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					Breakdown of data generated by project, technology, submitting centre



 Abbreviation Definitions
     Platform                           Definition
 LS454             454 Roche Genome Sequencer FLX System
 SLX               Illumina Genome Analyser
 ABI_SOLID         ABI SOLiD system

       Centre                              Definition
  454MSC            Roche
  ABI               Life Technologies
  BCM               Baylor College of Medicine
  BGI               BGI-Shenzhen
  BI                Broad Institute
  ILLUMINA          Illumina
  MPIMG             Max Planck Institute for Molecular Genetics
  SC                The Sanger Institute
  WUGSC             Washington University in St Louis


 Low Coverage
                             Sample        Total Base       Mapped Base
     Population      Centre
                               s             Count             Count
 CEU                454MSC       10      62,485,862,017     49,800,412,269
 CEU                ABI           7      ##########         89,897,498,650
 CEU                BCM          30      ##########        220,351,111,303
 CEU                BI           18      ##########        137,988,153,820
 CEU                ILLUMINA     10      ##########         92,261,736,966
 CEU                SC           21      ##########        154,606,818,706
 CEU                WUGSC        11      ##########         72,549,896,588
 CHB                BGI          30      ##########        231,234,717,242
 JPT                BI            5      64,595,729,387     42,877,586,814
 JPT                SC           15      ##########        113,559,505,261
 JPT                WUGSC        10      ##########         80,494,103,032
 YRI                BI           20      ##########        167,972,633,340
 YRI                MPIMG        10      ##########         56,572,201,003
 YRI                SC           20      ##########        238,958,001,903
 YRI                WUGSC        18      ##########        132,072,493,982
 total              454MSC       10      62,485,862,017     49,800,412,269
 total              ABI           7      ##########         89,897,498,650
 total              BCM          30      ##########        220,351,111,303
 total              BGI          30      ##########        231,234,717,242
 total              BI           43      ##########        348,838,373,974
 total              ILLUMINA     10      ##########         92,261,736,966
 total              MPIMG        10      ##########         56,572,201,003
 total              SC           56      ##########        507,124,325,870
 total              WUGSC        39      ##########        285,116,493,602
Low Coverage

                                                   Total Base
    Population   Platform   Layout   Samples         Count
CEU              ABI_SOLID PAIRED           31   636,252,317,468
CEU              ILLUMINA PAIRED            46   474,533,859,624
CEU              ILLUMINA SINGLE            16   121,867,362,644
CEU              LS454     PAIRED            6    43,265,065,818
CEU              LS454     SINGLE           18   125,639,767,507
CHB              ILLUMINA PAIRED            30   320,707,184,964
JPT              ILLUMINA PAIRED            20   188,575,086,669
JPT              ILLUMINA SINGLE             9   110,312,902,239
JPT              LS454     PAIRED            1     4,269,442,822
JPT              LS454     SINGLE            2     8,703,342,699
YRI              ABI_SOLID SINGLE            7    95,322,019,625
YRI              ILLUMINA PAIRED            43   554,724,240,212
YRI              ILLUMINA SINGLE            21   211,235,360,558
YRI              LS454     SINGLE            2    13,119,348,488
total            ABI_SOLID PAIRED           31   636,252,317,468
total            ABI_SOLID SINGLE            7    95,322,019,625
total            ILLUMINA PAIRED           139   ###########
total            ILLUMINA SINGLE            46   443,415,625,441
total            LS454     PAIRED            7    47,534,508,640
total            LS454     SINGLE           22   147,462,458,694
                Trio
                 Populatio            Sample     Total Base
Mapped Depth                 Centre
                      n                 s          Count
         17.5   CEU          ABI           1   32,303,393,493
         31.5   CEU          BCM           1   58,792,083,338
         77.3   CEU          BI            3   ##########
         48.4   CEU          MPIMG         1   24,065,310,896
         32.4   CEU          SC            3   ##########
         54.2   YRI          454MSC        1   17,632,987,644
         25.5   YRI          ABI           1   31,743,905,206
         81.1   YRI          BCM           1   ##########
         15.0   YRI          BGI           3   79,061,041,422
         39.8   YRI          ILLUMINA      1   23,870,910,232
         28.2   YRI          WUGSC         3   ##########
         58.9   total        454MSC        1   17,632,987,644
         19.8   total        ABI           2   64,047,298,699
         83.8   total        BCM           2   ##########
         46.3   total        BGI           3   79,061,041,422
         17.5   total        BI            3   ##########
         31.5   total        ILLUMINA      1   23,870,910,232
         77.3   total        MPIMG         1   24,065,310,896
         81.1   total        SC            3   ##########
        122.4   total        WUGSC         3   ##########
         32.4
         19.8
        177.9
        100.0
                           Trio
                  Mappe
 Mapped Base        d      Populatio
    Count         Depth       n      Platform   Layout   Samples
239,762,709,850    84.13   CEU      ABI_SOLID PAIRED               1
367,109,127,885   128.81   CEU      ILLUMINA PAIRED                3
 78,407,637,506    27.51   CEU      ILLUMINA SINGLE                3
 30,233,605,845    10.61   CEU      LS454     PAIRED               1
101,942,547,216    35.77   CEU      LS454     SINGLE               1
231,234,717,242    81.13   YRI      ABI_SOLID PAIRED               1
156,060,221,251    54.76   YRI      ABI_SOLID SINGLE               1
 71,250,532,380    25.00   YRI      ILLUMINA PAIRED                3
  2,705,589,821     0.95   YRI      ILLUMINA SINGLE                3
  6,914,851,655     2.43   YRI      LS454     SINGLE               1
 20,648,674,795     7.25   total    ABI_SOLID PAIRED               2
429,074,748,101   150.55   total    ABI_SOLID SINGLE               1
135,023,742,700    47.38   total    ILLUMINA PAIRED                6
 10,828,164,632     3.80   total    ILLUMINA SINGLE                6
239,762,709,850    84.13   total    LS454     PAIRED               1
 20,648,674,795     7.25   total    LS454     SINGLE               2
###########       415.26
284,681,912,586    99.89
 32,939,195,666    11.56
119,685,563,503    41.99
                               Exon
 Mapped Base                    Populatio            Sample      Total Base
               Mapped Depth                 Centre
    Count                            n                 s           Count
49,917,543,845          17.5   CEU          BCM           40   12,175,044,838
40,632,358,549          14.3   CEU          BI            30   ##########
##########              56.5   CEU          SC            18   14,401,851,078
18,946,754,496           6.6   CEU          WUGSC         20   22,191,013,052
98,327,871,498          34.5   CHB          BCM           63   30,305,411,535
16,819,082,789           5.9   CHB          BI            14   40,513,514,272
12,617,787,075           4.4   CHB          SC            14   10,575,413,376
62,306,064,045          21.9   CHB          WUGSC         18   11,683,046,440
50,585,677,379          17.7   CHD          BCM           79   37,698,245,871
21,222,957,828           7.4   CHD          BI            28   92,155,536,454
##########              62.8   JPT          BCM           16    7,469,382,603
16,819,082,789           5.9   JPT          BI            54   ##########
62,535,330,920          21.9   JPT          SC             9    8,642,770,160
##########              36.1   JPT          WUGSC         26   20,677,748,520
50,585,677,379          17.7   LWK          BCM          108   53,424,277,066
##########              56.5   TSI          BI             4   11,903,481,128
21,222,957,828           7.4   TSI          SC            62   52,054,186,369
18,946,754,496           6.6   YRI          BCM           45   22,905,478,666
98,327,871,498          34.5   YRI          BI            31   84,829,554,799
##########              62.8   YRI          SC            14   14,810,256,382
                               YRI          WUGSC         29   23,977,510,755
                               total        BCM          351   ##########
                               total        BI           161   ##########
                               total        SC           117   ##########
                               total        WUGSC         93   78,529,318,767
                                           Exon
                                  Mappe
 Total Base      Mapped Base        d      Populatio   Platfor
   Count            Count         Depth       n          m        Layout   Samples
32,303,393,493   49,917,543,845    17.51   CEU         ILLUMINA   PAIRED          45
##########       ##########        75.07   CEU         ILLUMINA   SINGLE          27
##########       64,402,851,766    22.60   CEU         LS454      SINGLE          40
35,273,524,439   20,746,770,334     7.28   CHB         ILLUMINA   PAIRED          28
23,518,558,899   19,885,588,215     6.98   CHB         ILLUMINA   SINGLE          18
##########       45,434,209,400    15.94   CHB         LS454      SINGLE          63
##########       29,489,641,720    10.35   CHD         ILLUMINA   PAIRED          28
##########       ##########        83.50   CHD         LS454      SINGLE          79
19,324,720,739   12,756,731,648     4.48   JPT         ILLUMINA   PAIRED          62
17,632,987,644   16,819,082,789     5.90   JPT         ILLUMINA   SINGLE          30
##########       95,351,753,245    33.46   JPT         LS454      SINGLE          16
##########       29,489,641,720    10.35   LWK         LS454      SINGLE         108
##########       ##########       158.56   TSI         ILLUMINA   PAIRED          56
##########       77,159,583,414    27.07   TSI         ILLUMINA   SINGLE          15
35,273,524,439   20,746,770,334     7.28   YRI         ILLUMINA   PAIRED          32
41,151,546,543   36,704,671,004    12.88   YRI         ILLUMINA   SINGLE          45
                                           YRI         LS454      SINGLE          45
                                           total       ILLUMINA   PAIRED         251
                                           total       ILLUMINA   SINGLE         135
                                           total       LS454      SINGLE         351
 Mapped Base
    Count
 9,299,875,674
28,063,266,916
11,189,333,836
 5,903,705,889
24,090,627,426
11,555,941,284
 8,372,935,831
 3,302,704,512
29,723,737,289
32,684,399,976
 4,864,443,988
41,214,181,774
 6,395,445,338
 5,883,891,981
41,781,889,022
 1,751,914,380
39,367,296,791
17,768,795,035
23,421,120,066
11,445,477,066
 6,781,574,681
##########
##########
76,770,488,862
21,871,877,063
 Total Base      Mapped Base
   Count            Count
##########       35,664,371,229
38,398,672,226    9,489,917,316
12,177,140,755    9,301,893,770
51,088,927,648   19,928,877,115
11,683,046,440    3,302,704,512
30,305,411,535   24,090,627,426
92,155,536,454   32,684,399,976
37,698,245,871   29,723,737,289
##########       46,530,315,966
24,638,423,042    6,963,203,127
 7,469,382,603    4,864,443,988
53,424,277,066   41,781,889,022
60,333,295,224   38,217,204,773
 3,624,372,273    2,902,006,398
93,418,214,789   32,752,076,260
30,199,107,147    8,896,095,553
22,905,478,666   17,768,795,035
##########       ##########
##########       31,553,926,906
##########       ##########
Fraction of genomic features passing filters in the Low Coverage Project.

    Percentage of each mask category (CEU autosomes) intersecting repeats.
            Mask              LINE           SINE            LTR
             -                   3.22%            1.69%         6.06%
             0                  20.13%            9.11%         9.18%
             B                  16.30%            7.39%         4.64%
             D                  18.73%            6.03%         8.87%
             M                  29.16%          44.33%          8.17%

    Percentage of each mask category (CEU autosomes) intersecting segmental duplications and co
            Mask             segdup     repeat_or_segdup
             -                  19.89%            84.59%
             0                   1.70%            45.03%
             B                  50.19%            97.73%
             D                  34.21%            70.19%
             M                  24.22%            97.90%

    Percentage of all repeats, segmental duplications and combined repeats & segmental duplicatio
                                  -               0              B
         all_repeats                0.00%           76.11%         0.23%
           segdup                   0.00%           30.16%         1.54%
      repeat_or_segdup              0.00%           74.16%         0.28%

    Percentage of each mask category (CEU autosomes) intersecting HapMap2 loci
            Mask            HapMap2
             -                   0.00%
             0                   0.17%
             B                   0.02%
             D                   0.21%
             M                   0.01%

    Percentage of HapMap2 loci intersecting each mask category (CEU autosomes)
                                -               0               B
          HapMap2                 0.00%           99.11%          0.02%

    Percentage of each mask category (CEU autosomes) intersecting all gene extents, all exon exte
            Mask            all genes       all exons     coding genes
             -                   32.20%             0.85%       28.98%
             0                   36.25%             2.55%       31.96%
             B                   17.29%             1.50%        9.50%
             D                   38.28%             1.97%       32.77%
             M                   33.49%             1.59%       27.66%

    Percentage of all gene extents, all exon extents, all coding gene extents, and all coding exon ex
                                 -                0                 B
          all genes                0.00%            87.14%            0.07%
          all exons                0.00%            90.93%            0.09%
    coding genes             0.00%           87.87%         0.05%
    coding exons             0.00%           93.07%         0.03%

Percentage of each mask category intersecting each uniqueness category
        Mask          Uniqueness 0     Uniqueness 1    Uniqueness 2
         -                   0.00%            75.99%          2.62%
         0                   0.00%             0.79%          5.33%
         B                   0.00%            66.93%         22.63%
         D                   0.00%             1.11%         18.07%
         M                   0.00%            85.26%         12.66%

Percentage of each uniqueness category intersecting each mask category
                           -                0              B
    Uniqueness 0             0.00%           100.00%         0.00%
    Uniqueness 1             0.00%             5.51%         0.81%
    Uniqueness 2             0.00%            72.18%         0.53%
    Uniqueness 3             0.00%            99.55%         0.02%


Totals
Non-N autosomal bases   2681301101

         -                   0.00%
         0                  86.17%
         B                   0.15%
         D                   0.08%
         M                  13.60%

          LINE              21.35%
          SINE              13.90%
          LTR                9.03%
          DNA                3.46%
    Simple_repeat            0.89%
   Low_complexity            0.59%
       Satellite             0.38%
      all repeats           49.86%
       SegDups               4.87%

      HapMap2                0.14%

    Uniqueness   0           0.00%
    Uniqueness   1          12.38%
    Uniqueness   2           6.37%
    Uniqueness   3          81.26%

      all genes             35.85%
      all exons              2.42%
    coding genes            31.35%
    coding exons             2.00%
cting repeats.
                 DNA     Simple_repeat Low_complexity      Satellite all_repeats   no_repeat
                   0.19%       29.96%         28.84%         10.46%       80.63%      19.37%
                   3.88%        0.73%          0.63%          0.24%       44.04%      55.96%
                   1.42%        3.72%          0.70%         42.72%       77.13%      22.87%
                   3.23%        2.10%          0.55%         12.34%       52.34%      47.66%
                   0.82%        1.86%          0.34%          0.75%       86.43%      13.57%

cting segmental duplications and combined repeats & segmental duplications
          Mask Key
          - : no coverage
          0 : passes filters
          B : failed both M and D filters
          D : failed DEPTH filter: total depth is greater than twice the average depth at HapMap3 sites
          M : failed MAPQ0 filter: more than 20% of Illumina reads have mapping quality 0

ned repeats & segmental duplications intersecting each mask category (CEU autosomes)
                D             M
                  0.09%        23.58%
                  0.58%        67.72%
                  0.11%        25.45%

cting HapMap2 loci




y (CEU autosomes)
               D                M
                     0.12%          0.75%

cting all gene extents, all exon extents, all coding gene extents, and all coding exon extents from gencode leve
             coding exons
                     0.38%
                     2.16%
                     0.43%
                     1.05%
                     1.01%

ene extents, and all coding exon extents from gencode level 1+2 intersecting each mask category
                D               M
                   0.09%        12.70%
                   0.07%          8.91%
                    0.09%   12.00%
                    0.04%    6.85%

ness category
           Uniqueness 3              Uniqueness Key
                 21.39%              0: all 35mers covering site cannot be mapped due to "N" in the refere
                 93.88%              3: >=35*0.5 reads 2-away unique
                 10.44%              2: if not 3, >=35*0.5 reads 1-away unique
                 80.81%              1: otherwise (>35*0.5 reads are exact repeats)
                  2.08%

mask category
                D           M
                    0.00%    0.00%
                    0.01%   93.68%
                    0.24%   27.05%
                    0.08%    0.35%
th at HapMap3 sites
quality 0




extents from gencode level 1+2




mask category
ed due to "N" in the reference


ats)
Validation Data

            Low Coverage Project

                                                       Total Polymorphi Monomorphi
                               Validation Set          Sites          c          c
            Sequenom random novel SNPs CEU              154         139         15
            Sequenom random novel SNPs YRI              210         192         18
            Sequenom random novel SNPs
            CHB+JPT                                     141        119          22

            Sequenom LOF SNPs CEU                        87         80           7
            Sequenom LOF SNPs YRI                       100         92           8
            Sequenom LOF SNPs CHB+JPT                    64         58           6

            Sequenom HighDiff SNPs CEU                   50         48           2
            Sequenom HighDiff SNPs YRI                   46         44           2
            Sequenom HighDiff SNPs CHB+JPT               41         39           2

            CEU indels                                   79         78          1
            CHB+JPT indels                               59         56          3
            YRI indels                                  152        151          1


            Trio Project
                                                       Total Polymorphi Monomorphi
            Validation Set                             Sites          c          c
            CEU_in_dbSNP                                286         285          1
            CEU_not_dbSNP                               682         671         11
            CEU overall                                 968


            Exon Project
                                                       Total Polymorphi Monomorphi
            Validation Set                             Sites          c          c
            CEU Random Sampling                           10          9          1
            CHB Random Sampling                           16         16          0
            CHD Random Sampling                           16         16          0
            JPT Random Sampling                           10          8          2
            LWK Random Sampling                           30         30          0
            TSI Random Sampling                           17         16          1
            YRI Random Sampling                           29         29          0

            CEU vs Population Specific Discovery CEU     43         43          0
            CHB vs Population Specific Discovery CHB     40         38          2
            YRI vs Population Specific Discovery YRI     42         41          1

            CEU Low Frequency Non-singletons              4          4          0
            CHB Low Frequency Non-singletons             13         13          0
CHD Low Frequency Non-singletons    9    9   0
JPT Low Frequency Non-singletons    8    8   0
LWK Low Frequency Non-singletons   11   11   0
TSI Low Frequency Non-singletons    5    5   0
YRI Low Frequency Non-singletons   11   11   0

CEU Low Frequency Singletons        4    4   0
CHB Low Frequency Singletons        5    5   0
CHD Low Frequency Singletons        7    6   1
JPT Low Frequency Singletons        4    4   0
LWK Low Frequency Singletons        4    4   0
TSI Low Frequency Singletons        5    5   0
YRI Low Frequency Singletons        5    5   0
          dbSNP rate of
           SNPs in this
    TP            class FDR
90.26%         66.58% ####
91.43%         52.97% ####

84.40%         72.22% ####

91.95%         73.60% ####
92.00%         49.00% ####
90.63%         67.20% ####

96.00%         94.00% ####
95.65%         91.30% ####
95.12%         97.60% ####

98.73%         61.40% ####
94.92%         61.30% ####
99.34%         47.90% ####




TP      dbSNP rate     FDR
 99.65%        100.00% ####
 98.40%          0.00% ####
 99.50%         88.83% ####




TP      dbSNP rate       FDR
 90.00%         65.90%   ####
#####           52.56%   ####
#####           50.24%   ####
 80.00%         57.89%   ####
#####           50.12%   ####
 94.12%         65.59%   ####
#####           53.82%   ####

#####          65.90% ####
95.00%         52.56% ####
97.62%         53.82% ####

#####
#####
#####
#####
#####
#####
#####

#####
#####
85.71%
#####
#####
#####
#####
Abbreviations: RD, read depth analysis; PE, paired-end analysis; SR, split-read analysis; AS, assembly; IN,
AS); DEL, deletion; DUP, duplication; INS, insertion; TEINS, transposable element insertion; TANDUP, tand

Supplementary table part A. SV discovery sets trio sequencing data
                                                      Genome
                                                         s
                Callset                        Plat- analyze
  Approach      Origin      Algorithm name     form      d
                 UCSD     Event-wise testingIllumina     6
         RD




                      Seattle         mrFAST        Illumina       6
                       Yale          CNVnator       Illumina       6
                        AB       AB large indel tool SOLiD         1
                        AB       AB large indel tool SOLiD         1
                        BC            Spanner       Illumina       6
                        BC            Spanner       Illumina       6
         PE




                   EMBL/Yale       PEMer         454               1
                     Seattle  VariationHunter Illumina             6
                     WashU     BreakDancer    Illumina             6
                      WTSI          N/A       Illumina             6
                       BC         Mosaik         454               2
         SR




                  Leiden/WTSI      Pindel     Illumina             6
                      Yale          N/A          454               1
                       BGI     SOAPdenovo     Illumina             6
                       BGI     SOAPdenovo     Illumina             6
         AS




                     Oxford        Cortex     Illumina             1
                     Oxford        Cortex     Illumina             1
                     Seattle        N/A       Illumina             6
         IN




                        BC             Spanner        Illumina     6

*
    In cases where only one validation method was applied, FDR (heirarch.) inherits that value

#FDR (PCR) was calculated on a preliminary set of the data, using the same method, and was not included
**In addition, the AB large indel tool also produced an inversion dataset, which received a 8.7% FDR on 29


Supplementary table part B. SV discovery sets low-coverage sequencing data
                                                      Genome
                                                         s
                Callset                        Plat- analyze
  Approach      Origin      Algorithm name     form      d
                AECOM             N/A        Illumina    8
         RD




                       UCSD      Event-wise testingIllumina      162
                      Yale           CNVnator         Illumina   65
                       BC             Spanner         Illumina   138
                       BC             Spanner         Illumina   138
         PE




                    EMBL/Yale          PEMer           SOLiD     25
                     WashU          BreakDancer       Illumina   138
         PE
                      WTSI             N/A            Illumina   144
                        BC            Mosaik             454     22

         SR
                  Leiden/WTSI         Pindel          Illumina   145
                       Yale            N/A               454      5
                        BC           Spanner          Illumina   138
         IN


                      Broad        Genome STRiP       Illumina   168

*
    In cases where only one validation method was applied, FDR (heirarch.) inherits that value

#FDR (PCR) was calculated on a preliminary set using the same method and was not included with FDR (hi
alysis; SR, split-read analysis; AS, assembly; IN, integrated approaches using more than one of the four different rationale
 , transposable element insertion; TANDUP, tandem duplication.




             SV types discovered (size-range of SV calls    SVs     FDR    FDR
                 validated SVs in basepairs)        made validated (PCR) (array)
           DEL (200 - 221,800); DUP (200 - 415,700) 5,762  1,952   0.279# 0.230
                    DEL (10,472 - 195,514)             2,100       187     0.692#   0.887
                     DEL (100 - 412,475)              17,036      2,361       -     0.142
                      DEL (67 - 83,391)                1,138       480     0.188    0.084
                     INS (448 - 2,213)**                632         42     0.176      -
                      TEINS (51 - 6,012)               2,013       179     0.022      -
                      DEL (50-192,167)                 4,718      3,619    0.100    0.033
                     DEL (941 - 960,004)               1,062       483     0.095#   0.363
                     DEL (52 - 498,738)               11,028      4,231    0.103    0.419
                    DEL (51 - 1,035,808)               5,973      3,587    0.115    0.145
                     DEL (276 - 959,518)               3,419      2,584    0.136    0.085
                     TEINS (300 - 6,000)               1,463       172     0.055      -
                      DEL (51 - 46,384)                3,879      2,960    0.201    0.127
              DEL (51 - 703,404); INS (52 - 295)      32,187      3,845    0.545    0.519
                       DEL (64 - 3,907)                 160         55     0.531    0.531
                       INS (55 – 4,116)                3,894        22     0.810      -
               DEL(52-39,512);DUP(83-2,090)            2,787       896     0.415    0.415
                         INS(50-828)                    389         84     0.398      -
                      INS (200 - 8,224)                 657         30     0.791      -
                      TANDUP (55-64,230)                256        88      0.049       -

DR (heirarch.) inherits that value

a, using the same method, and was not included when calculating the FDR (hierarch.)
ersion dataset, which received a 8.7% FDR on 29 handpicked calls assessed by PCR and will be incorporated into future rel


 verage sequencing data


             SV types discovered (size-range of SV calls  SVs    FDR    FDR
                 validated SVs in basepairs)     made validated (PCR) (array)
                      DEL (200 - 77,700)         10,965  1,049    -    0.535
                       DEL (200 - 67,500)             10,019      3,436       -     0.234
                      DEL (200 - 402,150)              5,507       402       -      0.695
                       TEINS (56 - 6,049)              3,276       182     0.052      -
                      DEL (53 - 195,139)               5,555      4,615    0.054    0.067
                      DEL (773 - 184,792)              2,177      1,188    0.258    0.434
                      DEL (51 - 959,495)               7,643      4,425    0.337    0.271
                      DEL (210 - 959,499)           8,011     5,541   0.214   0.245
                      TEINS (300 - 6,000)           2,833      172    0.044     -
                       DEL (51 - 47,040)           11,189     5,400   0.211   0.309
                DEL (54 - 6,047); INS (51 - 268)   10,697       74    0.575     -
                     TANDUP (55 – 64,230)            407        55    0.125     -
                      DEL (100 - 471,351)           7,015     5,852   0.057   0.019

DR (heirarch.) inherits that value

same method and was not included with FDR (hierarch.) calculation
ore than one of the four different rationales (RD, PE, SR, or




                                                  SVs qualified
                    FDR (hierarch.)               for inclusion
                         0.230                        1,952
                          0.887                        187
                          0.142*                      2,361
                           0.143                       480
                          0.176*                        42
                          0.022*                      2,013
                           0.087                      4,718
                           0.363                       483
                           0.190                      4,231
                           0.121                      3,587
                           0.121                      2,584
                           0.055                      1,463
                           0.189                      2,960
                           0.543                      3,845
                           0.497                        55
                          0.810*                        23
                           0.410                       896
                          0.398*                        84
                          0.791*                        30
                          0.049                        256
             Total algorithm-level SV calls
                 qualified for inclusion              31,994
             Independent (post-merging)
                SVs in 1kg data release               11,321
CR and will be incorporated into future releases of the 1000 Genomes Project.




                                                  SVs qualified
                    FDR (hierarch.)               for inclusion
                        0.535*                        1,049
                          0.234*                      3,436
                                *
                          0.695                        402
                          0.052                       3,276
                          0.059                       5,555
                          0.380                       1,188
                          0.320                       4,425
             0.227               5,541
            0.044*               2,833
             0.229               5,400
            0.575*                 74
            0.125*                407
             0.037               7,015
Total algorithm-level SV calls
    qualified for inclusion      40,601
Independent (post-merging)
   SVs in 1kg data release       15,947
Disease Variants (HGMD)

   Low Coverage Project
   chr pos        dbSNP_id gencode_id          HGNC_gene_name   ref_allele
      1   2224651 .          ENSG00000157933   SKI              C
      1   5862830 rs17472401 ENSG00000131697   NPHP4            G
      1   7952033 rs11548937 ENSG00000116288   PARK7            C
      1   9246497 rs6688832 ENSG00000049239    H6PD             G
      1 11029235 rs56392418 ENSG00000009724    MASP2            G
      1 11773514 rs2274976 ENSG00000177000     MTHFR            C
      1 16243654 rs2015352 ENSG00000184908     CLCNKB           G
      1 17226884 rs33927012 ENSG00000117118    SDHB             A
      1 17253094 rs11203289 ENSG00000117118    SDHB             G
      1 20844695 rs55831733 ENSG00000158828    PINK1            G
      1 20848249 .           ENSG00000158828   PINK1            G
      1 24067335 rs2070956 ENSG00000179163     FUCA1            G
      1 25762834 rs41291058 ENSG00000157978    LDLRAP1          C
      1 34999949 .           ENSG00000189433   GJB4             C
      1 35023044 rs1805063 ENSG00000188910     GJB3             C
      1 35023479 .           ENSG00000188910   GJB3             T
      1 35023530 .           ENSG00000188910   GJB3             G
      1 36337405 .           ENSG00000171812   COL8A2           C
      1 43576927 rs12731981 ENSG00000117400    MPL              G
      1 45252819 rs36033115 ENSG00000126088    UROD             T
      1 45253605 .           ENSG00000126088   UROD             G
      1 45569486 .           ENSG00000132781   MUTYH            C
      1 46428232 .           ENSG00000085998   POMGNT1          C
      1 53440651 .           ENSG00000157184   CPT2             C
      1 53448989 rs2229291 ENSG00000157184     CPT2             T
      1 55296390 rs28362261 ENSG00000169174    PCSK9            A
      1 55296443 rs28362263 ENSG00000169174    PCSK9            G
      1 63644620 rs35383149 ENSG00000088035    ALG6             T
      1 63654140 rs4630153 ENSG00000088035     ALG6             C
      1 68669590 rs34627040 ENSG00000116745    RPE65            G
      1 75971865 .           ENSG00000117054   ACADM            A
      1 91936234 rs35352606 ENSG00000069702    TGFBR3           G
      1 92721526 rs34631763 ENSG00000162676    GFI1             C
      1 94234305 rs6666652 ENSG00000198691     ABCA4            C
      1 94268627 rs56357060 ENSG00000198691    ABCA4            C
      1 94268641 rs1800549 ENSG00000198691     ABCA4            G
      1 94270151 rs61750129 ENSG00000198691    ABCA4            C
      1 94275476 .           ENSG00000198691   ABCA4            A
      1 94278192 rs61750126 ENSG00000198691    ABCA4            A
      1 94285153 rs1801581 ENSG00000198691     ABCA4            C
      1 94289842 .           ENSG00000198691   ABCA4            C
      1 94300730 rs61754024 ENSG00000198691    ABCA4            A
      1 94316822 rs3112831 ENSG00000198691     ABCA4            T
      1 94336943 .           ENSG00000198691   ABCA4            G
      1 94337071 rs6657239 ENSG00000198691     ABCA4            C
1    97753983   rs1801159 ENSG00000188641    DPYD      T
1    97754009   rs1801158 ENSG00000188641    DPYD      C
1    97937618   .          ENSG00000188641   DPYD      T
1    97937679   rs2297595 ENSG00000188641    DPYD      T
1    98121473   rs1801265 ENSG00000188641    DPYD      G
1   100099676   rs35278779 ENSG00000162688   AGL       A
1   100444648   rs12021720 ENSG00000137992   DBT       T
1   113258069   rs1049434 ENSG00000155380    SLC16A1   A
1   115023760   rs34526199 ENSG00000116748   AMPD1     T
1   115032777   rs61752479 ENSG00000116748   AMPD1     G
1   115377546   rs10776792 ENSG00000134200   TSHB      A
1   119766354   rs35887327 ENSG00000203859   HSD3B2    T
1   153528321   .          ENSG00000143627   PKLR      G
1   153528333   .          ENSG00000143627   PKLR      G
1   154413264   rs41265017 ENSG00000196189   SEMA4A    G
1   155115542   rs6336     ENSG00000198400   NTRK1     C
1   155115570   rs6339     ENSG00000198400   NTRK1     G
1   156899207   rs7418956 ENSG00000163554    SPTA1     G
1   158357332   rs55858252 ENSG00000018625   ATP1A2    T
1   167765599   rs6030     ENSG00000198734   F5        T
1   167788473   rs6035     ENSG00000198734   F5        T
1   169872010   rs56314834 ENSG00000034971   MYOC      T
1   169888148   rs2234926 ENSG00000034971    MYOC      C
1   169888318   rs2234925 ENSG00000034971    MYOC      C
1   177792798   rs61747727 ENSG00000116218   NPHS2     G
1   194973300   rs515299 ENSG00000000971     CFH       G
1   194977690   rs534399 ENSG00000000971     CFH       G
1   194979219   rs35274867 ENSG00000000971   CFH       A
1   195233977   rs35662416 ENSG00000134389   CFHR5     G
1   199597052   rs3730238 ENSG00000118194    TNNT2     T
1   214490898   rs696723 ENSG00000042781     USH2A     C
1   214605014   rs45500891 ENSG00000042781   USH2A     C
1   224637371   rs3219062 ENSG00000143799    PARP1     G
1   225138072   rs58973334 ENSG00000143801   PSEN2     G
1   226570189   .          ENSG00000154358   OBSCN     G
1   240108987   rs12122770 ENSG00000174371   EXO1      A
1   245655481   rs35829419 ENSG00000162711   NLRP3     C
2    10105574   rs34336420 ENSG00000172059   KLF11     C
2    20069022   rs52826764 ENSG00000132031   MATN3     C
2    21081484   .          ENSG00000084674   APOB      C
2    21085029   rs676210 ENSG00000084674     APOB      G
2    21087477   rs533617 ENSG00000084674     APOB      T
2    21091872   rs12713843 ENSG00000084674   APOB      C
2    26286166   rs10200182 ENSG00000084754   HADHA     G
2    31464647   rs45523133 ENSG00000158125   XDH       C
2    38151673   rs4986888 ENSG00000138061    CYP1B1    G
2    39094611   rs56219475 ENSG00000115904   SOS1      G
2    47496961   rs4987188 ENSG00000095002    MSH2      G
2    47510476   rs17224367 ENSG00000095002   MSH2      C
2    71594405   rs34999029 ENSG00000135636   DYSF       C
2    71594461   rs13407355 ENSG00000135636   DYSF       C
2    71615921   rs61740288 ENSG00000135636   DYSF       G
2    71761691   .          ENSG00000135636   DYSF       G
2    74952985   rs2229621 ENSG00000159399    HK2        A
2    74970035   rs2229629 ENSG00000159399    HK2        G
2    98379470   .          ENSG00000144191   CNGA3      G
2   157114495   rs2116665 ENSG00000115159    GPD2       G
2   166807404   rs6746030 ENSG00000169432    SCN9A      A
2   179033981   rs17304212 ENSG00000204311   DFNB59     C
2   179034062   .          ENSG00000204311   DFNB59     G
2   190427424   rs1145231 ENSG00000064933    PMS1       T
2   190427744   rs1145232 ENSG00000064933    PMS1       G
2   201782343   rs13010627 ENSG00000003400   CASP10     G
2   203128957   rs2228545 ENSG00000204217    BMPR2      G
2   215521576   rs726070 ENSG00000144452     ABCA12     C
2   215560703   .          ENSG00000144452   ABCA12     G
2   216996633   rs2066518 ENSG00000138375    SMARCAL1   G
2   219387121   rs41272687 ENSG00000135929   CYP27A1    C
2   219998918   .          ENSG00000175084   DES        G
2   220148070   rs12720061 ENSG00000123999   INHA       G
2   233894083   .          ENSG00000130561   SAG        C
2   233915700   .          ENSG00000130561   SAG        C
2   237909660   rs11903206 ENSG00000163359   COL6A3     G
2   237945215   .          ENSG00000163359   COL6A3     C
2   241456981   .          ENSG00000172482   AGXT       C
2   241461134   rs34664134 ENSG00000172482   AGXT       G
3     8762263   .          OTTHUMG00000090519CAV3       G
3    10064689   rs35782247 OTTHUMG00000128670FANCD2     T
3    15474717   rs6782980 OTTHUMG00000156233 COLQ       T
3    15661538   rs35034250 OTTHUMG00000129861BTD        C
3    15661697   rs13078881 OTTHUMG00000129861BTD        G
3    33030725   rs4302331 OTTHUMG00000155781 GLB1       A
3    33113553   rs7637099 OTTHUMG00000155781 GLB1       G
3    37028554   rs2308317 OTTHUMG00000130797 MLH1       G
3    37028572   rs1799977 OTTHUMG00000130797 MLH1       A
3    37064024   rs63751684 OTTHUMG00000130797MLH1       C
3    37065078   rs55907433 OTTHUMG00000130797MLH1       A
3    37067029   rs2020873 OTTHUMG00000130797 MLH1       C
3    38567178   rs45465995 OTTHUMG00000156166SCN5A      G
3    38591880   rs41261344 OTTHUMG00000156166SCN5A      C
3    38646822   .          OTTHUMG00000156166SCN5A      T
3    48594782   rs2229824 OTTHUMG00000133541 COL7A1     C
3    49431762   .          OTTHUMG00000156847AMT        C
3    49910507   rs9819888 OTTHUMG00000156709 MST1R      T
3    57207544   rs9878928 OTTHUMG00000158597 HESX1      T
3    77695032   .          ENSG00000185008   ROBO2      A
3    95128785   rs6122     OTTHUMG00000150354PROS1      G
3    95128899   rs7614835 OTTHUMG00000150354 PROS1      C
3   130263738   rs3796130 ENSG00000169704    GP9       G
3   133883496   .          ENSG00000113971   NPHP3     C
3   166183497   .          OTTHUMG00000158065SI        A
4     5806425   rs35953626 OTTHUMG00000090427EVC       G
4     6343846   .          OTTHUMG00000090431WFS1      G
4     6354750   rs56002719 OTTHUMG00000090431WFS1      A
4     6355034   .          OTTHUMG00000090431WFS1      G
4    55259401   .          OTTHUMG00000128713KIT       G
4    55667703   rs34231037 OTTHUMG00000128734KDR       A
4    70933492   rs1136511 ENSG00000205649    HTN3      G
4    70933511   rs17147990 ENSG00000205649   HTN3      T
4    88752564   rs36094464 ENSG00000152591   DSPP      A
4    89148477   .          OTTHUMG00000130595PKD2      G
4   100740828   rs17029215 OTTHUMG00000131023MTTP      A
4   110902232   .          ENSG00000205403   CFI       T
4   155709058   rs6054     OTTHUMG00000150331FGB       C
4   155747337   .          OTTHUMG00000150329FGG       C
4   178468213   rs34007209 ENSG00000109674   NEIL3     C
4   187395028   rs3733402 OTTHUMG00000150347 KLKB1     G
5     7938907   rs10064631 ENSG00000124275   MTRR      C
5    39377971   rs34000044 ENSG00000113600   C9        G
5    42754685   rs6182     ENSG00000112964   GHR       G
5    42755101   rs6184     ENSG00000112964   GHR       C
5    74017026   rs820878 ENSG00000049860     HEXB      T
5    74028637   rs10805890 ENSG00000049860   HEXB      A
5    78112128   .          ENSG00000113273   ARSB      T
5    78170997   rs25414    ENSG00000113273   ARSB      C
5    80099652   .          ENSG00000113318   MSH3      C
5    96144608   rs27044    ENSG00000164307   ERAP1     G
5   110460693   .          ENSG00000134987   WDR36     G
5   110473878   .          ENSG00000134987   WDR36     G
5   112201798   rs33974176 ENSG00000134982   APC       C
5   112206694   rs2229995 ENSG00000134982    APC       G
5   121814302   rs28937592 ENSG00000064692   SNCAIP    C
5   127772368   rs28763954 ENSG00000138829   FBN2      G
5   131439359   rs25882    ENSG00000164400   CSF2      T
5   131939434   rs28903085 ENSG00000113522   RAD50     A
5   137234459   rs41431944 ENSG00000120729   MYOT      A
5   147191298   rs35877720 ENSG00000164266   SPINK1    C
5   149281416   rs61733363 ENSG00000132915   PDE6A     G
5   149340823   .          ENSG00000155850   SLC26A2   C
5   149341070   rs30832    ENSG00000155850   SLC26A2   T
5   149341414   rs3776070 ENSG00000155850    SLC26A2   A
5   149720925   rs56180593 ENSG00000070814   TCOF1     C
5   151182669   .          ENSG00000145888   GLRA1     C
5   172592610   .          ENSG00000183072   NKX2-5    C
5   172594620   rs28936670 ENSG00000183072   NKX2-5    G
5   177353903   rs2233783 ENSG00000175325    PROP1     C
6     7530410   .          ENSG00000096696   DSP       G
6    18230485   rs10949483 ENSG00000187566   NHLRC1     G
6    25958824   rs56027330 ENSG00000124564   SLC17A3    C
6    26199164   rs1800730 ENSG00000010704    HFE        A
6    31936344   rs28940583 ENSG00000204386   NEU1       C
6    42774039   rs434102 ENSG00000112619     PRPH2      T
6    42797918   rs61755770 ENSG00000112619   PRPH2      G
6    43041442   rs35830695 ENSG00000124587   PEX6       G
6    43044048   .          ENSG00000124587   PEX6       G
6    43689733   rs56307355 ENSG00000170734   POLH       A
6    49511241   rs8589     ENSG00000146085   MUT        T
6    49520392   rs1141321 ENSG00000146085    MUT        C
6    49534934   .          ENSG00000146085   MUT        T
6    49688206   rs16879498 ENSG00000112077   RHAG       C
6    51631957   .          ENSG00000170927   PKHD1      C
6    51820718   rs7766366 ENSG00000170927    PKHD1      T
6    52025946   .          ENSG00000170927   PKHD1      G
6    52425533   .          ENSG00000096093   EFHC1      G
6    55147372   rs41271310 ENSG00000137252   HCRTR2     C
6   129677493   rs2306942 ENSG00000196569    LAMA2      G
6   129729089   .          ENSG00000196569   LAMA2      G
6   132239932   .          ENSG00000197594   ENPP1      C
6   132242769   .          ENSG00000197594   ENPP1      G
6   132247772   rs28933977 ENSG00000197594   ENPP1      C
6   134252293   rs56412384 ENSG00000118526   TCF21      G
6   135792717   rs13312995 ENSG00000135541   AHI1       G
6   162126866   .          ENSG00000185345   PARK2      A
6   162126882   rs9456711 ENSG00000185345    PARK2      T
6   162542229   rs55654276 ENSG00000185345   PARK2      G
6   166494336   .          ENSG00000164458   T          G
7     5993234   rs63750668 ENSG00000122512   PMS2       C
7    44195047   .          ENSG00000106633   GCK        C
7    44542007   .          ENSG00000015520   NPC1L1     A
7    65063329   rs9530     ENSG00000169919   GUSB       A
7    75448812   rs17853284 ENSG00000127948   POR        C
7    86887281   rs8187801 ENSG00000005471    ABCB4      C
7    86894112   rs2230028 ENSG00000005471    ABCB4      T
7    86907066   rs8187797 ENSG00000005471    ABCB4      C
7    86920228   rs1202283 ENSG00000005471    ABCB4      G
7   100064838   rs41303501 ENSG00000106327   TFR2       C
7   100558437   rs6092     ENSG00000106366   SERPINE1   G
7   107111187   rs36039758 ENSG00000091137   SLC26A4    A
7   107129530   rs17154335 ENSG00000091137   SLC26A4    T
7   107137863   rs17154353 ENSG00000091137   SLC26A4    G
7   116936379   .          ENSG00000001626   CFTR       C
7   116967520   .          ENSG00000001626   CFTR       C
7   116967572   rs1800086 ENSG00000001626    CFTR       C
7   117015110   .          ENSG00000001626   CFTR       A
7   117019459   rs1800100 ENSG00000001626    CFTR       C
7   117055048   rs34911792 ENSG00000001626   CFTR       T
7   117092070   .          ENSG00000001626   CFTR       G
7   117094312   rs4148725 ENSG00000001626    CFTR       C
7   127041787   rs2233578 ENSG00000106331    PAX4       G
7   138068331   rs3807153 ENSG00000105929    ATP6V0A4   A
7   142139408   .          ENSG00000204983   PRSS1      C
7   142738032   .          ENSG00000188037   CLCN1      G
8    11442985   rs55758736 ENSG00000136573   BLK        G
8    11651993   .          ENSG00000136574   GATA4      G
8    11680962   rs8191664 ENSG00000154328    NEIL2      G
8    11748297   rs12338    ENSG00000164733   CTSB       G
8    16070630   .          ENSG00000038945   MSR1       A
8    17971607   rs1049874 ENSG00000104763    ASAH1      T
8    17973091   rs1071645 ENSG00000104763    ASAH1      C
8    22032655   rs7014851 ENSG00000168453    HR         T
8    22037163   .          ENSG00000168453   HR         C
8    24831447   rs196863 ENSG00000104722     NEFM       C
8    38390458   rs56234888 ENSG00000077782   FGFR1      G
8    41671370   rs35213384 ENSG00000029534   ANK1       G
8    43171996   .          ENSG00000165102   HGSNAT     A
8    55700113   .          ENSG00000104237   RP1        C
8    55704792   .          ENSG00000104237   RP1        C
8    91052636   rs34767364 ENSG00000104320   NBN        G
8   106883455   rs28374544 ENSG00000169946   ZFPM2      A
8   133215798   .          ENSG00000184156   KCNQ3      G
8   143953695   rs4541     ENSG00000160882   CYP11B1    G
8   143958104   rs4534     ENSG00000160882   CYP11B1    C
8   143991043   rs4545     ENSG00000179142   CYP11B2    C
8   143991268   rs61757294 ENSG00000179142   CYP11B2    A
8   145611043   rs7823979 ENSG00000147804    SLC39A4    C
8   145611219   rs2977838 ENSG00000147804    SLC39A4    A
8   145612225   .          ENSG00000147804   SLC39A4    G
8   145670543   .          ENSG00000160973   FOXH1      G
9    21960979   rs6413464 ENSG00000147889    CDKN2A     C
9    35066755   rs2237857 ENSG00000221829    FANCG      G
9    97251393   rs2236405 ENSG00000185920    PTCH1      T
9    97270921   rs28936404 ENSG00000185920   PTCH1      G
9   102048725   .          ENSG00000119509   INVS       G
9   106618441   .          ENSG00000165029   ABCA1      G
9   107406320   rs34006675 ENSG00000106692   FKTN       G
9   119515647   rs5030718 ENSG00000136869    TLR4       G
9   129620396   .          ENSG00000106991   ENG        C
9   129656442   rs35400405 ENSG00000106991   ENG        G
9   134193831   rs61742937 ENSG00000107290   SETX       T
9   134194849   .          ENSG00000107290   SETX       G
9   134194999   .          ENSG00000107290   SETX       T
9   134775792   .          ENSG00000165699   TSC1       G
9   135209269   .          ENSG00000148290   SURF1      C
9   135297646   rs41314453 ENSG00000160323   ADAMTS13   C
9   135300738   .          ENSG00000160323   ADAMTS13   C
 9   136782475   rs61735045 ENSG00000130635   COL5A1    G
 9   138519141   .          ENSG00000148400   NOTCH1    C
 9   138529596   .          ENSG00000148400   NOTCH1    C
10    13206082   rs523747 ENSG00000123240     OPTN      A
10    13218772   rs28939689 ENSG00000123240   OPTN      G
10    13380242   rs28938169 ENSG00000107537   PHYH      G
10    42920613   rs35118262 ENSG00000165731   RET       C
10    42926862   rs9282834 ENSG00000165731    RET       G
10    50348728   rs4253208 ENSG00000225830    ERCC6     G
10    55261259   rs61731387 ENSG00000150275   PCDH15    G
10    70311866   rs1341667 ENSG00000165730    STOX1     T
10    70315302   rs41278530 ENSG00000165730   STOX1     C
10    70315382   rs10509305 ENSG00000165730   STOX1     A
10    73160277   rs41281314 ENSG00000107736   CDH23     A
10    90997319   rs1051339 ENSG00000107798    LIPA      C
10    92668894   .          ENSG00000148677   ANKRD1    C
10    99499241   rs35077384 ENSG00000155256   ZFYVE27   G
10   101593621   rs8187699 ENSG00000023839    ABCC2     A
10   101819504   rs61751507 ENSG00000120054   CPN1      C
10   102739059   rs17113613 ENSG00000107815   C10orf2   G
10   104587047   rs61754263 ENSG00000148795   CYP17A1   C
10   117839343   rs2072276 ENSG00000151892    GFRA1     T
10   123300861   rs755793 ENSG00000066468     FGFR2     A
11     2825705   rs1800172 ENSG00000053918    KCNQ1     G
11     5204808   .          ENSG00000244734   HBB       T
11     6369758   rs35824453 ENSG00000166311   SMPD1     G
11     6372039   rs1050239 ENSG00000166311    SMPD1     G
11     7017553   .          ENSG00000158077   NLRP14    A
11     7048174   .          ENSG00000158077   NLRP14    G
11    17421384   .          ENSG00000006071   ABCC8     T
11    18260109   rs61884288 ENSG00000110756   HPS5      G
11    20632895   rs16906628 ENSG00000165970   SLC6A5    G
11    47320765   rs11570082 ENSG00000134571   MYBPC3    C
11    47320810   rs35736435 ENSG00000134571   MYBPC3    C
11    47326617   rs3729989 ENSG00000134571    MYBPC3    T
11    61481029   .          ENSG00000167995   BEST1     C
11    64283799   .          ENSG00000068976   PYGM      G
11    64332081   rs607969 ENSG00000133895     MEN1      C
11    66043772   rs35520756 ENSG00000174483   BBS1      G
11    68318904   rs2229738 ENSG00000110090    CPT1A     C
11    68462250   rs17612126 ENSG00000132740   IGHMBP2   C
11    73394895   rs2229707 ENSG00000175564    UCP3      C
11    87685231   rs217086 ENSG00000109861     CTSC      A
11    95208229   .          ENSG00000087053   MTMR2     G
11    95209096   rs558018 ENSG00000087053     MTMR2     T
11   104374918   rs523104 ENSG00000137757     CASP5     G
11   107626943   rs2235000 ENSG00000149311    ATM       G
11   107627802   rs2227924 ENSG00000149311    ATM       C
11   107643255   rs3218673 ENSG00000149311    ATM       C
11   107655526   rs56398245 ENSG00000149311   ATM        A
11   107664942   rs3092856 ENSG00000149311    ATM        C
11   107665560   rs1800058 ENSG00000149311    ATM        C
11   111462875   rs34677591 ENSG00000204370   SDHD       G
11   111463887   rs11214077 ENSG00000204370   SDHD       A
11   113362871   rs35815285 ENSG00000166736   HTR3A      G
11   118720796   rs61736238 ENSG00000235718   MFRP       C
11   125821982   .          ENSG00000149571   KIRREL3    C
11   128214336   rs59172778 ENSG00000151704   KCNJ1      A
12     5973333   rs2229446 ENSG00000110799    VWF        C
12     5998328   rs61750100 ENSG00000110799   VWF        G
12     6010920   rs33978901 ENSG00000110799   VWF        C
12     6014239   rs41276738 ENSG00000110799   VWF        C
12     6015910   rs57950734 ENSG00000110799   VWF        A
12     6026211   rs16932374 ENSG00000110799   VWF        C
12     6089948   rs61753991 ENSG00000110799   VWF        G
12     6313262   rs4149637 ENSG00000067182    TNFRSF1A   G
12     6343013   rs55797039 ENSG00000111319   SCNN1A     G
12    32913201   rs1046116 ENSG00000057294    PKP2       A
12    39003325   rs35602796 ENSG00000188906   LRRK2      T
12    46812979   rs2228500 ENSG00000152556    PFKM       G
12    46825175   rs41291971 ENSG00000152556   PFKM       G
12    51110618   rs2232398 ENSG00000170454    KRT75      C
12    51199935   rs11170164 ENSG00000186081   KRT5       C
12    55717669   rs33962952 ENSG00000166866   MYO1A      C
12    68030281   rs1800973 ENSG00000090382    LYZ        C
12    97585453   .          ENSG00000120868   APAF1      A
12    97617357   .          ENSG00000120868   APAF1      A
12   101758401   rs5030858 ENSG00000171759    PAH        G
12   101830709   .          ENSG00000171759   PAH        C
12   108483986   rs35648932 ENSG00000139428   MMAB       C
12   118116037   rs4628742 ENSG00000152137    HSPB8      C
12   119916500   rs56348580 ENSG00000135100   HNF1A      G
12   119918784   .          ENSG00000135100   HNF1A      T
12   120779718   rs1154510 ENSG00000158104    HPD        T
13    19661113   .          ENSG00000165474   GJB2       A
13    19661305   .          ENSG00000165474   GJB2       C
13    19661380   rs2274083 ENSG00000165474    GJB2       T
13    19661472   .          ENSG00000165474   GJB2       G
13    19661642   rs2274084 ENSG00000165474    GJB2       C
13    31804558   .          ENSG00000139618   BRCA2      T
13    31812236   rs4987117 ENSG00000139618    BRCA2      C
13    31812592   rs1799954 ENSG00000139618    BRCA2      C
13    31827387   rs169547 ENSG00000139618     BRCA2      T
13    31851529   rs4987047 ENSG00000139618    BRCA2      A
13    31870884   rs1801426 ENSG00000139618    BRCA2      A
13    47837089   .          ENSG00000139687   RB1        C
13    47853459   rs4151539 ENSG00000139687    RB1        C
13    51411267   rs7334118 ENSG00000123191    ATP7B      T
13 51413355 rs1801249 ENSG00000123191     ATP7B       A
13 99760157 rs35719359 ENSG00000175198    PCCA        A
13 99818759 .           ENSG00000175198   PCCA        G
13 112820773 .          ENSG00000057593   F7          G
14 20859880 rs10151259 ENSG00000092200    RPGRIP1     G
14 20881036 rs17103671 ENSG00000092200    RPGRIP1     A
14 22956249 rs3729823 ENSG00000092054     MYH7        G
14 23794503 rs35312232 ENSG00000092295    TGM1        C
14 37130397 rs33984772 ENSG00000129514    FOXA1       C
14 37131493 rs7144658 ENSG00000129514     FOXA1       C
14 54380567 rs41298442 ENSG00000131979    GCH1        T
14 63746504 rs36215895 ENSG00000054654    SYNE2       C
14 74583287 rs17102999 ENSG00000119684    MLH3        G
14 74583891 rs28756990 ENSG00000119684    MLH3        C
14 76824873 .           ENSG00000009830   POMT2       C
14 80491931 rs2234919 ENSG00000165409     TSHR        C
14 87470966 rs421262 ENSG00000054983      GALC        T
14 87483911 rs34134328 ENSG00000054983    GALC        G
14 87520523 rs1805078 ENSG00000054983     GALC        G
14 93820239 rs2232710 ENSG00000140093     SERPINA10   T
14 93826249 .           ENSG00000140093   SERPINA10   A
14 93914596 rs1303      ENSG00000197249   SERPINA1    T
14 93914700 rs28929474 ENSG00000197249    SERPINA1    C
14 93917015 rs17580     ENSG00000197249   SERPINA1    T
14 93917168 rs6647      ENSG00000197249   SERPINA1    A
14 93918954 rs709932 ENSG00000197249      SERPINA1    C
14 94155395 rs17473     ENSG00000196136   SERPINA3    C
14 94159872 .           ENSG00000196136   SERPINA3    A
14 101799639 rs34931752 ENSG00000080823   RAGE        G
15 25902148 .           ENSG00000104044   OCA2        C
15 26000537 rs61738394 ENSG00000104044    OCA2        C
15 40465756 rs17592     ENSG00000092529   CAPN3       C
15 40467295 rs35889956 ENSG00000092529    CAPN3       C
15 43179367 rs269868 ENSG00000140279      DUOX2       G
15 43179569 .           ENSG00000140279   DUOX2       C
15 43185730 rs57659670 ENSG00000140279    DUOX2       T
15 46566822 rs140598 ENSG00000166147      FBN1        G
15 49316404 rs700518 ENSG00000137869      CYP19A1     T
15 50430856 rs1058219 ENSG00000197535     MYO5A       G
15 56625302 rs6083      ENSG00000166035   LIPC        A
15 56640371 rs3829462 ENSG00000166035     LIPC        C
15 56643040 rs28933094 ENSG00000166035    LIPC        C
15 83287734 rs45584739 ENSG00000156222    SLC28A1     T
15 87662830 rs2307441 ENSG00000140521     POLG        T
15 87666077 rs41549716 ENSG00000140521    POLG        T
16   1190393 .          ENSG00000196557   CACNA1H     C
16   2048756 rs1800748 ENSG00000103197    TSC2        A
16   2073799 rs45517323 ENSG00000103197   TSC2        G
16   2083956 .          ENSG00000008710   PKD1        C
16    2084183   rs45478794 ENSG00000008710   PKD1      G
16    2092866   rs13337123 ENSG00000008710   PKD1      C
16    2309593   .          ENSG00000167972   ABCA3     C
16    3239469   rs11466024 ENSG00000103313   MEFV      C
16    3239587   rs11466023 ENSG00000103313   MEFV      G
16    3244159   .          ENSG00000103313   MEFV      C
16    3244464   rs224222 ENSG00000103313     MEFV      C
16    8814415   rs34258285 ENSG00000140650   PMM2      A
16   16159032   rs58694313 ENSG00000091262   ABCC6     C
16   16159100   rs2238472 ENSG00000091262    ABCC6     C
16   46106974   rs56257827 ENSG00000102893   PHKB      G
16   46255119   rs16945474 ENSG00000102893   PHKB      A
16   49303497   rs5743278 ENSG00000167207    NOD2      C
16   49314777   rs5743291 ENSG00000167207    NOD2      G
16   55106002   rs4784677 ENSG00000125124    BBS2      C
16   55462088   rs1529927 ENSG00000070915    SLC12A3   C
16   55475498   .          ENSG00000070915   SLC12A3   C
16   55479341   rs36049418 ENSG00000070915   SLC12A3   G
16   55493820   rs12708965 ENSG00000070915   SLC12A3   C
16   55574793   rs2303790 ENSG00000087237    CETP      A
16   66533821   rs4986970 ENSG00000213398    LCAT      A
16   67413542   rs33935154 ENSG00000039068   CDH1      G
16   79968592   .          ENSG00000127688   GAN       C
16   87411936   .          ENSG00000141012   GALNS     C
16   88333978   rs17227354 ENSG00000187741   FANCA     C
16   88342653   rs17233497 ENSG00000187741   FANCA     G
16   88397205   rs17225943 ENSG00000187741   FANCA     T
16   88402257   rs17232246 ENSG00000187741   FANCA     G
16   88410501   .          ENSG00000187741   FANCA     G
17    1328505   rs61750783 ENSG00000197879   MYO1C     G
17    3497549   rs35086888 ENSG00000040531   CTNS      G
17    3791094   rs9895012 ENSG00000074370    ATP2A3    G
17    6269533   rs61757484 ENSG00000129221   AIPL1     G
17    6272486   rs8069375 ENSG00000129221    AIPL1     G
17    6272541   rs62619924 ENSG00000129221   AIPL1     C
17    6312281   .          ENSG00000091622   PITPNM3   C
17    7064230   rs2230178 ENSG00000072778    ACADVL    G
17    7064562   rs28934585 ENSG00000072778   ACADVL    C
17    7475403   rs6258     ENSG00000129214   SHBG      C
17    7847151   rs9905402 ENSG00000132518    GUCY2D    T
17    7853604   rs28743021 ENSG00000132518   GUCY2D    C
17    7856637   rs34598902 ENSG00000132518   GUCY2D    C
17   17066604   .          ENSG00000154803   FLCN      G
17   17992831   .          ENSG00000091536   MYO15A    G
17   21144803   rs55796947 ENSG00000034152   MAP2K3    C
17   24310977   rs1976165 ENSG00000063015    SEZ6      T
17   37252053   .          ENSG00000161594   KLHL10    A
17   38476574   rs4986854 ENSG00000012048    BRCA1     A
17   38496506   .          ENSG00000012048   BRCA1     C
17   38497626   .          ENSG00000012048   BRCA1     G
17   38497955   rs4986852 ENSG00000012048    BRCA1     C
17   38498553   rs1800709 ENSG00000012048    BRCA1     G
17   38498616   rs56082113 ENSG00000012048   BRCA1     T
17   38498997   rs4986850 ENSG00000012048    BRCA1     C
17   38499937   rs56128296 ENSG00000012048   BRCA1     A
17   39694519   rs45562031 ENSG00000004939   SLC4A1    C
17   45627826   .          ENSG00000108821   COL1A1    C
17   53711913   .          ENSG00000005381   MPO       T
17   59388289   rs62070884 ENSG00000007314   SCN4A     C
17   71338086   rs35037984 ENSG00000092929   UNC13D    G
17   71343548   .          ENSG00000092929   UNC13D    G
17   75693251   rs1800299 ENSG00000171298    GAA       G
18    2927815   rs34676691 ENSG00000101577   LPIN2     G
18   13874685   rs28926182 ENSG00000185231   MC2R      A
18   19394365   .          ENSG00000141458   NPC1      G
18   19767886   rs61752346 ENSG00000053747   LAMA3     C
18   27376616   .          ENSG00000046604   DSG2      G
18   27426863   rs1800458 ENSG00000118271    TTR       G
18   27432616   rs28933980 ENSG00000118271   TTR       G
18   32039091   rs678560 ENSG00000075643     MOCOS     G
18   45367163   .          ENSG00000101670   LIPG      C
18   53524791   rs34719006 ENSG00000081923   ATP8B1    C
18   56189812   rs52820871 ENSG00000166603   MC4R      T
19     807015   rs17216656 ENSG00000197561   ELANE     G
19    1174125   rs59912467 ENSG00000118046   STK11     C
19    1348443   rs17851582 ENSG00000130005   GAMT      G
19    5783209   rs778805 ENSG00000156413     FUT6      G
19    5795537   rs778986 ENSG00000171124     FUT3      A
19    5795649   rs812936 ENSG00000171124     FUT3      G
19    5795792   rs28362459 ENSG00000171124   FUT3      A
19   11082357   .          ENSG00000130164   LDLR      G
19   11091842   rs5926     ENSG00000130164   LDLR      C
19   15152576   rs35769976 ENSG00000074181   NOTCH3    C
19   17427610   rs10408265 ENSG00000171773   NXNL1     T
19   18047618   rs11575934 ENSG00000096996   IL12RB1   T
19   38044901   rs1007160 ENSG00000021488    SLC7A9    G
19   38046895   rs12150889 ENSG00000021488   SLC7A9    A
19   38046952   .          ENSG00000021488   SLC7A9    G
19   38398535   .          ENSG00000130876   SLC7A10   C
19   41014441   rs4806213 ENSG00000161270    NPHS1     T
19   41022117   rs34736717 ENSG00000161270   NPHS1     C
19   41031087   rs33950747 ENSG00000161270   NPHS1     C
19   41031849   .          ENSG00000161270   NPHS1     G
19   41034052   rs3814995 ENSG00000161270    NPHS1     C
19   43656115   rs34694816 ENSG00000196218   RYR1      A
19   43687838   rs35180584 ENSG00000196218   RYR1      C
19   43749455   .          ENSG00000196218   RYR1      C
19   46210061   rs28399499 ENSG00000197408   CYP2B6    T
  19   50103781   rs429358 ENSG00000130203     APOE              T
  19   50103880   rs769455 ENSG00000130203     APOE              C
  19   50103919   rs7412     ENSG00000130203   APOE              C
  19   53034608   rs61748445 ENSG00000105392   CRX               G
  19   56542102   rs1130426 ENSG00000105379    ETFB              G
  19   57160104   rs4986771 ENSG00000197619    ZNF350            A
  19   60142467   rs61743949 ENSG00000167634   NLRP7             T
  19   60143532   rs61746625 ENSG00000167634   NLRP7             C
  19   60359419   .          ENSG00000129991   TNNI3             G
  20    4628378   rs16990018 ENSG00000171867   PRNP              A
  20    5230850   .          ENSG00000101292   PROKR2            C
  20    5231039   .          ENSG00000101292   PROKR2            G
  20   10334059   rs1547     ENSG00000125863   MKKS              G
  20   10570501   rs35761929 ENSG00000101384   JAG1              G
  20   18461350   rs41309927 ENSG00000101310   SEC23B            G
  20   22976934   rs41400249 ENSG00000178726   THBD              C
  20   32983491   .          ENSG00000100983   GSS               G
  20   42475778   rs1800961 ENSG00000101076    HNF4A             C
  20   42685097   .          ENSG00000196839   ADA               C
  20   42688634   rs11555566 ENSG00000196839   ADA               T
  20   61515971   .          ENSG00000075043   KCNQ2             C
  21   18607163   .          ENSG00000154646   PRSS7             G
  21   34664672   rs16991652 ENSG00000159197   KCNE2             C
  21   37231489   rs61732504 ENSG00000159267   HLCS              C
  21   42682161   rs45598239 ENSG00000160183   TMPRSS3           C
  21   43353660   .          ENSG00000160200   CBS               G
  21   43356253   rs5742905 ENSG00000160200    CBS               A
  21   43361700   rs34040148 ENSG00000160200   CBS               T
  21   44534070   rs34397615 ENSG00000160224   AIRE              C
  21   46228730   rs11553519 ENSG00000142156   COL6A1            G
  21   46370508   .          ENSG00000142173   COL6A2            G
  21   46376629   .          ENSG00000142173   COL6A2            C
  22   16946288   rs12484657 ENSG00000215193   PEX26             C
  22   19464223   rs5907     ENSG00000099937   SERPIND1          G
  22   28969969   .          ENSG00000128342   LIF               C
  22   30775946   rs17683011 ENSG00000100170   SLC5A1            A
  22   30817700   rs17683430 ENSG00000100170   SLC5A1            G
  22   30836050   rs33954001 ENSG00000100170   SLC5A1            C
  22   35663603   rs1801122 ENSG00000100368    CSF2RB            C
  22   37264552   rs2227914 ENSG00000100206    DMC1              T
  22   40606771   rs2229440 ENSG00000198911    SREBF2            G
  22   45110353   rs11090865 ENSG00000100416   TRMU              G
  22   49311102   rs11479    ENSG00000025708   TYMP              G


Trio Project
chr pos          dbSNP_id gencode_id           HGNC_gene_name    ref_allele
    1    9246497 rs6688832 H6PD                ENSG00000049239   G
    1 16243654 rs2015352 CLCNKB                ENSG00000184908   G
1    20847608   rs45515602 PINK1     ENSG00000158828   G
1    25762834   rs41291058 LDLRAP1   ENSG00000157978   C
1    53451641   rs1871748 CPT2       ENSG00000157184   C
1    63654140   rs4630153 ALG6       ENSG00000088035   C
1    94234305   rs6666652 ABCA4      ENSG00000198691   C
1    94285153   rs1801581 ABCA4      ENSG00000198691   C
1    94337071   rs6657239 ABCA4      ENSG00000198691   C
1    97753983   rs1801159 DPYD       ENSG00000188641   T
1    97754009   rs1801158 DPYD       ENSG00000188641   C
1    98121473   rs1801265 DPYD       ENSG00000188641   G
1   100444648   rs12021720 DBT       ENSG00000137992   T
1   113258069   rs1049434 SLC16A1    ENSG00000155380   A
1   115377546   rs10776792 TSHB      ENSG00000134200   A
1   167765599   rs6030     F5        ENSG00000198734   T
1   169872010   rs56314834 MYOC      ENSG00000034971   T
1   194973300   rs515299 CFH         ENSG00000000971   G
1   194977690   rs534399 CFH         ENSG00000000971   G
1   199597052   rs3730238 TNNT2      ENSG00000118194   T
1   240115303   rs4150001 EXO1       ENSG00000174371   G
1   245655481   rs35829419 NLRP3     ENSG00000162711   C
2    26286166   rs10200182 HADHA     ENSG00000084754   G
2    71651270   rs34211915 DYSF      ENSG00000135636   G
2    71736867   .          DYSF      ENSG00000135636   A
2    74952985   rs2229621 HK2        ENSG00000159399   A
2    74970035   rs2229629 HK2        ENSG00000159399   G
2   157114495   rs2116665 GPD2       ENSG00000115159   G
2   166807404   rs6746030 SCN9A      ENSG00000169432   A
2   179033981   rs17304212 DFNB59    ENSG00000204311   C
2   190427424   rs1145231 PMS1       ENSG00000064933   T
2   190427744   rs1145232 PMS1       ENSG00000064933   G
2   201782343   rs13010627 CASP10    ENSG00000003400   G
2   216996633   rs2066518 SMARCAL1   ENSG00000138375   G
2   219998918   .          DES       ENSG00000175084   G
3    15474717   rs6782980 COLQ       OTTHUMG00000156233T
3    33030725   rs4302331 GLB1       OTTHUMG00000155781A
3    33113553   rs7637099 GLB1       OTTHUMG00000155781G
3    37028554   rs2308317 MLH1       OTTHUMG00000130797G
3    37028572   rs1799977 MLH1       OTTHUMG00000130797A
3    49910507   rs9819888 MST1R      OTTHUMG00000156709T
3    57207544   rs9878928 HESX1      OTTHUMG00000158597T
4     5806425   rs35953626 EVC       OTTHUMG00000090427G
4    55259401   .          KIT       OTTHUMG00000128713G
4    88752564   rs36094464 DSPP      ENSG00000152591   A
4   187395028   rs3733402 KLKB1      OTTHUMG00000150347G
4   187434514   rs5969     F11       OTTHUMG00000150311A
5     7938907   rs10064631 MTRR      ENSG00000124275   C
5    74017026   rs820878 HEXB        ENSG00000049860   T
5    96144608   rs27044    ERAP1     ENSG00000164307   G
5   112201798   rs33974176 APC       ENSG00000134982   C
 5   131439359   rs25882    CSF2       ENSG00000164400   T
 5   131748961   .          SLC22A5    ENSG00000197375   C
 5   137234459   rs41431944 MYOT       ENSG00000120729   A
 5   149341070   rs30832    SLC26A2    ENSG00000155850   T
 5   149341414   rs3776070 SLC26A2     ENSG00000155850   A
 6    25958824   rs56027330 SLC17A3    ENSG00000124564   C
 6    42774039   rs434102 PRPH2        ENSG00000112619   T
 6    43041442   rs35830695 PEX6       ENSG00000124587   G
 6    49511241   rs8589     MUT        ENSG00000146085   T
 6    49520392   rs1141321 MUT         ENSG00000146085   C
 6   129677493   rs2306942 LAMA2       ENSG00000196569   G
 6   134252293   rs56412384 TCF21      ENSG00000118526   G
 6   155623126   .          TFB1M      ENSG00000029639   C
 6   161047491   .          PLG        ENSG00000122194   A
 6   162126882   rs9456711 PARK2       ENSG00000185345   T
 7    44195047   .          GCK        ENSG00000106633   C
 7    65063329   rs9530     GUSB       ENSG00000169919   A
 7    86894112   rs2230028 ABCB4       ENSG00000005471   T
 7    86898780   rs45575636 ABCB4      ENSG00000005471   C
 7   100558437   rs6092     SERPINE1   ENSG00000106366   G
 7   116969314   .          CFTR       ENSG00000001626   A
 8    11748297   rs12338    CTSB       ENSG00000164733   G
 8    17971607   rs1049874 ASAH1       ENSG00000104763   T
 8    17973091   rs1071645 ASAH1       ENSG00000104763   C
 8    41671370   rs35213384 ANK1       ENSG00000029534   G
 8    43171996   .          HGSNAT     ENSG00000165102   A
 8   106883455   rs28374544 ZFPM2      ENSG00000169946   A
 8   145611219   rs2977838 SLC39A4     ENSG00000147804   A
 9    35066755   rs2237857 FANCG       ENSG00000221829   G
 9    97251393   rs2236405 PTCH1       ENSG00000185920   T
 9   107406320   rs34006675 FKTN       ENSG00000106692   G
 9   129656442   rs35400405 ENG        ENSG00000106991   G
10    13206082   rs523747 OPTN         ENSG00000123240   A
10    42940341   rs17158558 RET        ENSG00000165731   C
10    70311866   rs1341667 STOX1       ENSG00000165730   T
10    70315382   rs10509305 STOX1      ENSG00000165730   A
10    72028728   rs28933375 PRF1       ENSG00000180644   T
10    73160277   rs41281314 CDH23      ENSG00000107736   A
10    90997319   rs1051339 LIPA        ENSG00000107798   C
10   102739059   rs17113613 C10orf2    ENSG00000107815   G
10   123300861   rs755793 FGFR2        ENSG00000066468   A
11     2825577   rs34516117 KCNQ1      ENSG00000053918   C
11     6372039   rs1050239 SMPD1       ENSG00000166311   G
11    17406753   rs58241708 ABCC8      ENSG00000006071   G
11    66034730   rs55848325 BBS1       ENSG00000174483   T
11    68462250   rs17612126 IGHMBP2    ENSG00000132740   C
11    73394537   .          UCP3       ENSG00000175564   G
11    73394895   rs2229707 UCP3        ENSG00000175564   C
11    87685231   rs217086 CTSC         ENSG00000109861   A
11    95209096   rs558018 MTMR2        ENSG00000087053   T
11   104374918   rs523104 CASP5        ENSG00000137757   G
11   118720796   rs61736238 MFRP       ENSG00000235718   C
12     5965032   rs61750625 VWF        ENSG00000110799   G
12     5973333   rs2229446 VWF         ENSG00000110799   C
12    32913201   rs1046116 PKP2        ENSG00000057294   A
12    46812979   rs2228500 PFKM        ENSG00000152556   G
12    51584873   rs57749775 KRT8       ENSG00000170421   A
12    68030281   rs1800973 LYZ         ENSG00000090382   C
12   101758382   rs5030860 PAH         ENSG00000171759   T
12   120779718   rs1154510 HPD         ENSG00000158104   T
13    31812839   rs55953736 BRCA2      ENSG00000139618   A
13    31827387   rs169547 BRCA2        ENSG00000139618   T
13    31870884   rs1801426 BRCA2       ENSG00000139618   A
13    51413355   rs1801249 ATP7B       ENSG00000123191   A
14    20859880   rs10151259 RPGRIP1    ENSG00000092200   G
14    23794503   rs35312232 TGM1       ENSG00000092295   C
14    37131493   rs7144658 FOXA1       ENSG00000129514   C
14    74584242   rs28756986 MLH3       ENSG00000119684   C
14    87470966   rs421262 GALC         ENSG00000054983   T
14    87483911   rs34134328 GALC       ENSG00000054983   G
14    93914596   rs1303     SERPINA1   ENSG00000197249   T
14    93917015   rs17580    SERPINA1   ENSG00000197249   T
14    93917168   rs6647     SERPINA1   ENSG00000197249   A
15    43179367   rs269868 DUOX2        ENSG00000140279   G
15    43185730   rs57659670 DUOX2      ENSG00000140279   T
15    49316404   rs700518 CYP19A1      ENSG00000137869   T
15    50430856   rs1058219 MYO5A       ENSG00000197535   G
15    56625302   rs6083     LIPC       ENSG00000166035   A
15    56640371   rs3829462 LIPC        ENSG00000166035   C
16    16159100   rs2238472 ABCC6       ENSG00000091262   C
16    46255119   rs16945474 PHKB       ENSG00000102893   A
16    55106002   rs4784677 BBS2        ENSG00000125124   C
16    55462088   rs1529927 SLC12A3     ENSG00000070915   C
16    55493820   rs12708965 SLC12A3    ENSG00000070915   C
16    88333978   rs17227354 FANCA      ENSG00000187741   C
16    88397205   rs17225943 FANCA      ENSG00000187741   T
17     7064230   rs2230178 ACADVL      ENSG00000072778   G
17     7925204   .          ALOX12B    ENSG00000179477   G
17    21144803   rs55796947 MAP2K3     ENSG00000034152   C
17    24310977   rs1976165 SEZ6        ENSG00000063015   T
17    38476766   rs56119278 BRCA1      ENSG00000012048   A
18    27426863   rs1800458 TTR         ENSG00000118271   G
18    32039091   rs678560 MOCOS        ENSG00000075643   G
19     5783209   rs778805 FUT6         ENSG00000156413   G
19     5795537   rs778986 FUT3         ENSG00000171124   A
19     5795649   rs812936 FUT3         ENSG00000171124   G
19     5795792   rs28362459 FUT3       ENSG00000171124   A
19    15152576   rs35769976 NOTCH3     ENSG00000074181   C
  19   18047618   rs11575934 IL12RB1         ENSG00000096996    T
  19   38044901   rs1007160 SLC7A9           ENSG00000021488    G
  19   38046895   rs12150889 SLC7A9          ENSG00000021488    A
  19   41031087   rs33950747 NPHS1           ENSG00000161270    C
  19   43656115   rs34694816 RYR1            ENSG00000196218    A
  19   46611870   rs34442879 BCKDHA          ENSG00000142046    C
  19   56542102   rs1130426 ETFB             ENSG00000105379    G
  19   57160104   rs4986771 ZNF350           ENSG00000197619    A
  20   10334059   rs1547     MKKS            ENSG00000125863    G
  21   45133740   rs5030672 ITGB2            ENSG00000160255    G
  22   16946288   rs12484657 PEX26           ENSG00000215193    C
  22   35018124   .          MYH9            ENSG00000100345    G


Exon Project
chr pos           dbSNP_id gencode_id          HGNC_gene_name   ref_allele
   1 119766354    rs35887327 ENSG00000203859   HSD3B2           T
   1 195657157    .          ENSG00000134376   CRB1             C
   1 195663584    .          ENSG00000134376   CRB1             C
   1 195665239    .          ENSG00000134376   CRB1             G
   1 195678032    rs62636285 ENSG00000134376   CRB1             G
   1 206025069    rs35366573 ENSG00000117335   CD46             C
   2 127754674    .          ENSG00000163161   ERCC3            T
   2 157114495    rs2116665 ENSG00000115159    GPD2             G
   2 201782343    rs13010627 ENSG00000003400   CASP10           G
   2 233364380    .          ENSG00000204120   GIGYF2           A
   2 233367789    .          ENSG00000204120   GIGYF2           A
   2 234341611    rs34946978 ENSG00000167165   UGT1A1           C
   2 237909660    rs11903206 ENSG00000163359   COL6A3           G
   2 237945215    .          ENSG00000163359   COL6A3           C
   2 237950184    .          ENSG00000163359   COL6A3           T
   2 237952485    rs35227432 ENSG00000163359   COL6A3           C
   3 15474717     rs6782980 OTTHUMG00000156233 COLQ             T
   3 33146467     .          OTTHUMG00000130746CRTAP            C
   3 106978032    .          OTTHUMG00000150654CBLB             G
   3 167030339    .          OTTHUMG00000158131BCHE             C
   3 167030632    .          OTTHUMG00000158131BCHE             T
   3 167031334    .          OTTHUMG00000158131BCHE             T
   3 167031361    rs56309853 OTTHUMG00000158131BCHE             G
   4 178468213    rs34007209 ENSG00000109674   NEIL3            C
   4 178520440    rs36005630 ENSG00000109674   NEIL3            G
   5    7938907   rs10064631 ENSG00000124275   MTRR             C
   5 37851869     rs36119840 ENSG00000168621   GDNF             G
   5 149337637    .          ENSG00000155850   SLC26A2          A
   5 149340823    .          ENSG00000155850   SLC26A2          C
   5 149341070    rs30832    ENSG00000155850   SLC26A2          T
   5 149341414    rs3776070 ENSG00000155850    SLC26A2          A
   6 25958824     rs56027330 ENSG00000124564   SLC17A3          C
   6 31937868     .          ENSG00000204386   NEU1             G
 7     5993234   rs63750668 ENSG00000122512   PMS2      C
 7    44522224   rs52815063 ENSG00000015520   NPC1L1    A
 7    44540660   .          ENSG00000015520   NPC1L1    G
 7    44542007   .          ENSG00000015520   NPC1L1    A
 7    44545025   rs35803101 ENSG00000015520   NPC1L1    G
 7    44545221   .          ENSG00000015520   NPC1L1    C
 7    44545676   .          ENSG00000015520   NPC1L1    G
 7    44546000   .          ENSG00000015520   NPC1L1    C
 7    44546126   .          ENSG00000015520   NPC1L1    T
 7    44546339   .          ENSG00000015520   NPC1L1    G
 7   127041787   rs2233578 ENSG00000106331    PAX4      G
 7   127041823   .          ENSG00000106331   PAX4      G
 7   127042702   rs35155575 ENSG00000106331   PAX4      G
 8    11645044   .          ENSG00000136574   GATA4     G
 8    11651892   .          ENSG00000136574   GATA4     C
 8    11651993   .          ENSG00000136574   GATA4     G
 8    11653284   .          ENSG00000136574   GATA4     C
 8    11653337   rs56208331 ENSG00000136574   GATA4     G
 8    65671818   .          ENSG00000172817   CYP7B1    G
 8    94862366   .          ENSG00000164953   TMEM67    A
 8    94867689   .          ENSG00000164953   TMEM67    C
 8   133969844   rs2229843 ENSG00000042832    TG        G
 8   133979096   .          ENSG00000042832   TG        C
 8   133979109   .          ENSG00000042832   TG        C
 8   134049325   .          ENSG00000042832   TG        A
 9    21960928   .          ENSG00000147889   CDKN2A    G
 9    21960979   rs6413464 ENSG00000147889    CDKN2A    C
 9   102048725   .          ENSG00000119509   INVS      G
10    50348728   rs4253208 ENSG00000225830    ERCC6     G
10    72313765   .          ENSG00000166228   PCBD1     C
11    64275394   .          ENSG00000068976   PYGM      G
11    64275703   .          ENSG00000068976   PYGM      C
11    64278072   .          ENSG00000068976   PYGM      G
11    95208229   .          ENSG00000087053   MTMR2     G
11    95209096   rs558018 ENSG00000087053     MTMR2     T
12    51631849   .          ENSG00000111057   KRT18     C
12    52111428   .          ENSG00000135409   AMHR2     C
15    41285829   rs45495503 ENSG00000166947   EPB42     C
15    41294681   rs28933988 ENSG00000166947   EPB42     C
15    56090181   .          ENSG00000128918   ALDH1A2   C
16     2079815   .          ENSG00000008710   PKD1      G
16     2080181   .          ENSG00000008710   PKD1      G
16     2083956   .          ENSG00000008710   PKD1      C
16     2084183   rs45478794 ENSG00000008710   PKD1      G
16     2092866   rs13337123 ENSG00000008710   PKD1      C
16     8812511   rs28936415 ENSG00000140650   PMM2      G
16     8814415   rs34258285 ENSG00000140650   PMM2      A
16    16159032   rs58694313 ENSG00000091262   ABCC6     C
16    16159100   rs2238472 ENSG00000091262    ABCC6     C
16   67403548   .          ENSG00000039068   CDH1     A
16   67413542   rs33935154 ENSG00000039068   CDH1     G
16   88140646   rs61755320 ENSG00000197912   SPG7     C
17   37948886   .          ENSG00000108784   NAGLU    G
19   15152576   rs35769976 ENSG00000074181   NOTCH3   C
19   15163649   rs2285981 ENSG00000074181    NOTCH3   C
19   17788781   .          ENSG00000105639   INSL3    G
19   41022117   rs34736717 ENSG00000161270   NPHS1    C
19   41022296   .          ENSG00000161270   NPHS1    C
19   41025229   .          ENSG00000161270   NPHS1    G
19   41030884   rs28939695 ENSG00000161270   NPHS1    C
19   41031087   rs33950747 ENSG00000161270   NPHS1    C
19   41031849   .          ENSG00000161270   NPHS1    G
19   41032027   rs34982899 ENSG00000161270   NPHS1    G
19   41032346   .          ENSG00000161270   NPHS1    A
19   41034052   rs3814995 ENSG00000161270    NPHS1    C
19   41034408   .          ENSG00000161270   NPHS1    G
alt_allele   disease_allele YRI_alt_allele_frequenceCEU_alt_allele_frequence
T            T              -                                          0.008
A            A              -                                          0.033
T            T                                 0.11 -
A            A                                0.517                    0.233
A            A                                0.136 -
T            T                                0.025                    0.058
T            G                                 0.28                    0.625
G            G              -                                          0.017
C            C                                0.051 -
A            A              -                                          0.008
A            A                                0.034 -
C            C                                0.068                      0.1
T            T              -                                          0.025
G            G              -                                          0.033
T            T              -                                          0.067
G            G                                0.042 -
A            A              -                       -
T            T              -                       -
A            A              -                                          0.067
A            A              -                                          0.017
A            A                                0.008 -
G            G              -                       -
T            T              -                                          0.008
T            T                                0.042 -
G            G              -                       -
G            G                                0.034 -
A            A                                0.127 -
C            C              -                                          0.017
T            C                                0.864                    0.717
A            A                                 0.11 -
C            C                                0.178 -
A            A              -                                          0.017
T            T              -                                          0.042
A            A                                0.551                    0.042
T            T              -                       -
A            A              -                       -
T            T                                0.093 -
G            G              -                       -
C            C                                0.085 -
T            T              -                                          0.042
G            G              -                                          0.017
C            C              -                                          0.008
C            C                                0.169                     0.25
A            A                                0.008 -
T            T                                0.017                     0.05
C   C       0.127        0.15
T   T   -               0.017
C   C       0.042 -
C   C   -               0.083
A   G       0.593        0.85
G   G       0.076 -
C   T       0.703       0.933
T   A       0.915        0.65
A   A   -               0.033
A   A   -               0.158
G   A           1       0.958
C   C       0.051 -
A   A   -         -
A   A   -               0.008
A   A   -               0.042
T   T   -               0.042
T   T   -               0.042
T   T       0.076 -
A   A   -               0.008
C   T       0.195        0.25
C   T       0.025       0.092
C   C   -
T   T   -               0.125
A   A   -         -
A   A       0.051 -
T   T       0.178 -
T   T       0.288 -
T   T   -               0.033
A   A   -               0.058
C   C       0.203 -
G   G        0.22       0.017
T   T   -               0.025
T   T   -               0.008
A   A       0.085 -
A   A       0.136 -
G   G   -               0.008
A   A   -               0.092
T   T       0.034 -
T   T   -                0.05
T   T       0.008 -
A   A       0.136         0.2
C   C   -               0.042
T   T   -               0.017
T   T       0.169 -
T   T       0.008       0.017
C   C       0.042 -
A   A   -               0.017
A   A   -               0.025
T   T   -           -
A   A   -               0.025
G   G       0.119 -
A   A   -               0.025
A   A   -               0.008
T   T       0.203       0.167
A   A       0.644 -
A   A   -         -
A   G       0.475       0.742
G   A       0.898       0.883
T   T   -               0.117
A   A   -                0.05
C   C       0.034 -
A   A       0.042 -
A   A   -               0.025
A   A   -               0.017
T   T   -               0.033
A   A   -               0.008
C   C       0.068 -
T   T   -               0.017
A   A       0.025   -
A   A        0.11   -
T   T       0.025   -
T   T       0.034   -
A   A       0.102   -
T   T   -           -
A   A   -               0.025
A   A   -         -
A   A       0.119 -
G   G       0.127 -
C   C       0.212       0.017
T   T   -               0.058
C   C   -               0.033
G   A        0.72           1
A   A   -               0.658
A   A       0.017 -
G   G       0.034       0.325
T   T   -         -
G   G       0.008 -
T   T       0.119 -
A   A   -               0.008
T   T   -         -
C   C   -         -
T   T       0.042 -
T   T   -               0.017
A   A       0.017 -
C   C       0.347 -
T   T       0.017 -
A   A   -               0.008
A   A       0.051 -
A   A   -         -
G   G       0.042 -
C   C   -               0.008
A   A       0.237 -
A   A       0.008 -
T   T   -               0.025
A   A   -               0.017
A   A       0.025 -
G   G   -               0.033
A   A       0.203 -
A   A       0.195 -
T   T       0.407       0.042
A   A   -         -
C   C       0.144       0.033
C   C       0.008 -
T   T   -               0.008
T   T       0.008 -
T   T       0.373 -
A   G       0.805       0.492
G   G        0.22 -
T   T   -               0.008
T   T   -           -
A   A   -           -
C   T           1       0.983
G   G   -               0.225
C   C   -               0.008
T   T   -               0.042
T   T   -               0.008
C   C       0.712       0.775
A   A   -               0.008
A   A   -               0.008
T   T       0.025 -
A   A   -               0.008
T   T   -               0.017
A   A   -               0.017
C   C       0.381       0.242
C   C   -               0.017
C   A       0.932       0.992
G   G       0.119 -
C   C       0.017 -
T   T   -               0.042
C   T           1       0.992
T   T       0.305       0.158
T   T   -               0.008
T   T   -               0.017
T   T   -               0.008
A   A       0.008 -
G   G       0.119 -
A   A   -         -
A   A       0.153       0.442
T   T   -               0.117
T   T   -               0.033
T   T       0.008 -
C   T        0.72       0.808
A   A       0.034 -
A   A       0.153       0.033
A   A       0.025 -
G   G   -         -
C   T       0.551       0.675
T   C       0.203       0.367
C   C       0.008       0.008
T   T       0.076       0.008
T   T   -               0.008
C   C       0.008 -
C   C       0.034 -
A   A       0.025 -
T   T   -               0.008
A   A       0.161       0.042
A   A   -               0.033
G   G       0.068 -
A   A       0.059 -
T   T   -                0.05
T   T       0.271       0.008
A   A   -               0.033
G   G       0.008 -
C   C       0.237 -
C   C       0.025 -
A   A   -               0.025
A   A   -               0.017
T   T       0.034 -
T   T       0.017 -
G   A       0.322       0.517
T   T   -               0.017
T   T        0.11 -
C   C       0.449       0.092
G   G       0.051 -
A   A   -               0.617
T   T   -               0.008
A   A   -               0.108
T   T       0.042   -
G   G       0.127   -
A   A       0.051   -
T   T       0.017   -
T   T       0.008   -
G   G   -               0.008
G   G   -           -
T   T   -               0.017
G   G   -               0.017
C   C   -         -
T   T   -         -
A   A       0.068 -
G   G       0.153       0.042
T   T   -         -
A   A   -               0.008
A   A   -               0.025
A   A       0.042 -
T   T   -               0.008
C   C       0.364         0.4
G   G   -               0.008
C   T       0.195       0.475
T   C       0.186       0.475
C   C       0.339 -
T   T   -               0.017
A   A       0.034   -
A   A       0.025   -
A   G       0.068   -
C   C        0.11   -
T   T   -               0.025
T   T   -           -
A   A   -               0.008
G   G       0.178 -
A   A   -               0.017
A   A   -         -
T   T       0.008 -
T   T   -         -
G   G   -               0.058
T   T       0.093 -
G   A           1       0.958
A   A   -               0.025
C   C   -               0.017
A   A       0.034   -
A   A       0.136   -
A   A       0.169   -
A   A       0.017   -
A   A       0.034   -
A   A   -               0.008
A   A       0.093   -
A   A       0.051   -
T   T       0.025   -
A   A       0.136   -
C   C   -               0.008
T   T       0.017 -
C   C       0.017 -
A   A   -         -
G   G   -         -
T   T   -               0.025
T   T   -           -
A   A   -               0.042
T   T   -               0.008
T   T   -               0.008
G   A       0.983       0.992
A   A   -           -
A   A       0.085        0.15
A   A   -         -
A   A   -         -
C   C       0.042 -
T   T       0.025 -
C   C       0.322       0.558
T   T   -               0.008
C   C       0.017       0.317
G   G       0.169   -
T   T       0.186       0.125
A   A       0.025   -
T   T       0.085   -
G   G       0.025   -
T   T   -               0.025
A   A       0.059 -
T   T   -               0.008
C   C       0.153       0.067
G   G       0.356 -
A   A   -         -
A   A       0.119 -
A   A       0.076 -
A   A       0.161       0.208
T   T   -         -
A   A       0.008 -
C   C   -               0.008
A   A   -               0.025
A   A       0.017       0.008
T   T       0.008 -
T   T       0.017 -
C   C       0.042       0.167
A   A       0.051 -
A   A   -               0.008
T   T   -               0.025
A   A       0.051 -
T   T   -               0.083
A   A   -               0.333
T   T       0.178 -
G   A       0.924       0.833
C   C   -         -
C   C       0.068 -
C   G       0.525       0.442
A   A        0.11 -
G   G       0.059 -
T   T       0.068 -
G   G       0.034 -
T   T       0.119 -
T   T   -               0.042
A   A   -               0.017
G   G   -               0.033
A   A       0.127 -
T   T       0.085 -
T   T       0.008 -
G   G   -               0.042
T   T       0.246 -
A   A   -               0.117
T   T   -               0.033
T   T   -               0.008
T   T       0.195   -
T   T       0.271   -
T   T       0.017   -
A   A       0.093   -
A   A   -               0.017
G   G       0.203       0.283
C   C   -               0.008
A   A       0.042       0.208
A   A   -               0.025
T   T   -               0.017
T   T   -                0.05
T   T   -               0.025
A   A   -               0.042
G   G   -               0.017
C   C   -               0.008
A   A   -               0.008
T   T   -         -
T   T       0.008 -
T   T       0.288 -
C   C       0.102       0.208
G   G       0.008 -
C   T           1       0.875
G   G   -         -
T   T   -               0.008
C   C   -           -
C   C   -               0.008
T   T   -           -
A   A   -           -
T   T   -               0.017
T   T   -               0.008
C   T       0.907       0.992
T   T       0.085 -
G   G       0.186 -
T   T   -               0.008
G   G       0.025 -
C   C       0.034 -
G   G       0.559       0.483
G   G   -               0.025
T   T   -         -
A   A       0.025 -
T   T       0.297       0.175
G   G       0.102 -
C   C   -               0.017
T   T   -               0.025
T   T   -               0.067
T   T       0.305       0.617
C   C   -               0.008
T   T   -               0.017
A   A   -         -
A   A       0.034 -
G   G   -               0.008
A   A   -               0.067
C   T       0.805       0.992
C   C       0.017 -
A   A   -               0.117
C   C   -               0.017
C   C   -               0.008
G   G       0.076         0.3
T   T   -               0.017
A   A   -                0.05
G   G       0.661       0.242
T   T   -               0.175
G   G   -               0.017
G   G   -           -
A   A        0.11        0.05
T   T   -               0.008
T   T       0.025 -
G   G       0.085 -
T   T       0.068 -
A   G       0.136       0.967
T   T   -               0.017
C   C       0.432       0.025
C   C   -           -
C   C       0.127       0.558
A   A       0.119       0.183
G   G       0.627       0.383
A   C       0.839       0.983
T   T   -               0.008
C   C       0.008 -
C   C   -               0.025
C   C   -               0.008
T   T   -         -
G   G   -         -
A   A       0.051 -
T   T   -         -
A   A   -         -
G   G       0.127 -
T   T   -               0.008
T   T       0.008 -
A   A       0.008 -
T   T   -         -
T   T   -               0.242
C   C   -               0.008
T   T       0.051 -
T   T       0.076       0.233
T   T   -               0.017
G   G       0.153       0.033
G   G       0.076 -
A   A   -                 0.1
T   C           1       0.992
G   C   -               0.925
T   T       0.008 -
A   A   -               0.008
T   T       0.068 -
G   G   -         -
T   T   -               0.058
A   A       0.068 -
G   G   -               0.025
T   T   -         -
T   T       0.085 -
A   A   -                0.05
C   C       0.085   -
A   A       0.169   -
C   C       0.119   -
A   A       0.017   -
A   A       0.085   -
A   A   -               0.033
A   A       0.051 -
A   A       0.051 -
T   T   -               0.008
G   G   -               0.025
A   A   -         -
T   T       0.051 -
T   T   -               0.017
C   C       0.246 -
T   T       0.085 -
T   T   -               0.008
A   A   -               0.008
A   A       0.025 -
T   T       0.373       0.442
C   C       0.441       0.192
C   C       0.008 -
G   G   -         -
T   T   -         -
A   A   -           -
T   T   -               0.042
A   A   -               0.008
C   C       0.076 -
T   T   -                 0.1
C   C       0.017 -
T   T   -               0.025
T   T       0.025 -
C   C   -               0.008
T   T   -           -
A   A   -               0.017
A   A       0.085 -
A   A   -               0.033
A   A   -               0.017
C   C       0.102 -
A   A   -               0.025
T   T   -               0.008
A   A   -                0.05
A   A   -               0.075
A   A       0.042 -
A   G       0.771       0.967
T   T   -               0.008
T   T   -               0.008
G   G   -               0.008
A   A       0.017 -
G   G   -         -
A   A   -               0.092
A   A       0.585        0.35
G   A       0.898       0.792
A   G       0.898       0.792
C   C       0.229       0.092
A   A       0.008 -
T   T   -               0.008
G   G       0.356       0.017
C   C       0.008 -
C   C       0.076       0.325
T   T       0.305       0.342
G   G       0.373       0.333
A   A   -               0.008
G   G       0.017 -
C   C       0.102       0.067
G   G       0.237 -
T   T   -               0.042
A   A   -               0.033
T   T   -               0.383
G   G       0.169   -
G   G       0.034   -
T   T       0.034   -
C   C       0.119   -
C        C                               0.144                0.092
T        T                               0.025 -
T        T                               0.093                0.067
A        A                               0.127 -
A        A                               0.466                0.567
G        G             -                                      0.042
C        C                               0.068 -
T        T             -                                      0.008
A        A                               0.017 -
G        G                               0.076 -
T        T             -                       -
A        A                               0.034 -
A        A                                0.22                0.075
C        C             -                                        0.1
A        A             -                                      0.033
T        T             -                       -
A        A                               0.008 -
T        T             -                                      0.042
T        T                               0.008 -
C        C             -                                      0.033
G        G             -                       -
C        C             -                                      0.008
G        G                               0.025 -
A        A                               0.102 -
T        T             -                                       0.05
A        A             -                                      0.008
G        G                               0.136                0.092
G        G                               0.051 -
T        T                               0.059 -
A        A             -                                      0.042
A        A             -                                      0.017
T        T             -                                      0.017
G        G             -                                      0.025
A        A             -                                      0.017
T        T                               0.076 -
G        G             -                                      0.058
A        A             -                                      0.058
G        G             -                                      0.058
A        A             -                                      0.033
C        C                               0.254 -
A        A                               0.051 -
T        T                               0.161                    0.15
A        A             -                                          0.15




alt_allele disease_allele NA19239_genotype     NA19238_genotype
A          A              GA                   GA
T          G              -                    -
A   A   GG   GA
T   T   -    -
G   G   CG   CG
T   C   TT   TT
A   A   CC   CA
T   T   -    -
T   T   CT   CC
C   C   -    -
T   T   -    -
A   G   GA   GG
C   T   TC   TC
T   A   TT   TT
G   A   GG   GG
C   T   TC   TT
C   C   -    -
T   T   GT   GT
T   T   GT   GT
C   C   TT   TC
A   A   -    -
A   A   -    -
T   T   TT   GT
A   A   -    -
C   C   AA   AC
T   T   -    -
A   A   AA   GG
A   G   GA   GA
G   A   GG   AG
T   T   -    -
C   C   TT   TC
A   A   GG   GA
A   A   -    -
C   C   GC   GG
A   A   GG   GA
C   C   TT   TC
G   A   AA   GG
A   A   -    -
A   A   GA   GG
G   G   -    -
A   A   TA   TT
C   C   TT   CC
A   A   GA   GA
A   A   GA   GG
T   T   AT   AA
A   G   AA   GA
G   G   AG   AA
G   G   CC   CG
C   T   CC   CC
C   C   GC   GC
T   T   CC   CT
C   C   CC   TC
T   T   CC   CT
C   A   CC   CC
C   T   CC   CC
T   T   AA   AT
T   T   -    -
C   T   TC   CC
A   A   GA   GG
C   T   CC   CC
T   C   CT   CC
A   A   GG   GA
T   T   GT   GG
T   T   CT   CC
G   G   -    -
C   C   TC   TT
T   T   CC   CT
G   A   AA   AG
C   C   TC   TT
T   T   -    -
A   A   -    -
C   C   -    -
C   C   GG   CC
C   T   -    -
T   C   -    -
A   G   GA   GG
C   C   AA   AC
G   G   AG   AG
G   A   GG   GG
A   A   GA   GG
A   A   TA   TT
A   A   GG   GA
A   A   GA   GG
G   A   GG   AG
T   T   -    -
C   C   TT   TC
C   C   -    -
C   C   TT   TC
G   G   AA   AG
T   T   CC   CT
A   A   GA   GA
G   G   AG   GG
T   T   CT   CC
A   A   -    -
A   A   GA   GG
C   C   -    -
A   A   -    -
A   A   GA   GG
T   T   CC   CT
G   A   GG   GG
C   C   TT   TC
C   G   GC   GC
T   T   CT   CC
A   A   GA   GG
T   T   CC   CT
G   G   AG   AG
A   A   -    -
G   G   AG   AA
A   A   -    -
C   C   -    -
C   T   CC   CC
G   G   AG   AA
C   T   CC   CC
G   G   AA   AG
G   G   GG   GG
T   T   GT   TT
T   T   -    -
T   T   CT   TT
G   G   -    -
C   T   CC   CC
C   C   GG   GC
G   G   -    -
A   A   -    -
G   G   GG   GG
A   G   GG   GA
C   C   TC   TT
C   C   TC   TC
A   A   -    -
G   G   AG   GG
A   C   AA   AA
T   T   CT   CC
G   G   AG   AA
T   C   TT   TT
G   C   GG   GG
T   T   CT   CC
T   T   CT   CC
C   C   TC   TT
A   A   GG   GA
A   A   -    -
T   T   -    -
C   C   CC   CC
G   G   AA   AG
A   A   -    -
A   G   GA   AA
A   A   GA   AA
G   A   GG   AG
A   G   AA   GA
C   C   AC   AA
G   G   CG   GG
C            C            TT                      TC
T            T            -                       -
G            G            -                       -
T            T            -                       -
G            G            AG                      AA
T            T            -                       -
A            A            AA                      AA
G            G            -                       -
A            A            GA                      GG
A            A            -                       -
G            G            -                       -
A            A            -                       -




alt_allele   disease_allele YRI_alt_allele_frequenceLWK_alt_allele_frequence
C            C                                 0.03                   0.037
T            T              -                       -
A            A                                0.009                   0.005
A            A              -                       -
A            A              -                       -
T            T              -                       -
C            C              -                       -
A            G                                0.505                   0.448
A            A              -                       -
G            G              -                       -
C            C              -                       -
T            T              -                       -
A            A                                0.045                   0.014
T            T              -                       -
C            C              -                       -
T            T                                0.018                   0.032
C            C                                0.179                    0.12
T            T              -                                         0.005
A            A              -                       -
G            G              -                       -
C            C              -                       -
C            C              -                       -
A            A              -                                         0.009
T            T                                0.316                   0.335
T            T              -                       -
G            G                                0.188                   0.086
A            A              -                       -
C            C              -                       -
T            T              -                       -
C            T                                    1                       1
T            T                                0.259                   0.287
T            T                                0.005                   0.014
A            A              -                       -
A   A   -               0.014
T   T   -         -
A   A       0.005 -
T   T       0.014 -
A   A   -         -
T   T   -               0.005
A   A   -           -
T   T   -           -
C   C   -               0.014
A   A   -               0.005
A   A       0.068       0.103
A   A   -         -
A   A        0.01 -
A   A   -         -
T   T   -         -
A   A       0.051       0.032
A   A   -         -
A   A   -         -
A   A   -         -
T   T   -                0.01
T   T   -           -
T   T   -           -
T   T   -               0.005
T   T   -           -
G   G   -           -
A   A       0.007       0.005
A   A       0.008       0.015
A   A       0.014       0.005
C   C       0.046       0.032
T   T   -               0.014
A   A   -           -
T   T   -               0.005
A   A   -           -
C   C   -           -
C   C       0.073       0.111
T   T       0.012 -
A   A       0.005 -
T   T   -         -
T   T   -         -
A   A   -               0.028
A   A   -           -
A   A   -                0.01
T   T   -           -
A   A   -           -
G   G       0.114       0.104
A   A   -           -
C   C   -           -
T   T       0.075        0.14
T   T       0.075       0.056
G   G   -           -
A   A       0.068       0.028
T   T   -           -
A   A   -           -
G   G       0.346       0.191
T   T   -           -
A   A   -           -
G   G       0.206       0.176
G   G   -           -
A   A   -           -
T   T   -           -
T   T   -           -
A   A   -               0.005
C   C       0.012       0.005
C   C   -           -
T   T       0.045       0.083
A   A   -           -
                           H
CHBJPT_alt_allele_frequence GMD_acc_num
-                          CM055541
-                          CM022976
-                          CM032394
                     0.425 CM031993
-                          CM073192
                       0.1 CM056008
                     0.783 CM042957
-                          CM056695
-                          CM083557
-                          CM044245
-                          CM042455
                     0.217 CM970536
-                          CM024704
                      0.05 CM073103
-                          CM001173
-                          CM045413
                     0.008 CM090827
                     0.075 CM013251
-                          CM010063
-                          CM961406
-                          CM961408
                      0.05 CM065323
-                          CM074441
-                          CM065096
                       0.2 CM065101
-                          CM066162
-                          CM054799
-                          CM033079
                     0.858 CM001812
-                          CM994071
-                          CM066527
-                          CM067721
-                          CM082792
-                          CM023000
                     0.008 CM990050
                     0.058 CM970011
-                          CM014300
                     0.033 HM080053
-                          CM990042
-                          CM024629
-                          CM970003
-                          CM074661
                     0.217 CM015072
-                          CM022997
-                          CM020912
    0.233 CM033371
-         CM033370
-         CM056580
    0.017 CM003589
    0.958 CM970421
-         CM023321
    0.958 CM983430
    0.658 CM003692
-         CM041235
-         CM920026
        1 CM991218
-         CM993170
    0.008 CM950959
-         CM950958
-         CM061191
-         CM990977
-         CM990978
-         CM920629
-         CM094721
      0.2 CM070090
-         CM070088
-         CM004363
    0.025 CM085579
    0.008 CM057724
-         CM044689
-         CM055120
-         CM070675
-         CM050548
-         CM077517
    0.058 CM034583
-         CM001809
-         CM001806
-         CM077830
-         CM981662
-         CM074391
-         CM013708
-         CM074947
-         CM057334
-         CM040093
-         CM980096
    0.625 CM980093
-         CM980092
-         CM040371
-         CM054759
    0.058 CM086585
-         CM014175
-         CM070277
-         CM950813
    0.033 CM983445
-         CM053208
    0.025 CM052853
-         CM074148
-         CM013386
    0.267 CM950629
-         CM950635
    0.017 CM085330
    0.725 CM012769
    0.958 CM051623
-         CM074143
    0.192 CM074141
-         CM991061
-         CM991062
-         CM990325
-         CM061663
-         CM050963
-         CM064935
    0.175 CM071094
-         CM005424
-         CM070889
-         CM041026
-         CM985505
-         CM985506
-         CM050237
    0.058 CM050231
-         CM056286
    0.083 CM087282
-         CM980305
-         CM071751
-         CM045572
-         CM051404
-         CM980257
        1 CM051080
    0.525 CM055955
-         CM000176
    0.075 CM970958
    0.008 CM066133
-         CM023747
-         CM014821
-         CM097690
    0.033 CM020303
      0.1 CM023447
-         CM083608
-         CM001954
-         CM071867
-         CM994541
-         CM084997
-         CM951045
-         CM951041
    0.175 CM014862
-         CM032021
-         CM060475
-         CM000509
-         CM073422
-         CM043880
-         CM021367
-         CM960907
-         CM087498
-         CM940960
-         CM940961
    0.008 CM040732
    0.283 CM044027
-         CM057721
-         CM076092
-         CM025213
-         CM074176
-         CM053344
    0.667 CM073166
-         CM992646
-         CM970206
    0.092 CM930316
    0.108 CM930317
        1 CM952225
     0.25 CM910221
-         CM040379
-         CM003999
-         CM015300
    0.558 CM078286
-         CM080626
-         CM050770
-         CM080070
-         CM042292
-         CM030964
-         CM090541
    0.617 CM004548
-         CM033672
    0.992 CM056011
-         HM030003
-         CM085637
-         CM010436
        1 CM016008
      0.1 CM980573
-         CM023458
-         CM012968
-         CM096566
-         CM993125
-         CM057201
    0.025 CM085968
    0.375 CM065338
-         CM043093
-         CM990718
-         CM003463
    0.833 CM971297
-         CM951114
    0.025 CM092994
-         CM091386
    0.017 CM003167
    0.375 CM920487
    0.142 CM920486
-         CM050667
    0.067 CM991100
-         CM051189
-         CM034276
-         CM051133
-         CM042022
-         CM043845
    0.158 CM087682
-         CM030232
-         CM031971
-         CM031972
-         CM031974
-         HM050002
-         CM074671
-         CM085991
-         CM024242
-         CM074975
-         CM086609
-         CM061908
-         CM950571
-         CM068032
    0.842 CM910199
-         CM057352
-         CM034771
-         CM072814
-         CM034639
    0.383 CM096001
-         CM025301
    0.108 CM055540
-         CM040266
-         CM050323
-         CM040117
-         CM930098
-         CM910070
-         CM930108
    0.042 CM920985
-         CM950247
-         CM930133
    0.017 CM931158
    0.017 CM993876
-         CM043322
    0.042 CM002227
    0.008 CM066596
-         CM940284
-         CM095028
    0.025 CM068344
     0.15 CM053343
     0.55 CM066015
-         CM023577
    0.375 CM962671
    0.375 CM962670
-         CM983990
-         CM980996
-         CM034442
-         CM030659
-         CM984605
-         CM065260
-         CM014381
    0.008 CM015009
-         CM044022
-         CM033078
-         CM083709
    0.417 HM972177
    0.417 HM972174
      0.5 CM033362
-         CM920222
-         CM032675
        1 CM021685
-         CM021683
-         CM082700
-         CM023043
    0.083 CM015016
    0.108 CM032347
-         CM020751
-         CM077940
-         CM041975
-         CM080364
-         CM035922
-         CM040739
-         CM004889
-         CM066226
-         CM076515
-         CM076516
    0.017 CM993761
    0.192 CM003624
-         CM030405
    0.025 CM058044
-           CM020927
-           CM083739
-           CM083742
        1   CM095002
    0.075   CM020164
-           CM001290
    0.025   CM066207
    0.025   CM033449
-           CM980632
-           CM050736
    0.875   CM057373
-           CM057370
    0.117   CM057372
-           CM021540
    0.092   CM014368
-           CM094350
    0.008   CM063234
-           CM065959
-           CM032216
-           CM012076
-           CM097202
    0.167   CM033380
    0.067   CM071761
    0.083   CM044650
-           CM880038
-           CM041854
    0.225   CM067719
    0.033   CM067435
-           CM067434
-           CM092537
-           CM045580
    0.033   CM064281
-           CM057197
-           CM032598
    0.033   CM043536
-           CM004432
-           CM930629
-           CM083722
-           CM030643
-           CM033597
    0.292   CM055288
-           CM981987
        1   CM002936
    0.033   CM013413
-           CM013412
    0.767   CM092500
-           CM024583
-           CM035888
-           CM023331
-         CM023332
    0.017 CM021944
-         CM000653
-         CM003169
-         CM022244
-         CM011786
-         CM082943
-         CM086841
-         CM960893
-         CM070322
    0.258 CM930731
-         CM064356
-         CM910395
-         CM910394
-         CM002120
-         CM070344
-         CM012481
-         CM055536
    0.042 CM091988
-         CM053300
    0.233 CM950928
-         CM950933
-         CM022677
-         CM076254
-         CM031289
-         CM060322
-         CM068144
-         CM068143
-         CM870016
    0.025 CM981427
-         CM023189
-         CM057989
-         CM067044
-         CM082848
      0.8 CM003889
    0.017 CM012138
-         CM013723
    0.192 CM013722
-         CM022367
      0.4 CM013720
    0.017 CM024726
-         CM010170
-         CM994286
        1 CM960194
-         CM050183
    0.017 CM970189
-         CM030499
-         CM030507
-         CM994115
    0.375 CM044579
-         CM083011
    0.025 CM992653
-         CM020934
-         CM032029
-         CM012463
-         CM050712
-         CM981918
-         CM005500
      0.9 CM985500
-         CM960729
-         CM075030
    0.033 CM062876
-         CM035903
-         CM074454
-         CM084868
    0.933 CM950521
-         CM970563
-         CM950518
-         CM043090
-         CM043088
    0.283 CM900187
-         CM830003
-         CM890097
-         CM860015
    0.217 CM900182
-         CM930002
    0.008 CM920002
    0.042 CM071966
    0.092 CM941112
-         CM971079
-         CM041734
-         CM990302
     0.95 CM085371
-         CM097377
    0.042 CM085365
    0.317 HM0656
    0.425 CM068495
    0.192 CM971009
    0.842 CM910256
      0.9 CM962679
-         CM910258
-         CM045807
-         CM042765
-         CM043327
    0.008 CM071582
    0.067 CM067057
-         CM983891
    0.008 CM014740
    0.033 CM013956
-         CM003338
-         CM064939
     0.05 CM990838
    0.042 CM990837
    0.033 CM025263
    0.042 CM044663
-         CM002843
-         CM072815
    0.133 CM001044
-         CM074412
-         CM031328
-         CM015864
-         CM074384
        1 CM012900
-         CM022671
-         CM002107
-         CM961298
    0.025 CM981836
    0.033 CM930092
-         CM071830
-         CM034216
-         CM040069
    0.025 CM950544
-         CM962611
    0.017 CM992318
-         CM962610
-         CM962608
-         CM973122
-         CM090121
-         CM992863
-         CM992303
-         CM003233
-         CM003228
-         CM003227
-         CM071921
    0.158 CM990080
-         CM034378
-         CM021325
-         CM057708
-         CM023932
    0.217 CM994059
-         CM083699
-         CM074372
    0.267 CM071857
    0.275 CM073339
-         CM066109
    0.033 CM065000
    0.008 CM087388
    0.008 CM041694
-         CM940175
-         CM004236
-         CM960173
-         CM960172
-         CM960167
-         CM930673
-         CM090256
-         CM983332
    0.017 CM951139
-         CM066259
-         CM080591
-         CM062749
-         CM082926
-         CM025932
-         CM990941
-         CM020025
-         CM068260
-         CM941338
-         CM900219
    0.875 CM015226
-         CM092684
-         CM043812
-         CM030483
-         CM041339
    0.067 CM041082
-         CM024106
    0.583 CM940794
    0.958 CM930259
    0.958 CM970545
     0.15 CM930258
-         CM983995
-         CM071834
-         CM085589
-         CM067477
    0.367 CM984025
    0.333 CM061204
    0.333 CM061206
-         CM010444
-         CM015365
-         CM024138
-         CM044918
-         CM990958
-         CM044680
    0.617 HM080063
-         CM064230
-         CM044256
-         CM091772
-         CM066043
-                          CM900020
-                          CM880008
                    0.05   CM860003
-                          CM000677
                   0.283   CM940379
-                          CM032056
-                          CM094534
-                          CM094531
-                          CM020189
-                          CM971239
                   0.042   CM065403
-                          CM065405
                   0.208   CM064119
                   0.033   CM023740
-                          CM094615
                   0.025   CM012661
-                          CM960790
-                          CM004479
-                          CM900007
-                          CM860001
                   0.075   CM095345
-                          CM020047
-                          CM993507
                   0.083   CM013738
-                          CM054156
-                          CM970239
-                          CM920136
-                          CM994315
-                          CM020261
-                          CM050211
-                          CM050224
-                          CM076126
-                          CM060428
-                          CM890060
-                          CM994371
-                          CM961319
-                          CM961335
-                          CM961339
-                          CM970401
-                          CM080200
-                          CM020773
-                          CM063224
                     0.2   CM003741




NA19240_genotype           NA12891_genotype
GA                         GG
-                          GG
GA   -
-    CC
CC   -
TT   CT
CA   -
-    CT
CT   -
-    TT
-    CT
GG   AA
CC   CC
TT   AT
GG   GG
TT   CC
-    TT
GT   -
GT   -
TC   -
-    GG
-    CA
TT   -
-    GG
AA   -
-    AA
GA   -
AA   GA
GG   GG
-    CT
TT   -
GG   -
-    GA
GG   -
GG   -
TC   -
AG   GG
-    GA
GG   -
-    AA
TT   -
TC   -
GA   -
GG   -
AT   -
AA   GA
AG   -
CC   -
CC   -
GC   GG
CC   -
CC   TT
CC   -
CC   CC
CC   CC
AA   -
-    CT
CC   TC
GA   -
CC   TC
CT   -
GA   -
GG   -
CT   -
-    AA
TC   -
CC   -
AG   GG
TT   -
-    CT
-    GG
-    AA
GC   -
-    TC
-    CT
GA   -
AC   -
AG   -
GG   AG
GG   -
TT   -
GG   -
GG   -
GG   GG
-    CT
TT   TC
-    AC
TT   -
AG   -
CC   -
GA   -
GG   -
CC   -
-    GA
GA   -
-    TC
-    CA
GG   -
CT   -
GG   GG
TC   -
GG   GC
CT   -
GA   -
CC   -
AG   -
-    GA
AA   -
-    CC
-    TC
CC   CC
AG   -
CC   CC
AA   -
GG   GG
TT   -
-    CT
CT   -
-    CG
CC   CC
GG   -
-    TG
-    TT
GG   -
GG   AA
TC   -
CC   CC
-    GA
AG   AA
AA   AA
CC   CT
AG   -
TT   TT
GG   GG
CC   -
CC   -
TC   -
GA   -
-    GA
-    CT
CC   TT
AA   -
-    GG
GA   AA
GA   GA
AG   AG
GA   -
AC   -
GG   -
TC                           TC
-                            GT
-                            AG
-                            CC
AA                           -
-                            CT
AA                           AA
-                            AG
GA                           -
-                            GA
-                            CC
-                            GG




CEU_alt_allele_frequence     TSI_alt_allele_frequence
-                            -
-                            -
-                            -
-                            -
-                                              0.008
                     0.006   -
                     0.006                     0.008
                     0.722                     0.774
                     0.039                     0.048
-                            -
-                                              0.008
-                            -
-                            -
-                            -
                     0.006   -
-                            -
                     0.011                     0.008
-                            -
-                            -
-                            -
-                            -
-                            -
-                            -
-                                              0.033
                     0.006                     0.016
-                            -
                     0.011                     0.008
-                                              0.008
                     0.028                     0.015
                     0.989                     0.992
                     0.142                     0.195
                     0.112                     0.102
-                            -
    0.012 -
    0.017 -
-         -
-         -
    0.017      0.03
-         -
-         -
    0.006 -
-         -
-         -
-         -
-         -
-         -
-         -
    0.006 -
-         -
-         -
-         -
    0.011 -
-         -
-         -
    0.011 -
-         -
-         -
-         -
-         -
-         -
-         -
-         -
-         -
-         -
-         -
    0.008 -
-         -
-         -
-         -
-         -
    0.006 -
-         -
-         -
    0.019 -
-         -
-         -
-         -
-         -
    0.017      0.03
    0.006     0.015
-             0.015
    0.241     0.287
-           -
-           -
    0.006       0.008
-         -
    0.014 -
-         -
    0.006 -
-         -
-         -
-               0.008
-           -
    0.074       0.023
    0.021       0.008
    0.019       0.008
-               0.008
    0.367       0.288
-           -
disease                                           hgvs
Cleft lip ?                                       1163C>T
Nephronophthisis 4                                2542C>T
Parkinson disease, autosomal recessive            234C>T
Cortisone reductase deficiency                    1358G>A
MASP2 deficiency                                  377C>T
Methylenetetrahydrofolate reductase deficiency    1781G>A
Bartter syndrome 3                                80T>G
Medullary thyroid carcinoma ?                     487T>C
Cowden-like syndrome                              8C>G
Parkinson disease, early-onset                    1015G>A
Parkinson disease, early-onset                    1426G>A
Fucosidosis                                       29C>G
Hypercholesterolaemia, autosomal recessive        712C>T
Deafness                                          507C>G
Deafness, non-syndromic, autosomal recessive      94C>T
Deafness, non-syndromic, autosomal dominant       529T>G
Deafness, non-syndromic, autosomal recessive      580G>A
Fuchs corneal dystrophy ?                         464G>A
Amegakaryocytic thrombocytopaenia, congenital     340G>A
Porphyria, cutanea tarda                          758T>A
Porphyria, cutanea tarda                          952G>A
Adenomatous polyposis coli?                       1389G>C
Muscular dystrophy, limb girdle                   1666G>A
Carnitine palmitoyltransferase 2 deficiency       302C>T
Carnitine palmitoyltransferase 2 deficiency       1055T>G
Hypocholesterolaemia                              1274A>G
Hypercholesterolaemia, autosomal dominant         1327G>A
Congenital disorder of glycosylation 1c           391T>C
Congenital disorder of glycosylation 1c, mild     911T>C
Retinitis pigmentosa                              1301C>T
Medium chain acyl CoA dehydrogenase deficiency   ?351A>C
Premature ovarian failure                         2329C>T
Neutropaenia, severe chronic                      107G>A
Cone-rod degeneration                             6764G>T
Stargardt disease                                 4297G>A
Macular degeneration, age related                 4283C>T
Stargardt disease                                 3899G>A
Macular dystrophy                                 3626T>C
Stargardt disease                                 3602T>G
Macular degeneration, age related                 2828G>A
Stargardt disease                                 2588G>C
Macular dystrophy, early-onset                    1928T>G
Stargardt disease ?                               1268A>G
Cone-rod degeneration                             763C>T
Macular degeneration, age related                 635G>A
Dihydropyrimidine dehydrogenase deficiency ?     1627A>G
Dihydropyrimidine dehydrogenase deficiency ?     1601G>A
Dihydropyrimidine dehydrogenase deficiency       557A>G
Dihydropyrimidine dehydrogenase deficiency ?     496A>G
Dihydropyrimidine dehydrogenase deficiency ?     85T>C
Glycogen storage disease 3                       112A>G
Maple syrup urine disease                        1150G>A
Erythrocyte lactate transport deficiency         1470A>T
Adenosine monophosphate deaminase deficiency     860A>T
Adenosine monophosphate deaminase deficiency     143C>T
Hypothyroidism                                   40G>A
3 beta-hydroxysteroid dehydrogenase deficiency   707T>C
Haemolytic anaemia                               1468C>T
Pyruvate kinase deficiency                       1456C>T
Retinitis pigmentosa                             2138G>A
Pain insensitivity, congenital                   1792C>T
Pain insensitivity, congenital                   1820G>T
Elliptocytosis                                   2373C>A
Hemiplegic migraine ?                            25T>A
Thrombosis ?                                     5290G>A
Thrombosis ?                                     1242G>A
Glaucoma 1, open angle ?                         1193A>G
Glaucoma 1, open angle ?                         227G>A
Glaucoma 1, open angle                           57G>T
Nephrotic syndrome, steroid resistant            725C>T
Factor H deficiency                              2669G>T
Haemolytic uraemic syndrome                      3019G>T
Haemolytic uraemic syndrome ?                    3148A>T
Haemolytic uraemic syndrome susceptibility ?     1067G>A
Cardiomyopathy, hypertrophic                     758A>G
Usher syndrome 2a                                2137G>C
Usher syndrome 2a                                688G>A
Breast cancer ?                                  1148C>A
Alzheimer disease ?                              185G>A
Cardiomyopathy, hypertrophic                     13031G>A
Colorectal cancer, non-polyposis                 1828A>G
Cryopyrin-associated periodic syndrome ?         2113C>A
Diabetes mellitus, type 2                        659C>T
Multiple epiphyseal dysplasia ?                  754G>A
Hypocholesterolaemia                             11761G>A
Hypocholesterolaemia                             8216C>T
Hypocholesterolaemia                             5768A>G
Hypobetalipoproteinaemia                         3383G>A
Mitochondrial trifunctional protein deficiency   1072C>A
Hypertension ?                                   514G>A
Glaucoma, primary congenital ?                   1328C>G
Noonan syndrome                                  1964C>T
Colorectal cancer, non-polyposis ?               965G>A
Colorectal cancer, non-polyposis ?               1168C>T
Dysferlinopathy                                 509C>A
Muscular dystrophy, limb girdle 2B?             565C>G
Miyoshi myopathy                                1369G>A
Miyoshi myopathy                                5999G>A
Diabetes, NIDDM                                 426A>T
Diabetes, NIDDM                                 2531G>A
Achromatopsia                                   1405G>A
Increased plasma FFA and glycerol levels        791A>G
Erythermalgia, primary                          3448C>T
Progressive hearing loss, autosomal recessive   793C>T
Progressive hearing loss, autosomal recessive   874G>A
Colorectal cancer, non-polyposis                1181T>C
Colorectal cancer, non-polyposis                1501G>A
Autoimmune lymphoproliferative syndrome II ?    1228G>A
Pulmonary hypertension, primary                 2324G>A
Ichthyosis, harlequin                           7093G>A
Ichthyosis, harlequin                           3889C>T
Schimke immuno-osseous dysplasia                1129G>C
Cerebrotendinous xanthomatosis                  1151C>T
Cardiomyopathy, dilated                         1375G>A
Adrenocortical tumour                           679G>A
Retinitis pigmentosa                            250C>T
Retinitis pigmentosa                            1091C>T
Bethlem myopathy                                8822C>T
Ullrich congenital muscular dystrophy           4184G>A
Hyperoxaluria                                   26C>A
Hyperoxaluria                                   590G>A
Muscular dystrophy, limb girdle                 166G>A
Fanconi anaemia                                 1367T>G
Endplate acetylcholinesterase deficiency        934A>G
Biotinidase deficiency                          1171C>T
Biotinidase deficiency, partial                 1330G>C
Gangliosidosis GM1                              1561C>T
Gangliosidosis GM1                              29C>T
Colorectal cancer, non-polyposis ?              637G>A
Colorectal cancer, non-polyposis ?              655A>G
Colorectal cancer, non-polyposis                1742C>T
Endometrial cancer                              1963A>G
Colorectal cancer, non-polyposis ?              2152C>T
Long QT syndrome                                5689C>T
Sudden unexplained nocturnal death syndrome     3578G>A
Brugada syndrome                                376A>G
Epidermolysis bullosa dystrophica               4613G>A
Hyperglycinaemia, non-ketotic                   631G>A
Protein kinase deficiency                       1861A>T
Pituitary hypoplasia                            374A>G
Vesicoureteral reflux                           1544A>T
Protein S deficiency                            233C>T
Protein S deficiency                            119G>T
Bernard-Soulier syndrome                            466G>A
Nephronophthisis 3                                  3941G>C
Sucrase isomaltase deficiency?                      5234T>G
Ellis-van Creveld syndrome                          1328G>A
Sensorineural hearing loss                          482G>A
Wolfram syndrome                                    2327A>T
Diabetes, type 1, and sensorineural hearing loss    2611G>A
Piebaldism                                          532G>A
Haemangioma, infantile                              1444T>C
Histatin 2 deficiency                               122G>A
Histatin 2 deficiency                               141T>A
Dentinogenesis imperfecta type II                   202A>T
Polycystic kidney disease 2                         568G>A
Microsomal triglyceride transfer protein defic. ?   1151A>C
Haemolytic uraemic syndrome                         548A>G
Haemorrhages                                        794C>T
Hypofibrinogenaemia ?                               1099G>A
Multiple colorectal adenoma                         112C>T
Prekallikrein deficiency                            428A>G
Methionine synthase reductase deficiency ?          997C>G
Complement C9 deficiency                            162C>A
Laron dwarfism ?                                    1319G>T
Laron dwarfism                                      1735C>A
Sandhoff disease                                    185C>T
Motor neuron disease                                619A>G
Mucopolysaccharidosis VI                            1450A>G
Mucopolysaccharidosis VI ?                          1151G>A
Colon cancer ?                                      2041C>T
Cervical carcinoma, association with                2188C>G
Glaucoma, primary open angle                        376G>A
Glaucoma, primary open angle                        1586G>A
Colorectal adenoma                                  2608C>T
Adenomatous polyposis coli ?                        7504G>A
Parkinson disease                                   1861C>T
Contractural arachnodactyly                         976C>T
Pulmonary alveolar proteinosis                      350T>C
Breast and/or ovarian cancer ?                      280A>C
Myotilinopathy                                      220C>A
Pancreatitis, chronic                               36G>C
Retinitis pigmentosa                                908C>G
Diastrophic dysplasia                               1474C>T
Diastrophic dysplasia ?                             1721C>T
Achondrogenesis 1B                                  2065A>T
Treacher-Collins syndrome                           122C>T
Hyperekplexia                                       1108G>A
Cardiac disease                                     543G>A
Cardiac disease                                     73C>T
Pituitary hormone deficiency                        152G>C
Dysplasia, arrhythmogenic right ventricular         7916G>A
Myoclonic epilepsy of Lafora                       332C>T
Glycogen storage disease 1c ?                      601G>A
Haemochromatosis                                   193A>T
Sialidosis                                         649G>A
Retinitis punctata albescens                       1013G>A
Retinitis pigmentosa                               133C>T
Zellweger syndrome ?                               2426C>T
Zellweger syndrome C                               1646C>T
Xeroderma pigmentosum, variant                     1603A>G
Methylmalonic aciduria                             2011G>A
Methylmalonic aciduria                             1595A>G
Methylmalonic aciduria                             205A>G
Rh-null syndrome                                   808G>A
Polycystic kidney disease                          10926G>A
Polycystic kidney disease ?                        7921A>G
Polycystic kidney disease                          2027C>G
Myoclonic epilepsy, juvenile                       662G>A
Tourette syndrome                                  28C>T
Muscular dystrophy, merosin deficient              3412G>A
Laminin alpha 2 chain deficiency, partial          4750G>A
Idiopathic infantile arterial calcification        1675C>G
Idiopathic infantile arterial calcification        1846G>A
Idiopathic infantile arterial calcification        2164C>T
Cardiomyopathy, dilated                            65G>T
Joubert syndrome ?                                 2488C>T
Parkinson disease, early-onset ?                   799T>C
Parkinson disease, autosomal recessive             783A>G
Parkinson disease, autosomal recessive             458C>G
Vertebral malformation                             1013C>T
Colorectal cancer, non-polyposis                   1688G>T
Diabetes, NIDDM                                    31G>A
Low dietary cholesterol absorption                 1940T>A
Mucopolysaccharidosis VII                          1946C>T
POR deficiency                                     683C>T
Low phospholipid associated cholelithiasis         2363G>A
Intrahepatic cholestasis, familial progressive ?   1954A>G
Low phospholipid associated cholelithiasis         1584G>C
Intrahepatic cholestasis of pregnancy, assoc. ?    504C>T
Phenotype modifier?                                1364G>A
Plasminogen activator inhibitor 1 deficiency       43G>A
Deafness, non-syndromic, autosomal recessive       970A>T
Pendred syndrome ?                                 1826T>G
Deafness, non-syndromic, autosomal recessive       2218G>A
Cystic fibrosis ?                                  220C>T
Cystic fibrosis                                    1000C>T
Cystic fibrosis                                    1052C>G
Cystic fibrosis ?                                  1666A>G
Cystic fibrosis ?                                  2002C>T
Cystic fibrosis                                    3705T>G
Cystic fibrosis                                      4056G>C
Cystic fibrosis                                      4357C>T
Diabetes, type 2                                     397C>T
Distal renal tubular acidosis, autosomal recessive   1739T>C
Pancreatitis, chronic ?                              410C>T
Myotonia congenita                                   899G>A
Diabetes, MODY                                       211G>A
Congenital heart defects                             1138G>A
Multiple colorectal adenoma                          770G>T
Tropical calcific pancreatitis                       76C>G
Prostate cancer?                                     338T>C
Farber disease                                       277G>A
Farber disease                                       214A>G
Alopecia universalis ?                               3064A>G
Congenital atrichia ?                                1859G>A
Parkinson disease                                    2174C>A
Kallmann syndrome                                    2314C>T
Spherocytosis                                        3224T>C
Mucopolysaccharidosis IIIC                           1567A>C
Retinitis pigmentosa                                 1118C>T
Photoreceptor protein deficiency?                    5797C>T
Colorectal cancer                                    643C>T
Tetralogy of Fallot                                  1969A>G
Epilepsy, rolandic without neonatal seizures         1720C>T
Adrenal hyperplasia                                  1157C>T
Adrenal hyperplasia                                  128G>A
Corticosterone methyl oxidase deficiency             1303G>A
Corticosterone methyl oxidase deficiency             1157T>C
Acrodermatitis enteropathica                         850G>A
Acrodermatitis enteropathica ?                       751C>T
Acrodermatitis enteropathica ?                       251C>T
Congenital heart defects                             984C>G
Oesophageal tumours                                  379G>T
Fanconi anaemia ?                                    890C>T
Nevoid basal cell carcinoma syndrome                 3583A>T
Holoprosencephaly                                    2183C>T
Nephronophthisis 2                                   913G>A
Reduced plasma HDL cholesterol ?                     3542C>T
Walker-Warburg syndrome                              373G>A
Meningococcal disease ?                              1420G>A
Haemorrhagic telangiectasia 1                        1510G>A
Haemorrhagic telangiectasia 1                        14C>T
Ataxia-ocular apraxia 2                              2975A>G
Cerebellar ataxia/tremor syndrome ?                  1957C>A
Cerebellar ataxia/tremor syndrome ?                  1807A>G
Tuberous sclerosis                                   1250C>T
Cytochrome c oxidase deficiency ?                    604G>C
Thrombotic thrombocytopaenic purpura ?               2195C>T
Thrombotic thrombocytopaenic purpura                 2708C>T
Ehlers-Danlos syndrome                          1588G>A
Aortic valve disease                            4823G>A
Aortic valve disease ?                          1981G>A
Glaucoma 1, open angle                          964G>A
Glaucoma 1, open angle                          1634G>A
Refsum disease                                  85C>T
Hirschsprung disease                            833C>A
Autonomic control, congenital failure of ?      1465G>A
Cockayne syndrome                               3284C>G
Usher syndrome 1f                               4024C>A
Preeclampsia                                    457T>C
Preeclampsia                                    1744C>T
Preeclampsia                                    1824A>C
Usher syndrome 1d                               3625A>G
Wolman syndrome                                 67G>A
Cardiomyopathy, dilated                         319G>T
Spastic paraplegia ?                            572G>T
Dubin-Johnson syndrome                          3817A>G
Carboxypeptidase N deficiency                   533G>A
Progressive external ophthalmoplegia            1102G>A
17-alpha-hydroxylase/17,20-lyase deficiency     62G>A
Central hypoventilation syndrome ?              1096A>G
Hypospadias                                     557T>C
Long QT syndrome ?                              1927G>A
Sickle cell anaemia                             20A>T
Niemann-Pick disease                            887G>A
Niemann-Pick disease                            1522G>A
Spermatogenic failure                           322A>T
Spermatogenic failure                           3057G>A
Hyperinsulinism of infancy ?                    1384A>G
Hermansky-Pudlak syndrome                       3293C>T
Hyperekplexia                                   2299G>A
Cardiomyopathy, hypertrophic                    1564G>A
Cardiomyopathy, hypertrophic                    1519G>A
Cardiomyopathy, hypertrophic ?                  706A>G
Best macular dystrophy                          619C>A
McArdle disease                                 148C>T
Multiple endocrine neoplasia 1 ?                512G>A
Bardet-Biedl syndrome?                          700G>A
Carnitine palmitoyltransferase 1 deficiency     823G>A
Spinal muscular atrophy with resp. distress 1   2636C>A
Obesity, severe, with diabetes                  304G>A
Papillon-Lefevre syndrome                       458C>T
Congenital hypomyelinating neuropathy ?         1805C>G
Congenital hypomyelinating neuropathy ?         1634A>G
Lung cancer, association with                   952G>C
Hodgkin disease ?                               1541G>A
Breast cancer, susceptibility to                1636C>G
Breast cancer, susceptibility to                2614C>T
Breast cancer, susceptibility to                    3383A>G
Breast cancer, susceptibility to                    4138C>T
Ataxia telangiectasia                               4258C>T
Paraganglioma ?                                     34G>A
Paraganglioma ?                                     149A>G
Schizophrenia ?                                     1031G>A
Primary angle closure glaucoma ?                    770G>A
Intellectual disability                             1007G>A
Bartter syndrome                                    1070T>C
Von Willebrand disease 1 ?                          6554G>A
Von Willebrand disease 2a                           4517C>T
Von Willebrand disease ?                            2771G>A
Von Willebrand, Normandy variant                    2561G>A
Von Willebrand, Normandy variant                    2451T>A
Von Willebrand disease 2m                           2220G>A
Von Willebrand disease 1 ?                          385C>A
Periodic fever, autosomal dominant                  224C>T
Cystic fibrosis, non-classic                        541C>T
Arrhythmogenic right ventricular cardiomyopathy     1097T>C
Parkinson disease                                   5606T>C
Glycogen storage disease 7 ?                        299G>A
Glycogen storage disease 7 ?                        2087G>A
Loose anagen hair syndrome?                         1009G>A
Epidermolysis bullosa simplex ?                     413G>A
Sensorineural deafness, nonsyndromic                1985G>A
ALys amyloidosis, systemic                          263C>A
Major depression                                    1394A>G
Major depression                                    2345A>C
Phenylketonuria                                     1222C>T
Phenylketonuria                                     158G>A
Methylmalonic aciduria and metabolic ketoacidosis   403G>A
Charcot-Marie-Tooth disease 2L                      582C>T
Diabetes, MODY3                                     864G>C
Diabetes, MODY3                                     1165T>G
Hawkinsinsuria                                      97G>A
Deafness ?                                          608T>C
Deafness, autosomal recessive 1                     416G>A
Deafness ?                                          341A>G
Deafness ?                                          249C>G
Deafness ?                                          79G>A
Oesophageal carcinoma ?                             943T>A
Breast cancer ?                                     5744C>T
Breast and/or ovarian cancer ?                      6100C>T
Breast cancer                                       7397C>T
Breast cancer ?                                     8830A>T
Breast cancer ?                                     10234A>G
Retinoblastoma                                      920C>T
Retinoblastoma                                      1574C>G
Wilson disease                                      3620A>G
Wilson disease ?                                     3419T>C
Propionic acidaemia                                  1423A>G
Propionic acidaemia                                  1676G>T
Factor VII deficiency                                851G>A
Cone-rod dystrophy                                   1639G>T
Leber congenital amaurosis                           3341A>G
Cardiomyopathy, hypertrophic ?                       4472C>G
Ichthyosis, lamellar                                 1552G>A
Impaired glucose homeostasis ?                       1343G>A
Impaired glucose homeostasis ?                       247G>A
Dystonia, dopa-responsive                            671A>G
Muscular dystrophy, Emery-Dreifuss                   18632C>T
Endometrial cancer                                   2825C>T
Colorectal cancer, increased risk                    2221G>T
Muscle-eye-brain syndrome/Fukuyama CMD               1238G>C
Hypothyroidism                                       154C>A
Krabbe disease                                       1921G>A
Krabbe disease                                       1403C>G
Krabbe disease ?                                     550C>T
Venous thromboembolic disease                        1151A>G
Venous thromboembolic disease                        435T>G
Antitrypsin alpha 1 deficiency                       1200A>C
Antitrypsin alpha 1 deficiency                       1096G>A
Antitrypsin alpha 1 deficiency                       863A>T
Antitrypsin alpha 1 deficiency                       710T>C
Antitrypsin alpha 1 deficiency                       374G>A
Obstructive lung disease                             754C>G
Occlusive cerebrovascular disease                    1240A>G
Protein kinase deficiency                            280C>T
Albinism, oculocutaneous II                          1441G>A
Albinism, oculocutaneous II                          79G>A
Muscular dystrophy, limb girdle                      479C>G
Muscular dystrophy, limb girdle                      551C>T
Hypothyroidism                                       3200T>C
Hypothyroidism                                       3155G>A
Hypothyroidism                                       2033A>G
Bicuspid aortic valve                                3442C>G
Increased cortical bone mass density, association    240A>G
                                                    with
Griscelli syndrome                                   3736C>T
Hepatic lipase deficiency ?                          644A>G
Hepatic lipase deficiency                            1068A>C
Hepatic lipase deficiency                            1214C>T
Concentrative nucleoside transporter deficiency ?    1636T>C
Ataxic neuropathy                                    3428A>G
Progressive external ophthalmoplegia                 2492A>G
Epilepsy, childhood absence                          940C>T
Tuberous sclerosis                                   856A>G
Tuberous sclerosis                                   3986G>A
Polycystic kidney disease 1                          10675G>A
Polycystic kidney disease 1                       10526C>T
Polycystic kidney disease 1                       8898G>C
Fatal surfactant deficiency                       863G>A
Mediterranean fever, familial                     1223G>A
Mediterranean fever, familial                     1105C>T
Mediterranean fever, familial                     910G>A
Mediterranean fever, familial ?                   605G>A
Congenital disorder of glycosylation 1a           590A>C
Pseudoxanthoma elasticum ?                        3871G>A
Pseudoxanthoma elasticum, autosomal recessive 3803G>A
Liver glycogenosis                                555G>T
Liver glycogenosis ?                              2309A>G
Crohn's disease, susceptibility to ?              2174C>G
Crohn's disease ?                                 2863G>A
Bardet-Biedl syndrome                             209A>G
Gitelman syndrome ?                               791G>C
Gitelman syndrome                                 1706C>T
Gitelman syndrome                                 2182G>A
Gitelman syndrome                                 2782C>T
Cholesterol ester transfer protein deficiency     1376A>G
Lecithin:cholesterol acyltransferase deficiency ? 694T>A
Gastric cancer                                    1849G>A
Giant axonal neuropathy                           1684C>G
Mucopolysaccharidosis IVa                         1462G>A
Fanconi anaemia ?                                 3859G>A
Fanconi anaemia ?                                 3263C>T
Fanconi anaemia ?                                 755A>G
Fanconi anaemia ?                                 542C>T
Fanconi anaemia                                   24C>G
Sensorineural hearing loss, bilateral ?           1139C>T
Cystinosis, non-classical                         124G>A
Diabetes, type 2                                  2020C>T
Leber congenital amaurosis IV                     1126C>T
Leber congenital amaurosis IV                     341C>T
Leber congenital amaurosis IV                     286G>A
Cone dystrophy, autosomal dominant                1878G>C
                                                   ?
Very long chain acyl-CoA dehydrogenase deficiency128G>A
Very long chain acyl-CoA dehydrogenase deficiency194C>T
Hyperandrogenism                                  554C>T
Leber congenital amaurosis                        61T>C
Leber congenital amaurosis                        1724C>T
Leber congenital amaurosis                        2101C>T
Renal cell carcinoma                              715C>T
Deafness, non-syndromic, autosomal recessive      6796G>A
Protein kinase deficiency                         304C>T
Febrile seizures ?                                1636A>G
Oligozoospermia                                   647A>C
Breast cancer                                     4883T>C
Breast cancer                                     4166G>A
Breast cancer                                      3448C>T
Breast cancer ?                                    3119G>A
Ovarian cancer ?                                   2521C>T
Breast cancer                                      2458A>G
Breast cancer ?                                    2077G>A
Breast cancer                                      1137T>G
Spherocytosis                                      118G>A
Osteogenesis imperfecta II                         1168G>A
Myeloperoxidase deficiency                         518A>G
Hyperkalaemic periodic paralysis                   2341G>A
Haemophagocytic lymphohistiocytosis, familial      2782C>T
Juvenile idiopathic arthritis                      1579C>T
Glycogen storage disease 2                         271G>A
Psoriasis                                          1043C>T
Cushing syndrome                                   833T>G
Niemann-Pick disease C ?                           709C>T
Epidermolysis bullosa, junctional                  4024C>T
Cardiomyopathy, arrhythmogenic right ventricular   2137G>A
Amyloidotic polyneuropathy ?                       76G>A
Amyloidotic polyneuropathy                         424G>A
Xanthinuria, type 2 ?                              1072A>G
Higher plasma HDL cholesterol ?                    1426C>T
Intrahepatic cholestasis, benign recurrent         208G>A
Obesity, autosomal dominant ?                      751A>C
Neutropaenia, cyclic                               655G>A
Peutz-Jeghers syndrome                             1062C>G
Arginine:glycine amidinotransferase deficiency ?   626C>T
Fucosyltransferase deficiency                      370C>T
Lewis antigen, absence                             314C>T
Lewis antigen, absence                             202T>C
Lewis antigen, absence                             59T>G
Hypercholesterolaemia                              970G>A
Hypercholesterolaemia ?                            1920C>T
CADASIL                                            3058G>C
Leber congenital amaurosis                         485A>G
Mycobacterial infection                            641A>G
Cystinuria                                         667C>A
Cystinuria                                         425T>C
Cystinuria, non-type I                             368C>T
Cystinuria ?                                       336G>C
Congenital nephrotic syndrome, Finnish type ?      3230A>G
Congenital nephrotic syndrome, Finnish type        2971G>C
Congenital nephrotic syndrome, Finnish type        1223G>A
Minimal change nephrotic syndrome ?                881C>T
Congenital nephrotic syndrome, Finnish type        349G>A
Malignant hyperthermia                             4024A>G
Multi-minicore disease                             8360C>G
Malignant hyperthermia                             13502C>T
Impaired efavirenz metabolism                      983T>C
Apolipoprotein E deficiency                       388T>C
Apolipoprotein E deficiency                       487C>T
Apolipoprotein E deficiency                       526C>T
Leber congenital amaurosis ?                      472G>A
Glutaricacidaemia 2b ?                            461C>T
Breast cancer ?                                   1414T>C
Hydatidiform mole                                 1532A>G
Hydatidiform mole                                 467G>A
Cardiomyopathy, hypertrophic                      244C>T
Schizophrenia                                     512A>G
Kallmann syndrome ?                               991G>A
Kallmann syndrome ?                               802C>T
Bardet-Biedl syndrome                             1549C>T
Biliary atresia, extrahepatic                     2612C>G
Anaemia, dyserythropoietic congenital, type II    1276G>A
Late foetal loss                                  1208G>A
Glutathione synthetase deficiency                 941C>T
Diabetes mellitus, type 2 ?                       416C>T
Adenosine deaminase deficiency                    643G>A
Adenosine deaminase deficiency                    239A>G
Epilepsy, benign neonatal                         1545G>C
Enteropeptidase deficiency                        2135C>G
Cardiac arrhythmia                                25C>G
Holocarboxylase synthetase deficiency?            126G>T
Deafness, childhood onset                         268G>A
Homocystinuria                                    1105C>T
Homocystinuria                                    833T>C
Homocystinuria                                    304A>C
APECED                                            755C>T
Bethlem myopathy                                  347G>A
Ullrich congenital muscular dystrophy             2351G>A
Bethlem myopathy                                  2795C>T
Peroxisome biogenesis disorder                    457C>G
Heparin cofactor 2 deficiency                     623G>A
Female infertility                                280G>A
Glucose / galactose malabsorption                 152A>G
Glucose / galactose malabsorption                 1231G>A
Glucose / galactose malabsorption                 1845C>G
Pulmonary alveolar proteinosis                    1807C>A
Premature ovarian failure                         598A>G
Hypercholesterolaemia ?                           1867G>A
Phenotype modifier                                28G>T
Mitochondrial neurogastrointestinal encephalopathy1412C>T




NA12892_genotype                                NA12878_genotype
GA                                              GA
GT                                              GG
-    -
CT   CC
-    -
CT   CC
-    -
CC   CT
-    -
TC   TC
CC   CT
AA   AA
CC   CC
AT   AA
AG   GG
TC   CC
TC   TC
-    -
-    -
-    -
GA   GG
CC   CC
-    -
GA   GG
-    -
AT   AA
-    -
GA   AA
GG   GG
CC   CT
-    -
-    -
GG   GG
-    -
-    -
-    -
GG   GG
AA   AA
-    -
AG   AA
-    -
-    -
-    -
-    -
-    -
AA   GA
-    -
-    -
-    -
GC   GC
-    -
TC   TC
-    -
CC   CC
CC   CC
-    -
CC   CC
CC   CC
-    -
TT   TC
-    -
-    -
-    -
-    -
AG   AG
-    -
-    -
GG   GG
-    -
CC   CC
GA   GA
AC   AA
-    -
CC   TC
TT   CT
-    -
-    -
-    -
GG   AG
-    -
-    -
-    -
-    -
GG   GG
CC   CC
CC   TC
AA   AC
-    -
-    -
-    -
-    -
-    -
-    -
GG   GG
-    -
TT   TC
CC   CA
-    -
-    -
GG   GG
-    -
GG   GC
-    -
-    -
-    -
-    -
GG   GG
-    -
CA   CC
TT   TC
TC   TC
-    -
CC   CC
-    -
AG   AG
-    -
CC   CC
-    -
CC   CC
CC   CC
-    -
TG   GG
TA   TT
-    -
AA   AA
-    -
TC   TC
GG   GG
AG   AA
AA   AA
CC   CT
-    -
TT   TT
GG   GG
-    -
-    -
-    -
-    -
GG   GA
CT   CT
CC   TC
-    -
GA   GG
AA   AA
GA   GA
AA   AG
-    -
-    -
-    -
CC                                 CC
GG                                 GG
AA                                 AA
CT                                 CT
-                                  -
CC                                 CT
AA                                 AA
AA                                 AA
-                                  -
GG                                 GG
CG                                 CG
GA                                 GA




CHB_alt_allele_frequence           CHD_alt_allele_frequence
-                                  -
-                                                    0.005
-                                  -
-                                                    0.005
-                                  -
-                                  -
-                                  -
                           0.782                     0.837
-                                  -
-                                                    0.005
-                                  -
                           0.032                     0.033
-                                  -
                           0.044                     0.072
-                                  -
-                                  -
-                                  -
-                                  -
-                                                    0.005
-                                  -
                           0.005   -
-                                                    0.005
-                                  -
-                                  -
-                                  -
-                                  -
-                                  -
                           0.005   -
                           0.005   -
                               1                         1
                           0.162                     0.154
                           0.032                     0.024
-                                                    0.005
-         -
-         -
-         -
-         -
-         -
-         -
    0.005 -
-         -
-         -
-         -
-         -
-         -
-         -
-               0.005
-         -
-         -
    0.009 -
-               0.005
-           -
-           -
-           -
-           -
-           -
    0.019       0.033
    0.014       0.005
-           -
-           -
-           -
-           -
-           -
-               0.005
-           -
-           -
    0.037       0.023
-         -
-         -
-         -
-         -
-         -
-         -
    0.008 -
-         -
    0.028 -
    0.047       0.038
-         -
-         -
-         -
-         -
    0.115       0.143
    0.009 -
-         -
-         -
-               0.005
-           -
    0.005       0.009
-           -
-           -
-               0.005
    0.019        0.01
    0.014       0.033
-           -
-           -
-           -
-           -
     0.61       0.612
    0.012       0.014
codon_change   aa_change
GCG-GTG        Ala-Val
tCGG-TGG       Arg-Trp
GGCg-GGT       Gly-Gly
CGG-CAG        Arg-Gln
CCG-CTG        Pro-Leu
CGG-CAG        Arg-Gln
CTC-CGC        Leu-Arg
aTCT-CCT       Ser-Pro
GCG-GGG        Ala-Gly
cGCC-ACC       Ala-Thr
cGAG-AAG       Glu-Lys
CCG-CGG        Pro-Arg
gCGG-TGG       Arg-Trp
TGCc-TGG       Cys-Trp
cCGG-TGG       Arg-Trp
cTAC-GAC       Tyr-Asp
cGCC-ACC       Ala-Thr
CGG-CAG        Arg-Gln
tGTG-ATG       Val-Met
CTG-CAG        Leu-Gln
cGGG-AGG       Gly-Arg
ACGc-ACC       Thr-Thr
gGAC-AAC       Asp-Asn
GCT-GTT        Ala-Val
TTT-TGT        Phe-Cys
AAT-AGT        Asn-Ser
cGCC-ACC       Ala-Thr
gTAC-CAC       Tyr-His
TTT-TCT        Phe-Ser
GCG-GTG        Ala-Val
ACAg-ACC       Thr-Thr
aCCA-TCA       Pro-Ser
AGC-AAC        Ser-Asn
AGT-ATT        Ser-Ile
cGTC-ATC       Val-Ile
ACG-ATG        Thr-Met
CGA-CAA        Arg-Gln
ATG-ACG        Met-Thr
CTG-CGG        Leu-Arg
CGG-CAG        Arg-Gln
GGA-GCA        Gly-Ala
GTG-GGG        Val-Gly
CAC-CGC        His-Arg
cCGT-TGT       Arg-Cys
CGC-CAC        Arg-His
tATA-GTA   Ile-Val
AGT-AAT    Ser-Asn
TAT-TGT    Tyr-Cys
aATG-GTG   Met-Val
gTGT-CGT   Cys-Arg
aACT-GCT   Thr-Ala
gGGT-AGT   Gly-Ser
GAAg-GAT   Glu-Asp
AAA-ATA    Lys-Ile
CCG-CTG    Pro-Leu
tGCA-ACA   Ala-Thr
TTG-TCG    Leu-Ser
tCGG-TGG   Arg-Trp
tCGG-TGG   Arg-Trp
CGG-CAG    Arg-Gln
cCAT-TAT   His-Tyr
GGT-GTT    Gly-Val
GACc-GAA   Asp-Glu
gTAC-AAC   Tyr-Asn
tGTG-ATG   Val-Met
AAGg-AAA   Lys-Lys
AAA-AGA    Lys-Arg
AGA-AAA    Arg-Lys
CAGc-CAT   Gln-His
GCC-GTC    Ala-Val
AGT-ATT    Ser-Ile
tGTG-TTG   Val-Leu
gAAT-TAT   Asn-Tyr
CGT-CAT    Arg-His
AAG-AGG    Lys-Arg
aGGC-CGC   Gly-Arg
cGTG-ATG   Val-Met
TCT-TAT    Ser-Tyr
CGC-CAC    Arg-His
CGG-CAG    Arg-Gln
tAGT-GGT   Ser-Gly
gCAG-AAG   Gln-Lys
ACG-ATG    Thr-Met
tGAG-AAG   Glu-Lys
cGTA-ATA   Val-Ile
CCA-CTA    Pro-Leu
CAT-CGT    His-Arg
CGT-CAT    Arg-His
aCAG-AAG   Gln-Lys
aGGA-AGA   Gly-Arg
GCT-GGT    Ala-Gly
CCA-CTA    Pro-Leu
GGC-GAC    Gly-Asp
aCTT-TTT   Leu-Phe
GCG-GAG    Ala-Glu
aCTA-GTA   Leu-Val
cGAA-AAA   Glu-Lys
CGG-CAG    Arg-Gln
CAAa-CAT   Gln-His
AGG-AAG    Arg-Lys
cGCC-ACC   Ala-Thr
CAT-CGT    His-Arg
aCGG-TGG   Arg-Trp
tCGT-TGT   Arg-Cys
aGGG-AGG   Gly-Arg
ATG-ACG    Met-Thr
gGGA-AGA   Gly-Arg
cGTA-ATA   Val-Ile
AGC-AAC    Ser-Asn
gGAT-AAT   Asp-Asn
gCGA-TGA   Arg-Term
gGAA-CAA   Glu-Gln
CCG-CTG    Pro-Leu
cGTC-ATC   Val-Ile
aGGG-AGG   Gly-Arg
cCGC-TGC   Arg-Cys
CCT-CTT    Pro-Leu
GCA-GTA    Ala-Val
CGG-CAG    Arg-Gln
ACC-AAC    Thr-Asn
CGG-CAG    Arg-Gln
cGGC-AGC   Gly-Ser
CTC-CGC    Leu-Arg
cAGT-GGT   Ser-Gly
tCCT-TCT   Pro-Ser
tGAT-CAT   Asp-His
gCGC-TGC   Arg-Cys
CCT-CTT    Pro-Leu
cGTG-ATG   Val-Met
cATC-GTC   Ile-Val
CCG-CTG    Pro-Leu
tATC-GTC   Ile-Val
aCAC-TAC   His-Tyr
cCGG-TGG   Arg-Trp
CGG-CAG    Arg-Gln
gAAG-GAG   Lys-Glu
CGC-CAC    Arg-His
gGAG-AAG   Glu-Lys
cAAG-TAG   Lys-Term
AAT-AGT    Asn-Ser
AAC-ATC    Asn-Ile
ACG-ATG    Thr-Met
CGT-CTT    Arg-Leu
cGCC-ACC   Ala-Thr
AGC-ACC    Ser-Thr
TTT-TGT    Phe-Cys
CGA-CAA    Arg-Gln
CGG-CAG    Arg-Gln
GAG-GTG    Glu-Val
cGTG-ATG   Val-Met
cGCC-ACC   Ala-Thr
tTGT-CGT   Cys-Arg
CGA-CAA    Arg-Gln
TATc-TAA   Tyr-Term
aAGG-TGG   Arg-Trp
gGCG-ACG   Ala-Thr
GAC-GCC    Asp-Ala
CAT-CGT    His-Arg
CCG-CTG    Pro-Leu
cGCT-ACT   Ala-Thr
cCGC-TGC   Arg-Cys
AAT-AGT    Asn-Ser
gCTT-GTT   Leu-Val
TGCg-TGA   Cys-Term
TGC-TTC    Cys-Phe
gCCT-ACT   Pro-Thr
TCG-TTG    Ser-Leu
gATT-GTT   Ile-Val
aAGA-GGA   Arg-Gly
AGC-AAC    Ser-Asn
tCCA-TCA   Pro-Ser
tCAA-GAA   Gln-Glu
gGAT-AAT   Asp-Asn
CGA-CAA    Arg-Gln
tCCA-TCA   Pro-Ser
tGGT-AGT   Gly-Ser
aCGC-TGC   Arg-Cys
tCCT-TCT   Pro-Ser
ATT-ACT    Ile-Thr
tATA-CTA   Ile-Leu
cCAG-AAG   Gln-Lys
TTGg-TTC   Leu-Phe
TCT-TGT    Ser-Cys
aCGG-TGG   Arg-Trp
ACT-ATT    Thr-Ile
cACT-TCT   Thr-Ser
GCT-GTT    Ala-Val
gGGC-AGC   Gly-Ser
CAGg-CAA   Gln-Gln
gCGC-TGC   Arg-Cys
GGG-GCG    Gly-Ala
CGG-CAG    Arg-Gln
CCC-CTC    Pro-Leu
cGGG-AGG   Gly-Arg
gAGT-TGT   Ser-Cys
cGTG-ATG   Val-Met
GGC-GAC    Gly-Asp
aCTC-TTC   Leu-Phe
GCC-GTC    Ala-Val
GCT-GTT    Ala-Val
gAAA-GAA   Lys-Glu
cGTA-ATA   Val-Ile
CAT-CGT    His-Arg
tATA-GTA   Ile-Val
gGTT-ATT   Val-Ile
ATGg-ATA   Met-Ile
aACC-GCC   Thr-Ala
CCC-CGC    Pro-Arg
CGT-CAT    Arg-His
cCCC-TCC   Pro-Ser
gGTG-ATG   Val-Met
cGGT-AGT   Gly-Ser
cCTG-GTG   Leu-Val
gGAA-AAA   Glu-Lys
gCGC-TGC   Arg-Cys
GGG-GTG    Gly-Val
cCGG-TGG   Arg-Trp
aTAC-CAC   Tyr-His
TTAg-TTG   Leu-Leu
CCC-CGC    Pro-Arg
GCC-GTC    Ala-Val
CGA-CTA    Arg-Leu
cGCC-ACC   Ala-Thr
ATC-AAC    Ile-Asn
CCG-CTG    Pro-Leu
CCG-CTG    Pro-Leu
CGG-CAG    Arg-Gln
tAGA-GGA   Arg-Gly
GAGa-GAC   Glu-Asp
AACg-AAT   Asn-Asn
CGG-CAG    Arg-Gln
gGCC-ACC   Ala-Thr
cAAT-TAT   Asn-Tyr
GTT-GGT    Val-Gly
aGGT-AGT   Gly-Ser
tCGG-TGG   Arg-Trp
cCGG-TGG   Arg-Trp
ACT-AGT    Thr-Ser
aATT-GTT   Ile-Val
cCGT-TGT   Arg-Cys
AGTc-AGG   Ser-Arg
CAGt-CAC   Gln-His
cCGG-TGG   Arg-Trp
aCGG-TGG   Arg-Trp
ATG-ACG    Met-Thr
ACG-ATG    Thr-Met
CGG-CAG    Arg-Gln
cGCT-ACT   Ala-Thr
cGTG-ATG   Val-Met
CGG-CTG    Arg-Leu
cCTG-GTG   Leu-Val
GTC-GCC    Val-Ala
aGTT-ATT   Val-Ile
aATG-GTG   Met-Val
cACA-GCA   Thr-Ala
CGG-CAG    Arg-Gln
CCA-CAA    Pro-Gln
gCCC-TCC   Pro-Ser
ATC-ACC    Ile-Thr
gAAG-CAG   Lys-Gln
ACA-ATA    Thr-Ile
cCGA-TGA   Arg-Term
aCGG-TGG   Arg-Trp
cAGT-GGT   Ser-Gly
cCCT-TCT   Pro-Ser
GCG-GTG    Ala-Val
CGG-CAG    Arg-Gln
cGGC-AGC   Gly-Ser
GTG-GCG    Val-Ala
gGAA-AAA   Glu-Lys
cCGG-TGG   Arg-Trp
CCG-CTG    Pro-Leu
GACg-GAG   Asp-Glu
cGCA-TCA   Ala-Ser
ACA-ATA    Thr-Ile
cACA-TCA   Thr-Ser
ACG-ATG    Thr-Met
gGTT-ATT   Val-Ile
TCT-TTT    Ser-Phe
aGGC-AGC   Gly-Ser
cGAA-AAA   Glu-Lys
cGTG-ATG   Val-Met
ACG-ATG    Thr-Met
AAA-AGA    Lys-Arg
gCAA-AAA   Gln-Lys
tAAC-GAC   Asn-Asp
ACA-ATA    Thr-Ile
gGAC-CAC   Asp-His
GCG-GTG    Ala-Val
TCG-TTG    Ser-Leu
cGGC-AGC   Gly-Ser
CGT-CAT    Arg-His
tGGC-AGC   Gly-Ser
cGAA-AAA   Glu-Lys
CGG-CAG    Arg-Gln
tCCC-TCC   Pro-Ser
ACC-AAC    Thr-Asn
cGAC-AAC   Asp-Asn
CCT-CGT    Pro-Arg
tCAG-AAG   Gln-Lys
tTAC-CAC   Tyr-His
cCTC-TTC   Leu-Phe
GAAg-GAC   Glu-Asp
cACA-GCA   Thr-Ala
tGGA-AGA   Gly-Arg
tGTA-TTA   Val-Leu
GGC-GTC    Gly-Val
aACT-GCT   Thr-Ala
GGC-GAC    Gly-Asp
cGTA-ATA   Val-Ile
AGG-AAG    Arg-Lys
cACT-GCT   Thr-Ala
ATG-ACG    Met-Thr
cGGC-AGC   Gly-Ser
GAG-GTG    Glu-Val
CGG-CAG    Arg-Gln
cGGG-AGG   Gly-Arg
cAAG-TAG   Lys-Term
ATGa-ATA   Met-Ile
aATT-GTT   Ile-Val
ACC-ATC    Thr-Ile
cGGG-AGG   Gly-Arg
cGCG-ACG   Ala-Thr
cGGG-AGG   Gly-Arg
cAGC-GGC   Ser-Gly
gCTC-ATC   Leu-Ile
aCGA-TGA   Arg-Term
CGG-CAG    Arg-Gln
cGAG-AAG   Glu-Lys
cGCC-ACC   Ala-Thr
ACG-AAG    Thr-Lys
cGTC-ATC   Val-Ile
ACA-ATA    Thr-Ile
GCT-GGT    Ala-Gly
AAC-AGC    Asn-Ser
aGTC-CTC   Val-Leu
GGT-GAT    Gly-Asp
aCTG-GTG   Leu-Val
aCCT-TCT   Pro-Ser
CAG-CGG    Gln-Arg
tCAT-TAT   His-Tyr
tCTT-TTT   Leu-Phe
cGGT-AGT   Gly-Ser
CAC-CGC    His-Arg
CGT-CAT    Arg-His
CGC-CAC    Arg-His
CGG-CAG    Arg-Gln
ATG-ACG    Met-Thr
CGG-CAG    Arg-Gln
TCG-TTG    Ser-Leu
CGG-CAG    Arg-Gln
CGG-CAG    Arg-Gln
CATg-CAA   His-Gln
ATGa-ATA   Met-Ile
gCTG-ATG   Leu-Met
CCG-CTG    Pro-Leu
gCGG-TGG   Arg-Trp
CTG-CCG    Leu-Pro
ATG-ACG    Met-Thr
CGA-CAA    Arg-Gln
CGT-CAT    Arg-His
cGAG-AAG   Glu-Lys
GGA-GAA    Gly-Glu
GGG-GAG    Gly-Glu
ACC-AAC    Thr-Asn
CAG-CGG    Gln-Arg
AAT-ACT    Asn-Thr
tCGG-TGG   Arg-Trp
CGC-CAC    Arg-His
gGCC-ACC   Ala-Thr
ACCt-ACT   Thr-Thr
GGGc-GGC   Gly-Gly
cTTG-GTG   Leu-Val
cGCG-ACG   Ala-Thr
ATC-ACC    Ile-Thr
AGC-AAC    Ser-Asn
GAA-GGA    Glu-Gly
TTCg-TTG   Phe-Leu
cGTC-ATC   Val-Ile
aTGT-AGT   Cys-Ser
ACG-ATG    Thr-Met
aCGT-TGT   Arg-Cys
GCA-GTA    Ala-Val
gATC-TTC   Ile-Phe
aATT-GTT   Ile-Val
ACA-ATA    Thr-Ile
GCC-GGC    Ala-Gly
CAC-CGC    His-Arg
GTC-GCC    Val-Ala
tATT-GTT   Ile-Val
TGG-TTG    Trp-Leu
CGG-CAG    Arg-Gln
aGCT-TCT   Ala-Ser
GAT-GGT    Asp-Gly
TCC-TGC    Ser-Cys
tGTG-ATG   Val-Met
AGC-AAC    Ser-Asn
aGCC-ACC   Ala-Thr
AAA-AGA    Lys-Arg
ACG-ATG    Thr-Met
ACA-ATA    Thr-Ile
cGTC-TTC   Val-Phe
CGA-CCA    Arg-Pro
gCCC-ACC   Pro-Thr
cGCC-ACC   Ala-Thr
ACT-AGT    Thr-Ser
gCGT-TGT   Arg-Cys
CAA-CGA    Gln-Arg
TTTa-TTG   Phe-Leu
GAAc-GAC   Glu-Asp
cGAG-AAG   Glu-Lys
GAA-GTA    Glu-Val
GTG-GCG    Val-Ala
CGT-CAT    Arg-His
aCCT-GCT   Pro-Ala
cATG-GTG   Met-Val
aCGA-TGA   Arg-Term
tGCC-ACC   Ala-Thr
cGGA-AGA   Gly-Arg
GCA-GGA    Ala-Gly
ACG-ATG    Thr-Met
TTG-TCG    Leu-Ser
TGT-TAT    Cys-Tyr
CAT-CGT    His-Arg
cCCC-GCC   Pro-Ala
GTAt-GTG   Val-Val
cCGT-TGT   Arg-Cys
AAT-AGT    Asn-Ser
TTAa-TTC   Leu-Phe
ACG-ATG    Thr-Met
cTCC-CCC   Ser-Pro
GAG-GGG    Glu-Gly
TAT-TGT    Tyr-Cys
gCCC-TCC   Pro-Ser
cATG-GTG   Met-Val
CGC-CAC    Arg-His
cGGG-AGG   Gly-Arg
ACG-ATG    Thr-Met
GAGt-GAC   Glu-Asp
AGG-AAG    Arg-Lys
CGG-CAG    Arg-Gln
cCCC-TCC   Pro-Ser
cGGA-AGA   Gly-Arg
CGG-CAG    Arg-Gln
GAA-GCA    Glu-Ala
cGCA-ACA   Ala-Thr
CGG-CAG    Arg-Gln
ATGa-ATT   Met-Ile
TAT-TGT    Tyr-Cys
GCT-GGT    Ala-Gly
cGTC-ATC   Val-Ile
AAC-AGC    Asn-Ser
GGC-GCC    Gly-Ala
GCG-GTG    Ala-Val
cGCA-ACA   Ala-Thr
cCGT-TGT   Arg-Cys
GAC-GGC    Asp-Gly
cTCT-ACT   Ser-Thr
tGCA-ACA   Ala-Thr
tCCA-GCA   Pro-Ala
cGTG-ATG   Val-Met
cGTT-ATT   Val-Ile
TCT-TTT    Ser-Phe
GAT-GGT    Asp-Gly
GCG-GTG    Ala-Val
AACt-AAG   Asn-Lys
ACG-ATG    Thr-Met
cGTC-ATC   Val-Ile
cCGC-TGC   Arg-Cys
cCCG-TCG   Pro-Ser
ACA-ATA    Thr-Ile
gGTC-ATC   Val-Ile
CAGg-CAC   Gln-His
GGT-GAT    Gly-Asp
CCG-CTG    Pro-Leu
CCG-CTG    Pro-Leu
gTGG-CGG   Trp-Arg
CCA-CTA    Pro-Leu
tCCC-TCC   Pro-Ser
cCGC-TGC   Arg-Cys
cGTG-ATG   Val-Met
aCAG-TAG   Gln-Term
cACA-GCA   Thr-Ala
CAA-CCA    Gln-Pro
ATG-ACG    Met-Thr
AGT-AAT    Ser-Asn
aCCT-TCT   Pro-Ser
AGC-AAC    Ser-Asn
tCGG-TGG   Arg-Trp
cAAA-GAA   Lys-Glu
tGAC-AAC   Asp-Asn
ATTc-ATG   Ile-Met
cGAG-AAG   Glu-Lys
tGCT-ACT   Ala-Thr
TAC-TGC    Tyr-Cys
cGTC-ATC   Val-Ile
gCGT-TGT   Arg-Cys
cCGG-TGG   Arg-Trp
cGAT-AAT   Asp-Asn
CCT-CTT    Pro-Leu
TTC-TGC    Phe-Cys
aCCA-TCA   Pro-Ser
tCGT-TGT   Arg-Cys
cGAG-AAG   Glu-Lys
cGGT-AGT   Gly-Ser
cGTC-ATC   Val-Ile
cATG-GTG   Met-Val
cCGG-TGG   Arg-Trp
cGAT-AAT   Asp-Asn
gATT-CTT   Ile-Leu
cGTC-ATC   Val-Ile
TTCg-TTG   Phe-Leu
ACG-ATG    Thr-Met
cCCG-TCG   Pro-Ser
ACG-ATG    Thr-Met
aTGG-CGG   Trp-Arg
CTG-CGG    Leu-Arg
cGGC-AGC   Gly-Ser
AACt-AAT   Asn-Asn
gGCC-CCC   Ala-Pro
AAC-AGC    Asn-Ser
CAG-CGG    Gln-Arg
cCTG-ATG   Leu-Met
GTG-GCG    Val-Ala
ACG-ATG    Thr-Met
GAGa-GAC   Glu-Asp
AAT-AGT    Asn-Ser
cGTA-CTA   Val-Leu
CGG-CAG    Arg-Gln
ACC-ATC    Thr-Ile
tGAG-AAG   Glu-Lys
gAGC-GGC   Ser-Gly
ACC-AGC    Thr-Ser
CCG-CTG    Pro-Leu
ATT-ACT    Ile-Thr
gTGC-CGC       Cys-Arg
gCGT-TGT       Arg-Cys
gCGC-TGC       Arg-Cys
gGCC-ACC       Ala-Thr
ACG-ATG        Thr-Met
aTCA-CCA       Ser-Pro
AAG-AGG        Lys-Arg
CGG-CAG        Arg-Gln
gCCG-TCG       Pro-Ser
AAC-AGC        Asn-Ser
cGTG-ATG       Val-Met
gCGC-TGC       Arg-Cys
aCGT-TGT       Arg-Cys
CCA-CGA        Pro-Arg
cGTA-ATA       Val-Ile
AGG-AAG        Arg-Lys
CCG-CTG        Pro-Leu
ACT-ATT        Thr-Ile
cGCC-ACC       Ala-Thr
AAA-AGA        Lys-Arg
GAGg-GAC       Glu-Asp
TCA-TGA        Ser-Term
aCAG-GAG       Gln-Glu
GAGc-GAT       Glu-Asp
aGCT-ACT       Ala-Thr
gCGC-TGC       Arg-Cys
ATT-ACT        Ile-Thr
gAAG-CAG       Lys-Gln
CCG-CTG        Pro-Leu
AGC-AAC        Ser-Asn
CGC-CAC        Arg-His
CCG-CTG        Pro-Leu
cCTT-GTT       Leu-Val
CGC-CAC        Arg-His
cGCC-ACC       Ala-Thr
AAT-AGT        Asn-Ser
cGCC-ACC       Ala-Thr
CACg-CAG       His-Gln
aCCT-ACT       Pro-Thr
gATG-GTG       Met-Val
cGTG-ATG       Val-Met
cGCC-TCC       Ala-Ser
TCG-TTG        Ser-Leu




HGMD_acc_num   disease
CM031993       Cortisone reductase deficiency
CM042957       Bartter syndrome 3
CM065379   Parkinson disease, autosomal recessive
CM024704   Hypercholesterolaemia, autosomal recessive
CM065098   Carnitine palmitoyltransferase 2 deficiency
CM001812   Congenital disorder of glycosylation 1c, mild
CM023000   Cone-rod degeneration
CM024629   Macular degeneration, age related
CM020912   Macular degeneration, age related
CM033371   Dihydropyrimidine dehydrogenase deficiency ?
CM033370   Dihydropyrimidine dehydrogenase deficiency ?
CM970421   Dihydropyrimidine dehydrogenase deficiency ?
CM983430   Maple syrup urine disease
CM003692   Erythrocyte lactate transport deficiency
CM991218   Hypothyroidism
CM070090   Thrombosis ?
CM004363   Glaucoma 1, open angle ?
CM055120   Factor H deficiency
CM070675   Haemolytic uraemic syndrome
CM034583   Cardiomyopathy, hypertrophic
CM013710   Colorectal cancer, non-polyposis
CM074947   Cryopyrin-associated periodic syndrome ?
CM054759   Mitochondrial trifunctional protein deficiency
CM090628   Muscular dystrophy, limb girdle ?
CM090631   Muscular dystrophy, limb girdle
CM950629   Diabetes, NIDDM
CM950635   Diabetes, NIDDM
CM012769   Increased plasma FFA and glycerol levels
CM051623   Erythermalgia, primary
CM074143   Progressive hearing loss, autosomal recessive
CM991061   Colorectal cancer, non-polyposis
CM991062   Colorectal cancer, non-polyposis
CM990325   Autoimmune lymphoproliferative syndrome II ?
CM071094   Schimke immuno-osseous dysplasia
CM070889   Cardiomyopathy, dilated
CM045572   Endplate acetylcholinesterase deficiency
CM051080   Gangliosidosis GM1
CM055955   Gangliosidosis GM1
CM000176   Colorectal cancer, non-polyposis ?
CM970958   Colorectal cancer, non-polyposis ?
CM071867   Protein kinase deficiency
CM994541   Pituitary hypoplasia
CM000509   Ellis-van Creveld syndrome
CM960907   Piebaldism
CM040732   Dentinogenesis imperfecta type II
CM073166   Prekallikrein deficiency
CM980651   Factor XI deficiency
CM992646   Methionine synthase reductase deficiency ?
CM952225   Sandhoff disease
CM078286   Cervical carcinoma, association with
CM080070   Colorectal adenoma
CM004548   Pulmonary alveolar proteinosis
CM051222   Carnitine deficiency, systemic primary
CM056011   Myotilinopathy
CM016008   Diastrophic dysplasia ?
CM980573   Achondrogenesis 1B
CM043093   Glycogen storage disease 1c ?
CM971297   Retinitis punctata albescens
CM092994   Zellweger syndrome ?
CM920487   Methylmalonic aciduria
CM920486   Methylmalonic aciduria
CM087682   Muscular dystrophy, merosin deficient
HM050002   Cardiomyopathy, dilated
CM087628   Cardiac hypertrophy ?
CM991050   Plasminogen deficiency
CM024242   Parkinson disease, autosomal recessive
CM950571   Diabetes, NIDDM
CM910199   Mucopolysaccharidosis VII
CM072814   Intrahepatic cholestasis, familial progressive ?
CM075942   Intrahepatic cholestasis, familial progressive
CM055540   Plasminogen activator inhibitor 1 deficiency
CM960277   Cystic fibrosis
CM066015   Tropical calcific pancreatitis
CM962671   Farber disease
CM962670   Farber disease
CM984605   Spherocytosis
CM065260   Mucopolysaccharidosis IIIC
CM033078   Tetralogy of Fallot
CM021685   Acrodermatitis enteropathica ?
CM015016   Fanconi anaemia ?
CM032347   Nevoid basal cell carcinoma syndrome
CM080364   Walker-Warburg syndrome
CM004889   Haemorrhagic telangiectasia 1
CM095002   Glaucoma 1, open angle
CM033451   Autonomic control, congenital failure of ?
CM057373   Preeclampsia
CM057372   Preeclampsia
CM992952   Haemophagocytic lymphohistiocytosis, familial ?
CM021540   Usher syndrome 1d
CM014368   Wolman syndrome
CM012076   Progressive external ophthalmoplegia
CM071761   Hypospadias
CM097256   Long QT syndrome
CM067719   Niemann-Pick disease
CM994416   Hypoglycaemia, persistent hyperinsulinaemic
CM085270   Bardet-Biedl syndrome
CM055288   Spinal muscular atrophy with resp. distress 1
CM981988   Obesity, severe, with diabetes
CM981987   Obesity, severe, with diabetes
CM002936   Papillon-Lefevre syndrome
CM013412   Congenital hypomyelinating neuropathy ?
CM092500   Lung cancer, association with
CM082943   Primary angle closure glaucoma ?
CM070343   Von Willebrand disease 1
CM070322   Von Willebrand disease 1 ?
CM091988   Arrhythmogenic right ventricular cardiomyopathy
CM950928   Glycogen storage disease 7 ?
CM011796   Cryptogenic liver disease
CM060322   ALys amyloidosis, systemic
CM910294   Phenylketonuria
CM003889   Hawkinsinsuria
CM022331   Breast and/or ovarian cancer
CM960194   Breast cancer
CM970189   Breast cancer ?
CM044579   Wilson disease ?
CM032029   Cone-rod dystrophy
CM981918   Ichthyosis, lamellar
CM985500   Impaired glucose homeostasis ?
CM013005   Colorectal cancer, non-polyposis
CM950521   Krabbe disease
CM970563   Krabbe disease
CM900187   Antitrypsin alpha 1 deficiency
CM890097   Antitrypsin alpha 1 deficiency
CM860015   Antitrypsin alpha 1 deficiency
CM085371   Hypothyroidism
CM085365   Hypothyroidism
CM068495   Increased cortical bone mass density, association with
CM971009   Griscelli syndrome
CM910256   Hepatic lipase deficiency ?
CM962679   Hepatic lipase deficiency
CM001044   Pseudoxanthoma elasticum, autosomal recessive
CM031328   Liver glycogenosis ?
CM012900   Bardet-Biedl syndrome
CM022671   Gitelman syndrome ?
CM981836   Gitelman syndrome
CM962611   Fanconi anaemia ?
CM962610   Fanconi anaemia ?
CM990080   Very long chain acyl-CoA dehydrogenase deficiency ?
CM053751   Ichthyosis, congenital, autosomal recessive
CM071857   Protein kinase deficiency
CM073339   Febrile seizures ?
CM990289   Breast cancer
CM941338   Amyloidotic polyneuropathy ?
CM015226   Xanthinuria, type 2 ?
CM940794   Fucosyltransferase deficiency
CM930259   Lewis antigen, absence
CM970545   Lewis antigen, absence
CM930258   Lewis antigen, absence
CM085589   CADASIL
CM984025             Mycobacterial infection
CM061204             Cystinuria
CM061206             Cystinuria
CM990958             Congenital nephrotic syndrome, Finnish type
CM064230             Malignant hyperthermia
CM021497             Maple syrup urine disease
CM940379             Glutaricacidaemia 2b ?
CM032056             Breast cancer ?
CM064119             Bardet-Biedl syndrome
CM920385             Leukocyte adhesion deficiency
CM060428             Peroxisome biogenesis disorder
CM024613             Epstein syndrome ?




JPT_alt_allele_frequenceHGMD_acc_num
-                       CM993170
-                       CM082582
-                       CM043271
-                       CM057654
-                       CM010805
-                       CM062497
-                       CM065144
                  0.768 CM012769
-                       CM990325
-                       CM096342
-                       CM081287
-                       CM045205
-                       CM050237
                  0.053 CM050231
-                       CM050228
-                       CM050227
-                       CM045572
-                       CM067660
                  0.005 CM080132
                  0.014 CM921036
-                       CM973661
-                       CM960153
-                       CM033750
-                       CM053344
-                       CM053345
-                       CM992646
-                       CM960732
-                       CM010428
-                       CM010436
                      1 CM016008
                  0.115 CM980573
-                       CM043093
-                       CM022431
-           CM061908
-           CM050303
-           CM068034
-           CM068032
-           CM068031
-           CM068040
-           CM068033
-           CM068043
-           CM068027
-           CM068029
-           CM043322
    0.024   CM013782
-           CM043321
-           CM068343
-           CM076205
    0.018   CM068344
    0.015   CM086819
-           CM076207
-           CM092984
-           CM081453
    0.005   CM073381
-           CM930702
-           CM063176
    0.019   CM063180
-           CM063179
-           CM942292
-           CM023043
-           CM077940
-           CM980632
-           CM981484
-           CM071957
-           CM071958
-           CM071069
    0.034   CM013413
-           CM013412
-           CM057878
-           CM035072
-           CM095605
    0.005   CM920241
-           CM097768
-           CM993192
-           CM992203
-           CM014740
    0.043   CM013956
-           CM003338
-           CM971228
-           CM002843
-           CM072815
    0.179   CM001044
-           CM020926
-           CM034216
-           CM085726
-           CM040464
-           CM085589
-           CM025913
-           CM002797
-           CM044918
    0.019   CM058019
-           CM044685
    0.062   CM004008
-           CM990958
-           CM044680
-           CM020471
-           CM024135
    0.603   HM080063
    0.019   CM044922
codon          strand
         388   +
         848   -
          78   +
         453   +
         111   -
         594   -
          27   +
         163   -
           3   -
         339   +
         476   +
           5   -
         238   +
         169   +
          32   +
         177   +
         194   +
         155   -
         114   +
         253   +
         318   +
         463   -
         556   -
         101   +
         352   +
         425   +
         443   +
         131   +
         304   +
         434   -
          92   +
         777   -
          36   -
        2255   -
        1433   -
        1428   -
        1300   -
        1209   -
        1201   -
         943   -
         863   -
         643   -
         423   -
         255   -
         212   -
 543   -
 534   -
 186   -
 166   -
  29   -
  38   +
 323   -
 490   -
 287   -
  48   -
  -7   +
 236   +
 490   -
 486   -
 713   +
 598   +
 607   +
 791   -
   9   +
1736   -
 386   -
 398   -
  76   -
  19   -
 242   -
 890   +
1007   +
1050   +
 356   +
 253   -
 713   -
 230   -
 383   -
  62   +
4344   +
 610   +
 703   +
 220   +
 252   -
3894   -
2712   -
1896   -
1101   -
 322   -
 172   -
 443   -
 655   -
 322   +
 390   +
 170   +
 189   +
 457   +
2000   +
 142   +
 844   +
 469   +
 264   +
1150   -
 265   +
 292   +
 394   +
 501   +
 410   +
 775   +
2365   -
1297   -
 377   +
 351   +
 459   +
 227   +
  84   +
 364   +
2941   -
1395   -
   9   +
 197   +
  56   +
 456   +
 312   -
 391   +
 444   +
 521   -
  10   -
 213   +
 219   +
 581   +
 655   +
 718   +
1897   -
1193   -
 126   -
1538   -
 211   -
 621   -
 125   -
 515   +
  37   -
  -2   -
 140   +
1314   -
1745   -
 443   +
 161   +
 776   +
 871   +
 178   +
 482   -
  22   +
  28   +
  68   +
 190   +
 384   +
 165   -
 235   +
 341   -
  38   +
 143   +
 333   +
  33   -
 422   +
 561   +
  62   +
 207   +
 484   -
 384   -
 681   +
 730   -
 126   +
 529   +
 870   +
2502   +
 621   +
 326   -
 117   +
  94   +
  74   +
  12   -
 303   -
 492   +
 574   +
 689   +
  41   +
 342   -
 181   -
  25   -
  51   -
2639   +
 111   -
 201   -
  65   +
 217   -
 338   -
  45   -
 809   -
 549   -
 535   +
 671   -
 532   -
  69   -
 270   -
3642   -
2641   -
 676   -
 221   +
  10   +
1138   +
1584   +
 559   +
 616   +
 722   +
  22   +
 830   -
 267   -
 261   -
 153   -
 338   -
 563   -
  11   -
 647   -
 649   -
 228   +
 788   -
 652   -
 528   -
 168   -
 455   -
  15   +
 324   +
 609   +
 740   +
  74   +
 334   +
 351   +
 556   +
 668   +
1235   +
1352   +
1453   +
 133   -
 580   -
 137   +
 300   +
  71   +
 380   +
 257   +
  26   -
 113   -
  93   -
  72   -
1022   -
 620   -
 725   +
 772   -
1075   -
 523   +
 373   +
1933   +
 215   -
 657   +
 574   -
 386   -
  43   -
 435   -
 386   -
 284   -
 251   -
  84   -
 328   -
 127   -
 297   -
1195   -
 728   -
 305   +
1121   -
 125   +
 474   +
 504   -
   5   -
 992   -
 653   -
 603   -
 417   -
 202   -
 732   +
 903   +
 493   +
1608   -
 661   -
 322   +
 545   +
  29   -
 278   +
 489   +
1095   -
1342   -
 153   +
 582   +
 608   +
1209   +
   2   -
 107   -
 191   +
1273   +
 178   -
 368   +
  21   -
 366   -
 186   -
 643   +
   6   -
 296   +
 508   +
 108   +
1019   +
 462   -
1098   -
 767   +
 522   -
 507   -
 236   -
 207   +
  49   -
 171   -
 234   +
 275   -
 879   +
 102   -
 153   -
 602   -
 545   -
 318   -
 514   +
 546   +
 872   +
1128   +
1380   +
1420   +
  12   +
  50   +
 344   +
 257   -
 336   -
 357   -
2185   -
1506   -
 924   -
 854   -
 817   -
 740   -
 129   -
  46   -
 181   -
 366   -
1869   +
 100   +
 696   +
 337   -
 138   -
 662   -
  70   +
 465   +
 782   +
 408   -
  53   -
 135   -
 194   +
 288   +
 389   +
  33   -
 203   -
 139   -
 114   -
  83   -
  27   -
 315   +
1915   +
2034   +
2466   +
2944   +
3412   +
 307   +
 525   +
1207   -
1140   -
 475   +
 559   +
 224   +
 547   +
1114   +
1491   -
 518   -
 448   -
  83   -
 224   -
6211   +
 942   -
 741   -
 413   -
  52   +
 625   -
 452   -
 168   -
 363   -
 124   -
 376   -
 342   -
 264   -
 213   -
 101   -
 227   +
 389   +
  94   -
 481   -
  27   -
 160   +
 184   +
1067   -
1052   -
 678   -
1148   -
  80   -
1246   -
 193   +
 334   +
 383   +
 546   +
1143   -
 831   -
 314   +
 286   +
1329   +
3559   -
3509   -
2966   -
 288   -
 408   -
 369   -
 304   -
 202   -
 197   +
1291   -
1268   -
 184   +
 769   +
 725   +
 955   +
  70   -
 264   +
 569   +
 728   +
 928   +
 442   +
 208   -
 617   +
 562   +
 488   -
1287   -
1088   -
 252   -
 181   -
   8   -
 380   -
  42   +
 674   -
 376   -
 114   -
  96   -
 626   -
  43   +
  65   +
 156   +
  21   +
 575   +
 701   +
 239   -
2266   +
 102   +
 546   -
 216   +
1628   -
1389   -
1150   -
1040   -
 841   -
 820   -
 693   -
 379   -
  40   -
 212   -
 173   -
 781   -
 928   -
 527   -
  91   +
 348   -
 278   -
 237   -
1342   +
 713   +
   6   +
 122   +
 358   +
 476   +
  70   -
 251   -
 190   +
 354   +
 209   -
 124   -
 105   -
  68   -
  20   -
 303   +
 619   +
1020   -
 162   -
 214   -
 223   -
 142   -
 123   -
 112   -
1077   -
 991   -
 408   -
 294   -
 117   -
1342   +
2787   +
4501   +
 328   +
          112   +
          145   +
          158   +
          158   +
          154   -
          472   -
          511   -
          156   -
           82   -
          171   +
          331   -
          268   -
          517   -
          871   -
          426   +
          385   -
          314   -
          130   +
          215   -
           80   -
          515   -
          712   -
            9   +
           42   -
           90   -
          369   -
          278   -
          102   -
          252   +
          116   +
          784   +
          932   +
          153   +
          189   +
           72   -
           51   +
          411   +
          615   +
          603   +
          200   -
          623   +
           10   +
          471   -




hgvs            codon_changeaa_change   codon       strand
1358G>A         CGG-CAG     Arg-Gln             453 +
80T>G           CTC-CGC     Leu-Arg              27 +
1147G>A   cGCA-ACA   Ala-Thr     383   +
712C>T    gCGG-TGG   Arg-Trp     238   +
1763C>G   TCC-TGC    Ser-Cys     588   +
911T>C    TTT-TCT    Phe-Ser     304   +
6764G>T   AGT-ATT    Ser-Ile    2255   -
2828G>A   CGG-CAG    Arg-Gln     943   -
635G>A    CGC-CAC    Arg-His     212   -
1627A>G   tATA-GTA   Ile-Val     543   -
1601G>A   AGT-AAT    Ser-Asn     534   -
85T>C     gTGT-CGT   Cys-Arg      29   -
1150G>A   gGGT-AGT   Gly-Ser     323   -
1470A>T   GAAg-GAT   Glu-Asp     490   -
40G>A     tGCA-ACA   Ala-Thr      -7   +
5290G>A   tGTG-ATG   Val-Met    1736   -
1193A>G   AAA-AGA    Lys-Arg     398   -
2669G>T   AGT-ATT    Ser-Ile     890   +
3019G>T   tGTG-TTG   Val-Leu    1007   +
758A>G    AAG-AGG    Lys-Arg     253   -
2276G>A   GGA-GAA    Gly-Glu     759   +
2113C>A   gCAG-AAG   Gln-Lys     703   +
1072C>A   aCAG-AAG   Gln-Lys     322   -
3065G>A   CGG-CAG    Arg-Gln    1022   +
4577A>C   AAG-ACG    Lys-Thr    1526   +
426A>T    CAAa-CAT   Gln-His     142   +
2531G>A   AGG-AAG    Arg-Lys     844   +
791A>G    CAT-CGT    His-Arg     264   +
3448C>T   aCGG-TGG   Arg-Trp    1150   -
793C>T    tCGT-TGT   Arg-Cys     265   +
1181T>C   ATG-ACG    Met-Thr     394   +
1501G>A   gGGA-AGA   Gly-Arg     501   +
1228G>A   cGTA-ATA   Val-Ile     410   +
1129G>C   gGAA-CAA   Glu-Gln     377   +
1375G>A   cGTC-ATC   Val-Ile     459   +
934A>G    cAGT-GGT   Ser-Gly     312   -
1561C>T   gCGC-TGC   Arg-Cys     521   -
29C>T     CCT-CTT    Pro-Leu      10   -
637G>A    cGTG-ATG   Val-Met     213   +
655A>G    cATC-GTC   Ile-Val     219   +
1861A>T   cAAG-TAG   Lys-Term    621   -
374A>G    AAT-AGT    Asn-Ser     125   -
1328G>A   CGA-CAA    Arg-Gln     443   +
532G>A    cGCC-ACC   Ala-Thr     178   +
202A>T    aAGG-TGG   Arg-Trp      68   +
428A>G    AAT-AGT    Asn-Ser     143   +
731A>G    CAG-CGG    Gln-Arg     226   +
997C>G    gCTT-GTT   Leu-Val     333   +
185C>T    TCG-TTG    Ser-Leu      62   +
2188C>G   tCAA-GAA   Gln-Glu     730   -
2608C>T   tCCA-TCA   Pro-Ser     870   +
350T>C    ATT-ACT    Ile-Thr     117   +
695C>T    ACG-ATG    Thr-Met     232   +
220C>A    cCAG-AAG   Gln-Lys      74   +
1721C>T   ACT-ATT    Thr-Ile     574   +
2065A>T   cACT-TCT   Thr-Ser     689   +
601G>A    cGGG-AGG   Gly-Arg     201   -
1013G>A   GGC-GAC    Gly-Asp     338   -
2426C>T   GCC-GTC    Ala-Val     809   -
2011G>A   cGTA-ATA   Val-Ile     671   -
1595A>G   CAT-CGT    His-Arg     532   -
3412G>A   gGTG-ATG   Val-Met    1138   +
65G>T     GGG-GTG    Gly-Val      22   +
767G>A    CGA-CAA    Arg-Gln     256   -
112A>G    tAAG-GAG   Lys-Glu      19   +
783A>G    TTAg-TTG   Leu-Leu     261   -
31G>A     cGCC-ACC   Ala-Thr      11   -
1946C>T   CCG-CTG    Pro-Leu     649   -
1954A>G   tAGA-GGA   Arg-Gly     652   -
1769G>A   CGA-CAA    Arg-Gln     590   -
43G>A     gGCC-ACC   Ala-Thr      15   +
1125A>C   TTAc-TTC   Leu-Phe     375   +
76C>G     cCTG-GTG   Leu-Val      26   -
277G>A    aGTT-ATT   Val-Ile      93   -
214A>G    aATG-GTG   Met-Val      72   -
3224T>C   ATC-ACC    Ile-Thr    1075   -
1567A>C   gAAG-CAG   Lys-Gln     523   +
1969A>G   cAGT-GGT   Ser-Gly     657   +
751C>T    cCGG-TGG   Arg-Trp     251   -
890C>T    ACA-ATA    Thr-Ile     297   -
3583A>T   cACA-TCA   Thr-Ser    1195   -
373G>A    aGGC-AGC   Gly-Ser     125   +
14C>T     ACG-ATG    Thr-Met       5   -
964G>A    cGAA-AAA   Glu-Lys     322   +
2944C>T   cCGC-TGC   Arg-Cys     982   +
457T>C    tTAC-CAC   Tyr-His     153   +
1824A>C   GAAg-GAC   Glu-Asp     608   +
755A>G    AAC-AGC    Asn-Ser     252   -
3625A>G   cACA-GCA   Thr-Ala    1209   +
67G>A     tGGA-AGA   Gly-Arg       2   -
1102G>A   cGTA-ATA   Val-Ile     368   +
557T>C    ATG-ACG    Met-Thr     186   -
1799C>T   ACG-ATG    Thr-Met     600   +
1522G>A   cGGG-AGG   Gly-Arg     508   +
1858C>T   cCGT-TGT   Arg-Cys     620   -
24T>C     GATt-GAC   Asp-Asp       8   +
2636C>A   ACG-AAG    Thr-Lys     879   +
427C>T    cCGA-TGA   Arg-Term    143   -
304G>A    cGTC-ATC   Val-Ile     102   -
458C>T    ACA-ATA    Thr-Ile     153   -
1634A>G    AAC-AGC    Asn-Ser     545   -
952G>C     aGTC-CTC   Val-Leu     318   -
770G>A     CGC-CAC    Arg-His     257   -
6859C>T    gCGG-TGG   Arg-Trp    2287   -
6554G>A    CGG-CAG    Arg-Gln    2185   -
1097T>C    CTG-CCG    Leu-Pro     366   -
299G>A     CGA-CAA    Arg-Gln     100   +
160T>C     cTAT-CAT   Tyr-His      54   -
263C>A     ACC-AAC    Thr-Asn      70   +
1241A>G    TAC-TGC    Tyr-Cys     414   -
97G>A      cGCG-ACG   Ala-Thr      33   -
6347A>G    CAC-CGC    His-Arg    2116   +
7397C>T    GCA-GTA    Ala-Val    2466   +
10234A>G   aATT-GTT   Ile-Val    3412   +
3419T>C    GTC-GCC    Val-Ala    1140   -
1639G>T    aGCT-TCT   Ala-Ser     547   +
1552G>A    tGTG-ATG   Val-Met     518   -
247G>A     aGCC-ACC   Ala-Thr      83   -
1870G>C    aGAA-CAA   Glu-Gln     624   -
1921G>A    cGCC-ACC   Ala-Thr     625   -
1403C>G    ACT-AGT    Thr-Ser     452   -
1200A>C    GAAc-GAC   Glu-Asp     376   -
863A>T     GAA-GTA    Glu-Val     264   -
710T>C     GTG-GCG    Val-Ala     213   -
3200T>C    TTG-TCG    Leu-Ser    1067   -
2033A>G    CAT-CGT    His-Arg     678   -
240A>G     GTAt-GTG   Val-Val      80   -
3736C>T    cCGT-TGT   Arg-Cys    1246   -
644A>G     AAT-AGT    Asn-Ser     193   +
1068A>C    TTAa-TTC   Leu-Phe     334   +
3803G>A    CGG-CAG    Arg-Gln    1268   -
2309A>G    TAT-TGT    Tyr-Cys     769   +
209A>G     AAC-AGC    Asn-Ser      70   -
791G>C     GGC-GCC    Gly-Ala     264   +
2782C>T    cCGT-TGT   Arg-Cys     928   +
3859G>A    cGTT-ATT   Val-Ile    1287   -
755A>G     GAT-GGT    Asp-Gly     252   -
128G>A     GGT-GAT    Gly-Asp      43   +
379C>T     cCCC-TCC   Pro-Ser     127   -
304C>T     aCAG-TAG   Gln-Term    102   +
1636A>G    cACA-GCA   Thr-Ala     546   -
4691T>C    CTG-CCG    Leu-Pro    1564   -
76G>A      cGGT-AGT   Gly-Ser       6   +
1072A>G    cATG-GTG   Met-Val     358   +
370C>T     cCCG-TCG   Pro-Ser     124   -
314C>T     ACG-ATG    Thr-Met     105   -
202T>C     aTGG-CGG   Trp-Arg      68   -
59T>G      CTG-CGG    Leu-Arg      20   -
3058G>C    gGCC-CCC   Ala-Pro    1020   -
641A>G                                    CAG-CGG     Gln-Arg           214   -
667C>A                                    cCTG-ATG    Leu-Met           223   -
425T>C                                    GTG-GCG     Val-Ala           142   -
1223G>A                                   CGG-CAG     Arg-Gln           408   -
4024A>G                                   gAGC-GGC    Ser-Gly          1342   +
452C>T                                    ACG-ATG     Thr-Met           106   +
461C>T                                    ACG-ATG     Thr-Met           154   -
1414T>C                                   aTCA-CCA    Ser-Pro           472   -
1549C>T                                   aCGT-TGT    Arg-Cys           517   -
1756C>T                                   gCGG-TGG    Arg-Trp           586   -
457C>G                                    cCTT-GTT    Leu-Val           153   +
4198C>T                                   gCGG-TGG    Arg-Trp          1400   -




disease                                     hgvs      codon_changeaa_change codon
                                            707T>C
3 beta-hydroxysteroid dehydrogenase deficiency        TTG-TCG     Leu-Ser      236
Leber congenital amaurosis                  1576C>T   cCGA-TGA    Arg-Term     526
Retinitis pigmentosa                        2506C>A   aCCT-ACT    Pro-Thr      836
Leber congenital amaurosis                  2714G>A   CGG-CAG     Arg-Gln      905
Leber congenital amaurosis                  3992G>A   CGC-CAC     Arg-His     1331
Haemolytic uraemic syndrome                 926C>T    GCC-GTC     Ala-Val      309
Lung cancer, susceptibility to              1346A>G   AAG-AGG     Lys-Arg      449
Increased plasma FFA and glycerol levels    791A>G    CAT-CGT     His-Arg      264
                                            1
Autoimmune lymphoproliferative syndrome II ? 228G>A   cGTA-ATA    Val-Ile      410
Parkinson disease ?                         1262A>G   AAA-AGA     Lys-Arg      421
Parkinson disease ?                         1370A>C   AAT-ACT     Asn-Thr      457
Gilbert syndrome                            1091C>T   CCG-CTG     Pro-Leu      364
Bethlem myopathy                            8822C>T   GCA-GTA     Ala-Val     2941
Ullrich congenital muscular dystrophy       4184G>A   CGG-CAG     Arg-Gln     1395
Bethlem myopathy                            3040A>G   aAAA-GAA    Lys-Glu     1014
Bethlem myopathy                            2030G>A   CGT-CAT     Arg-His      677
Endplate acetylcholinesterase deficiency    934A>G    cAGT-GGT    Ser-Gly      312
Osteogenesis imperfecta, recessive          826C>T    aCAG-TAG    Gln-Term     276
Diabetes, type 1                            464C>T    GCA-GTA     Ala-Val      155
Cholinesterasaemia                          1177G>C   tGGA-CGA    Gly-Arg      365
Butyrylcholinesterase deficiency            884A>G    AAA-AGA     Lys-Arg      267
Butyrylcholinesterase deficiency            182A>G    TAT-TGT     Tyr-Cys       33
Butyrylcholinesterase deficiency            155C>T    ACG-ATG     Thr-Met       24
Multiple colorectal adenoma                 112C>T    cCGC-TGC    Arg-Cys       38
Multiple colorectal adenoma                 1639G>T   gGCA-TCA    Ala-Ser      547
Methionine synthase reductase deficiency ?  997C>G    gCTT-GTT    Leu-Val      333
Hirschsprung disease                        277C>T    tCGG-TGG    Arg-Trp       93
Diastrophic dysplasia                       229A>C    gAAT-CAT    Asn-His       77
Diastrophic dysplasia                       1474C>T   aCGG-TGG    Arg-Trp      492
Diastrophic dysplasia ?                     1721C>T   ACT-ATT     Thr-Ile      574
Achondrogenesis 1B                          2065A>T   cACT-TCT    Thr-Ser      689
Glycogen storage disease 1c ?               601G>A    cGGG-AGG    Gly-Arg      201
Sialidosis 2                                239C>T    CCG-CTG     Pro-Leu       80
Colorectal cancer, non-polyposis           1688G>T    CGA-CTA    Arg-Leu     563
Ezetimibe non-response ?                   3698T>A    ATC-AAC    Ile-Asn    1233
Low dietary cholesterol absorption         2077C>T    cCGC-TGC   Arg-Cys     693
Low dietary cholesterol absorption         1940T>A    ATC-AAC    Ile-Asn     647
Low dietary cholesterol absorption         1496C>T    ACG-ATG    Thr-Met     499
Low dietary cholesterol absorption         1300G>A    cGGA-AGA   Gly-Arg     434
High dietary cholesterol absorption        845C>T     CCG-CTG    Pro-Leu     282
High dietary cholesterol absorption        521G>A     CGT-CAT    Arg-His     174
Low dietary cholesterol absorption         395A>G     AAT-AGT    Asn-Ser     132
Low dietary cholesterol absorption         182C>T     ACG-ATG    Thr-Met      61
Diabetes, type 2                           397C>T     aCGG-TGG   Arg-Trp     133
Diabetes, type 2                           361C>T     gCGG-TGG   Arg-Trp     121
Diabetes, type 2                           109C>T     aCGG-TGG   Arg-Trp      37
Congenital heart defects                   799G>A     aGTG-ATG   Val-Met     267
Congenital heart defects                   1037C>T    GCT-GTT    Ala-Val     346
Congenital heart defects                   1138G>A    cGTG-ATG   Val-Met     380
Congenital heart defects                   1220C>A    CCA-CAA    Pro-Gln     407
Congenital heart defects                   1273G>A    gGAC-AAC   Asp-Asn     425
Spastic paraplegia                         1456C>T    cCGC-TGC   Arg-Cys     486
Bardet-Biedl syndrome                      928A>T     cAGT-TGT   Ser-Cys     310
Meckel syndrome                            1321C>T    aCGA-TGA   Arg-Term    441
Goitre, simple                             2610G>T    CAGa-CAT   Gln-His     851
Hypothyroidism                             3022C>T    aCGC-TGC   Arg-Cys     989
Hypothyroidism                             3035C>T    CCG-CTG    Pro-Leu     993
Hypothyroidism                             5791A>G    cATC-GTC   Ile-Val    1912
Oesophageal tumours                        430C>T     cCGC-TGC   Arg-Cys     144
Oesophageal tumours                        379G>T     cGCA-TCA   Ala-Ser     127
Nephronophthisis 2                         913G>A     gGTT-ATT   Val-Ile     305
Cockayne syndrome                          3284C>G    CCT-CGT    Pro-Arg    1095
Hyperphenylalaninaemia                     263G>A     CGG-CAG    Arg-Gln      88
McArdle disease                            1948C>T    cCGA-TGA   Arg-Term    649
McArdle disease                            1769G>A    CGC-CAC    Arg-His     589
McArdle disease                            1094C>T    GCG-GTG    Ala-Val     364
Congenital hypomyelinating neuropathy ?    1805C>G    GCT-GGT    Ala-Gly     602
Congenital hypomyelinating neuropathy ?    1634A>G    AAC-AGC    Asn-Ser     545
Liver disease ?                            890C>T     ACA-ATA    Thr-Ile     296
Persistent Mullerian ducts syndrome ?      1626C>A    CTCc-CTA   Leu-Leu     542
Thalassaemia alpha ?                       1699G>A    tGCC-ACC   Ala-Thr     567
Spherocytosis                              424G>A     cGCT-ACT   Ala-Thr     142
Tetralogy of Fallot                        451G>T     cGCA-TCA   Ala-Ser     151
Polycystic kidney disease 1                12823C>T   cCGG-TGG   Arg-Trp    4275
Polycystic kidney disease 1                12457C>T   cCGC-TGC   Arg-Cys    4153
Polycystic kidney disease 1                10675G>A   cGGG-AGG   Gly-Arg    3559
Polycystic kidney disease 1                10526C>T   ACG-ATG    Thr-Met    3509
Polycystic kidney disease 1                8898G>C    GAGt-GAC   Glu-Asp    2966
Congenital disorder of glycosylation 1a    422G>A     CGC-CAC    Arg-His     141
Congenital disorder of glycosylation 1a    590A>C     GAA-GCA    Glu-Ala     197
Pseudoxanthoma elasticum ?                 3871G>A    cGCA-ACA   Ala-Thr    1291
                                           3803G>A
Pseudoxanthoma elasticum, autosomal recessive         CGG-CAG    Arg-Gln    1268
Gastric cancer                                  1018A>G   tACG-GCG   Thr-Ala    340
Gastric cancer                                  1849G>A   tGCA-ACA   Ala-Thr    617
Upper motor neuron syndrome                     1529C>T   GCA-GTA    Ala-Val    510
Sanfilippo syndrome B                           1336G>A   cGAG-AAG   Glu-Lys    446
CADASIL                                         3058G>C   gGCC-CCC   Ala-Pro   1020
CADASIL                                         709G>A    cGTG-ATG   Val-Met    237
Cryptorchidism                                  278C>T    CCC-CTC    Pro-Leu     69
Congenital nephrotic syndrome, Finnish   type   2971G>C   cGTA-CTA   Val-Leu    991
Nephrotic syndrome                              2869G>C   cGTG-CTG   Val-Leu    957
Minimal change nephrotic syndrome ?             2398C>T   gCGC-TGC   Arg-Cys    800
Congenital nephrotic syndrome, Finnish   type   1339G>A   tGAG-AAG   Glu-Lys    447
Congenital nephrotic syndrome, Finnish   type   1223G>A   CGG-CAG    Arg-Gln    408
Minimal change nephrotic syndrome ?             881C>T    ACC-ATC    Thr-Ile    294
Congenital nephrotic syndrome, Finnish   type   791C>G    CCG-CGG    Pro-Arg    264
Congenital nephrotic syndrome, Finnish   type   658T>G    gTCT-GCT   Ser-Ala    220
Congenital nephrotic syndrome, Finnish   type   349G>A    tGAG-AAG   Glu-Lys    117
Congenital nephrotic syndrome, Finnish   type   65C>T     GCG-GTG    Ala-Val     22
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Expression QTLs: Numbers of cis-eQTLs found in 100kb windows around expression probes with Spearman r


                                                   Genotype Set
         Population Sample Size      317K        610K        1M           1000G
        CEU                 43           321         375         420           522
        YRI                 42           504         273         345           518
        CHB+JPT             59           759         893         968          1154
        ALL                144          1052        1266        1428          1872
ssion probes with Spearman rank correlation, thresholds set by permutation to achieve FDR 0.05.
Table of SNPs that appear as near-fixed differences between populations

                                                                 ABS
                                                             FREQUENCY
    COMPARISON CHROMOSOME POSITION                 LRT       DIFFERENCE
   CEU vs CHB+JPT       15  46213776               204.953      0.992066
   CEU vs CHB+JPT       15  46273218               179.727      0.995497
   CEU vs YRI            1 157441307               198.792      0.992488
   CEU vs YRI           14 105170672               124.193      0.990592
   CEU vs YRI           15  42928665               189.429      0.993253
   CEU vs YRI           22  22690288               124.689      0.991467
   CHB+JPT vs YRI        1  24441391               218.751      0.994039
   CHB+JPT vs YRI        1 157441307               203.291      0.992486
   CHB+JPT vs YRI        2   9469158               201.654      0.995235
   CHB+JPT vs YRI        2  72314112               215.141      0.996552
   CHB+JPT vs YRI        2  72326877               217.928      0.993106
   CHB+JPT vs YRI        2  72354645                216.29      0.997074
   CHB+JPT vs YRI        2  72370804                   198      0.995403
   CHB+JPT vs YRI        2  72371995               234.669      0.997602
   CHB+JPT vs YRI        2  72373236               222.139      0.996523
   CHB+JPT vs YRI        2  72397638               234.281      0.996962
   CHB+JPT vs YRI        2  72426416               212.392      0.995567
   CHB+JPT vs YRI        2  72475988                208.85      0.991954
   CHB+JPT vs YRI        2  72496496                229.09      0.992102
   CHB+JPT vs YRI        2  72531996               212.619        0.9954
   CHB+JPT vs YRI        2  72565872               229.521       0.99761
   CHB+JPT vs YRI        2  72586634               175.251      0.992899
   CHB+JPT vs YRI        2  72606447               213.194      0.996461
   CHB+JPT vs YRI        2  72656947               220.712      0.996359
   CHB+JPT vs YRI        2  72676685               227.734      0.996876
   CHB+JPT vs YRI        2  72680620               225.176      0.997023
   CHB+JPT vs YRI        2  72686967               179.371      0.992624
   CHB+JPT vs YRI        2  72748589               216.363      0.994584
   CHB+JPT vs YRI        2  72761978               237.513       0.99773
   CHB+JPT vs YRI        2  72762206               236.503      0.996515
   CHB+JPT vs YRI        2  72777399               222.231      0.995461
   CHB+JPT vs YRI        2  72787692               223.942      0.993222
   CHB+JPT vs YRI        2  72823283               236.908      0.997006
   CHB+JPT vs YRI        2 177433874               213.572      0.992212
   CHB+JPT vs YRI        2 177469531               219.764      0.995995
   CHB+JPT vs YRI        2 177501473               197.332      0.994229
   CHB+JPT vs YRI        4  13302422               201.819      0.994804
   CHB+JPT vs YRI        4  41621468               195.627      0.996444
   CHB+JPT vs YRI        4  41821986               231.816      0.993669
   CHB+JPT vs YRI        5  27624800               145.838      0.999092
   CHB+JPT vs YRI        5 116976402               203.477       0.99233
   CHB+JPT vs YRI        5 116996995               209.284      0.990942
   CHB+JPT vs YRI        5 116997393               181.596      0.993739
   CHB+JPT vs YRI        5 117003144               222.913      0.997184
CHB+JPT   vs   YRI    5   117006587   213.427   0.997224
CHB+JPT   vs   YRI    5   117011477   188.036   0.995709
CHB+JPT   vs   YRI    5   117011538    161.72   0.992009
CHB+JPT   vs   YRI    5   117476897   174.944   0.991941
CHB+JPT   vs   YRI    5   117525764    208.64   0.996679
CHB+JPT   vs   YRI    5   117636276   188.357   0.992818
CHB+JPT   vs   YRI    5   117648160   196.275   0.994049
CHB+JPT   vs   YRI    5   117677374   209.267   0.997193
CHB+JPT   vs   YRI    5   119773883   177.194   0.992234
CHB+JPT   vs   YRI    5   175083501   178.881   0.994675
CHB+JPT   vs   YRI    6   105989840   196.869    0.99457
CHB+JPT   vs   YRI    6   106035509   218.697   0.992733
CHB+JPT   vs   YRI    6   153956275   202.796   0.991382
CHB+JPT   vs   YRI    6   153962242   211.119   0.996001
CHB+JPT   vs   YRI    6   153966274   232.717   0.997172
CHB+JPT   vs   YRI    6   153969844   170.443   0.992482
CHB+JPT   vs   YRI    7    74935424   174.672   0.994005
CHB+JPT   vs   YRI    8    10910563   167.629   0.992702
CHB+JPT   vs   YRI    8   109099179   199.822   0.996327
CHB+JPT   vs   YRI    8   109103595   195.758   0.996517
CHB+JPT   vs   YRI    9   135625230    192.31   0.994176
CHB+JPT   vs   YRI   12   122267223   167.598   0.994668
CHB+JPT   vs   YRI   17    59553682   220.627   0.997161
CHB+JPT   vs   YRI   20    52629121    175.89   0.993537
CHB+JPT   vs   YRI   20    52629520   220.084   0.996767
CHB+JPT   vs   YRI   20    52631503   199.007   0.995188
CHB+JPT   vs   YRI   20    52632255   215.047   0.996715
CHB+JPT   vs   YRI   20    52651191   236.697   0.996875
CHB+JPT   vs   YRI   20    52653368   240.966   0.997419
CHB+JPT   vs   YRI   20    52656285   216.584   0.996163
CHB+JPT   vs   YRI   20    52686047   220.394    0.99683
CHB+JPT   vs   YRI   20    52687274   231.872    0.99327
CHB+JPT   vs   YRI   22    44878828   159.457   0.993842
CHB+JPT   vs   YRI   22    44879637   201.093   0.995613
  NEAREST GENE    DISTANCE TO
(PROTEIN CODING, NEAREST EXON
   LEVELS 1+2)        (bp)
SLC24A5 (nonsynon)         29
SLC12A1                 12573
DARC                       26
TMEM121                  7224
TRIM69                  81350
GSTTP1                   8207
IL28RA                  54355
DARC                       26
ITGB1BP1                  490
EXOC6B                  29803
EXOC6B                  17038
EXOC6B                  10571
EXOC6B                  26730
EXOC6B                  27921
EXOC6B                  29162
EXOC6B                  17946
EXOC6B                   8439
EXOC6B                  15481
EXOC6B                  35989
EXOC6B                  10117
EXOC6B                   4485
EXOC6B                   6025
EXOC6B                  10056
EXOC6B                    642
EXOC6B                  20380
EXOC6B                  24315
EXOC6B                  30662
EXOC6B                  50151
EXOC6B                  36762
EXOC6B                  36534
EXOC6B                  21341
EXOC6B                  11048
EXOC6B                   1177
HNRNPA3                351663
HNRNPA3                316006
HNRNPA3                284064
BOD1L                   63977
TMEM33                  10435
SLC30A9                 37691
CDH9                   550369
RPS17P2                896157
RPS17P2                916750
RPS17P2                917148
RPS17P2                922899
RPS17P2            926342
RPS17P2            931232
RPS17P2            931293
DMXL1              958187
DMXL1              909320
DMXL1              798808
DMXL1              786924
DMXL1              757710
PRR16               54035
HRH2                37650
PREP                32188
PREP                77857
OPRM1              445861
OPRM1              439894
OPRM1              435862
OPRM1              432292
POM121C              6482
XKR6                13162
OXR1              1265081
OXR1              1269497
VAV2                   91
SETD8              167050
ACE                600741
DOK5                 9308
DOK5                 8909
DOK5                 6926
DOK5                 6174
DOK5                 9143
DOK5                 6966
DOK5                 4049
DOK5                 7357
DOK5                 6130
RP4-695O20__B.1      1035
RP4-695O20__B.1       316
Colours
Gene appears   in   both CEU vs CHB+JPT, and CHB+JPT vs YRI
Gene appears   in   both CEU vs CHB+JPT, and CEU vs YRI
Gene appears   in   both CEU vs YRI, and CHB+JPT vs YRI
Gene appears   in   all three pairwise comparisons
List of functional SNPs with high frequency differences between populations

                                                            FREQUENCY
     COMPARISON       CHROMOSOME      POSITION     LRT      DIFFERENCE
    CEU vs CHB+JPT              2     108880033    154.89      0.892013
    CEU vs CHB+JPT              2     135627892    148.64      0.820847
    CEU vs CHB+JPT              3     109671683   127.463       0.80769
    CEU vs CHB+JPT              3     124894279    122.33       0.82057
    CEU vs CHB+JPT              4      38475043   137.937      0.939426
    CEU vs CHB+JPT              4     100458342   117.427      0.816517
    CEU vs CHB+JPT              5      33987450   177.491      0.968179
    CEU vs CHB+JPT             10      55252911   116.601       0.83026
    CEU vs CHB+JPT             10      55625450   121.827      0.837906
    CEU vs CHB+JPT             11        298314   73.3066      0.866666
    CEU vs CHB+JPT             11     119604868   80.9807      0.819716
    CEU vs CHB+JPT             15      46213776   204.953      0.992066
    CEU vs CHB+JPT             15      61724262   122.029      0.809019
    CEU vs CHB+JPT             16      46815699   142.681      0.858173
    CEU vs CHB+JPT             16      88363824   130.925      0.833945
    CEU vs CHB+JPT             17      18937740   84.4623      0.894443
    CEU vs CHB+JPT             17      19187668   116.239      0.802636
    CEU vs CHB+JPT             20      61644006   104.337      0.814308
    CEU vs CHB+JPT             20      61645168   99.3601      0.804195
    CEU vs YRI                  1      39730500   45.9609      0.845461
    CEU vs YRI                  2       3669423   125.929       0.87029
    CEU vs YRI                  2      74495132   130.847      0.847237
    CEU vs YRI                  2      74541058   109.069      0.819257
    CEU vs YRI                  2      74543547   113.648      0.842857
    CEU vs YRI                  2      74563999   147.334      0.889086
    CEU vs YRI                  2     135627892   149.346      0.821061
    CEU vs YRI                  3      66633446   52.0528        0.8725
    CEU vs YRI                  3      66633452   52.6212      0.851777
    CEU vs YRI                  3     113667715   153.352      0.863153
    CEU vs YRI                  3     124894279   147.286       0.85425
    CEU vs YRI                  3     139830647   106.532      0.800107
    CEU vs YRI                  3     189810249   138.126      0.861665
    CEU vs YRI                  4      38475043   129.556      0.937328
    CEU vs YRI                  5      33987450   192.665      0.978825
    CEU vs YRI                  6       3209525   118.324      0.813168
    CEU vs YRI                  6     132214061   126.886      0.837711
    CEU vs YRI                  7      98885914   117.931      0.810099
    CEU vs YRI                  8      10517787   107.312      0.828434
    CEU vs YRI                  8      30822067   138.986      0.846453
    CEU vs YRI                  8      30822144   132.337      0.867334
    CEU vs YRI                  8     144873231   110.629      0.821243
    CEU vs YRI                  8     145610489   167.772      0.972345
    CEU vs YRI                  9     126302623   123.734      0.965823
    CEU vs YRI                  9     130605375   137.222      0.815588
    CEU vs YRI                 10        686237   91.1343      0.808199
CEU vs YRI         10    31691830   97.2662   0.827246
CEU vs YRI         11    66790842   45.4541   0.838335
CEU vs YRI         11    66921367   70.0337   0.853065
CEU vs YRI         11    66928312   101.147   0.846375
CEU vs YRI         12    78539038   123.799   0.909191
CEU vs YRI         14    23492930   88.3053   0.834615
CEU vs YRI         14    89499502   141.309   0.869391
CEU vs YRI         15    40769098   130.337   0.820846
CEU vs YRI         15    41366858   122.039   0.802619
CEU vs YRI         15    43179367   121.654   0.834531
CEU vs YRI         15    46213776   196.956   0.979102
CEU vs YRI         16    65594555   133.473   0.877287
CEU vs YRI         16    65873735   124.684   0.803517
CEU vs YRI         16    65875743   96.3464   0.843623
CEU vs YRI         16    65882328   122.571    0.82236
CEU vs YRI         17    26322430   71.7764   0.847639
CEU vs YRI         17    55863400   129.436   0.845422
CEU vs YRI         17    56141407    143.63   0.834914
CEU vs YRI         17    59371896    112.28   0.817403
CEU vs YRI         17    60251208   73.1841    0.87613
CEU vs YRI         17    71097779   93.6163   0.842255
CEU vs YRI         18    66022323    112.86   0.819609
CEU vs YRI         19    11211340   105.401   0.819493
CEU vs YRI         19    59495316   110.909   0.885632
CEU vs YRI         20    61644369   106.607   0.906625
CHB+JPT vs   YRI    1    11127645   150.084   0.856877
CHB+JPT vs   YRI    1    26013160   119.116   0.801805
CHB+JPT vs   YRI    1   153185704   125.893   0.833308
CHB+JPT vs   YRI    1   157441978   164.659   0.890296
CHB+JPT vs   YRI    1   173354352    127.51   0.848064
CHB+JPT vs   YRI    1   195379156   127.811   0.804591
CHB+JPT vs   YRI    2     3669423   164.924   0.870501
CHB+JPT vs   YRI    2     9445987   123.732   0.803948
CHB+JPT vs   YRI    2    17825931   125.459   0.826746
CHB+JPT vs   YRI    2    72561382   224.441   0.981011
CHB+JPT vs   YRI    2    73505475   201.427   0.937993
CHB+JPT vs   YRI    2    73531341    160.81   0.879896
CHB+JPT vs   YRI    2    73531406   191.439   0.931143
CHB+JPT vs   YRI    2    73532788   202.987   0.946528
CHB+JPT vs   YRI    2    73533498   183.023   0.925461
CHB+JPT vs   YRI    2    73534016   182.008   0.928179
CHB+JPT vs   YRI    2    73571075   181.205    0.93654
CHB+JPT vs   YRI    2    73571164   180.721     0.9051
CHB+JPT vs   YRI    2    73682880   165.939   0.883845
CHB+JPT vs   YRI    2    88168518   145.942   0.918631
CHB+JPT vs   YRI    2   108361240   159.094   0.870352
CHB+JPT vs   YRI    2   108880033   179.315   0.892015
CHB+JPT vs   YRI    2   219311063   142.298   0.835226
CHB+JPT vs   YRI    2   219318677   129.761   0.818889
CHB+JPT   vs   YRI    2   219905565   112.417   0.847973
CHB+JPT   vs   YRI    3     4333210   135.694   0.838618
CHB+JPT   vs   YRI    3    12588866   183.891    0.88311
CHB+JPT   vs   YRI    3    44667568   118.646    0.80168
CHB+JPT   vs   YRI    3    66633446   58.4499   0.844357
CHB+JPT   vs   YRI    3    66633452   61.5651   0.827005
CHB+JPT   vs   YRI    3   139830647   130.396   0.820666
CHB+JPT   vs   YRI    3   188929726   140.702   0.841338
CHB+JPT   vs   YRI    3   189810249   155.836   0.861667
CHB+JPT   vs   YRI    4     1155130   69.8392    0.80226
CHB+JPT   vs   YRI    4     6354255   143.337   0.852883
CHB+JPT   vs   YRI    4    41678875   165.167   0.859401
CHB+JPT   vs   YRI    4    41698428   142.534   0.908903
CHB+JPT   vs   YRI    4   100458342   139.869   0.831588
CHB+JPT   vs   YRI    4   159821126   131.767    0.83547
CHB+JPT   vs   YRI    5    37369484   124.859    0.81286
CHB+JPT   vs   YRI    5    81584972   133.085   0.806443
CHB+JPT   vs   YRI    5    81584996   131.029   0.810204
CHB+JPT   vs   YRI    5   140570950   122.228    0.82695
CHB+JPT   vs   YRI    6    10795732   134.087   0.823029
CHB+JPT   vs   YRI    6   105928142   156.429   0.831589
CHB+JPT   vs   YRI    6   132214061   149.086   0.858785
CHB+JPT   vs   YRI    6   167191706   124.994   0.850025
CHB+JPT   vs   YRI    7    14724798   144.033   0.863171
CHB+JPT   vs   YRI    7    82875687   110.488   0.807712
CHB+JPT   vs   YRI    7   120757005   125.398   0.845816
CHB+JPT   vs   YRI    7   120766325   136.319   0.828044
CHB+JPT   vs   YRI    7   138253063   162.117   0.889139
CHB+JPT   vs   YRI    8      353192   80.0883   0.957648
CHB+JPT   vs   YRI    8     8132136   141.485   0.832499
CHB+JPT   vs   YRI    8     8135987   141.157   0.809071
CHB+JPT   vs   YRI    8    10517787   119.994   0.828436
CHB+JPT   vs   YRI    8    23116201   156.129   0.851217
CHB+JPT   vs   YRI    8    30822067   161.459   0.866792
CHB+JPT   vs   YRI    8    30822144   157.824   0.881968
CHB+JPT   vs   YRI    8    30825766   152.475   0.856421
CHB+JPT   vs   YRI    8    32572900    136.78   0.829304
CHB+JPT   vs   YRI    8   144463743   136.815   0.814926
CHB+JPT   vs   YRI    8   145062516   78.6931   0.821969
CHB+JPT   vs   YRI    8   145063164   110.939   0.820947
CHB+JPT   vs   YRI    8   145064091   136.318   0.838702
CHB+JPT   vs   YRI    8   145064349   115.857   0.925792
CHB+JPT   vs   YRI    8   145065365   156.962   0.885137
CHB+JPT   vs   YRI    8   145068017   111.573   0.810585
CHB+JPT   vs   YRI    8   145610489    201.47   0.972348
CHB+JPT   vs   YRI    9    14712477   137.686    0.83156
CHB+JPT   vs   YRI    9   135633815   155.716   0.924812
CHB+JPT   vs   YRI   10    15185861    146.68   0.857229
CHB+JPT   vs   YRI   10    90956976   135.636   0.806124
CHB+JPT   vs   YRI   10   116063686   153.791   0.868732
CHB+JPT   vs   YRI   10   126905364    147.69   0.846752
CHB+JPT   vs   YRI   11     6086413   151.336   0.847482
CHB+JPT   vs   YRI   11    46344444   107.931   0.842526
CHB+JPT   vs   YRI   11   100352146   152.587   0.879313
CHB+JPT   vs   YRI   11   100352260   171.625   0.894678
CHB+JPT   vs   YRI   11   100352279   198.758   0.940315
CHB+JPT   vs   YRI   12     8267377   108.961   0.920149
CHB+JPT   vs   YRI   12    11135992   123.253   0.900124
CHB+JPT   vs   YRI   12    74740233   126.058   0.827401
CHB+JPT   vs   YRI   12    86904225   119.913   0.826267
CHB+JPT   vs   YRI   12   101770830   158.672   0.833938
CHB+JPT   vs   YRI   12   122211756   146.835   0.881329
CHB+JPT   vs   YRI   12   122745370   143.598   0.849857
CHB+JPT   vs   YRI   14    56742468   135.081   0.829878
CHB+JPT   vs   YRI   14    56746083   124.467   0.810946
CHB+JPT   vs   YRI   14    56811303   141.214   0.851973
CHB+JPT   vs   YRI   14    68772911   157.838   0.866524
CHB+JPT   vs   YRI   14    76913567   125.109   0.821593
CHB+JPT   vs   YRI   14    76914622   117.397   0.824482
CHB+JPT   vs   YRI   14    76914874   150.714    0.85146
CHB+JPT   vs   YRI   14    76995764   162.369   0.858324
CHB+JPT   vs   YRI   14    77005273   132.045   0.836994
CHB+JPT   vs   YRI   14    77020877   127.665   0.815758
CHB+JPT   vs   YRI   14    89499502   134.178   0.822352
CHB+JPT   vs   YRI   15    39936764   174.528   0.925786
CHB+JPT   vs   YRI   15    39936798   192.355   0.978402
CHB+JPT   vs   YRI   15    43179367   142.443   0.836643
CHB+JPT   vs   YRI   15    62295816   156.028   0.820645
CHB+JPT   vs   YRI   16    30444173   141.934   0.833157
CHB+JPT   vs   YRI   16    30982676   167.311   0.905893
CHB+JPT   vs   YRI   16    30995848   133.393   0.861965
CHB+JPT   vs   YRI   16    30996126   175.152   0.915563
CHB+JPT   vs   YRI   16    31029294   133.214   0.817196
CHB+JPT   vs   YRI   16    31061647   98.9842   0.917743
CHB+JPT   vs   YRI   16    46680083   146.675   0.871171
CHB+JPT   vs   YRI   16    46815699    224.87   0.967593
CHB+JPT   vs   YRI   16    65873735   134.756   0.803506
CHB+JPT   vs   YRI   16    65875743   134.699   0.840253
CHB+JPT   vs   YRI   16    65882328   136.228   0.822038
CHB+JPT   vs   YRI   16    66249169   161.979   0.875008
CHB+JPT   vs   YRI   17    26322430   103.851   0.849188
CHB+JPT   vs   YRI   17    33739279   118.122   0.800943
CHB+JPT   vs   YRI   17    46008353   130.372   0.859401
CHB+JPT   vs   YRI   17    55863364   139.244   0.802266
CHB+JPT   vs   YRI   17    59371896   146.897   0.817418
CHB+JPT   vs   YRI   17    60251208   104.999   0.975725
CHB+JPT   vs   YRI   17    70781271   170.013   0.871092
CHB+JPT   vs   YRI   17    71097779   109.675   0.848494
CHB+JPT   vs   YRI   17   71097953   128.467   0.806668
CHB+JPT   vs   YRI   18   66022323   187.152   0.948122
CHB+JPT   vs   YRI   19    3494397   115.872   0.902985
CHB+JPT   vs   YRI   19    3979783   95.0773   0.823996
CHB+JPT   vs   YRI   19    5843743   115.282    0.80498
CHB+JPT   vs   YRI   19   44480955   133.523   0.815844
CHB+JPT   vs   YRI   19   45621203   122.725   0.812594
CHB+JPT   vs   YRI   19   60516144   140.169   0.873255
CHB+JPT   vs   YRI   19   60571684   129.943   0.822517
CHB+JPT   vs   YRI   19   60587400   38.7397   0.839256
CHB+JPT   vs   YRI   20   29657199   127.327   0.835534
CHB+JPT   vs   YRI   20   29912986   93.4751   0.816393
CHB+JPT   vs   YRI   20   61642663   189.114     0.9611
CHB+JPT   vs   YRI   20   61644006   197.137   0.957066
CHB+JPT   vs   YRI   20   61644369   160.674   0.960353
CHB+JPT   vs   YRI   20   61645168   175.226   0.962797
CHB+JPT   vs   YRI   22   21315303   33.0489   0.834338
CHB+JPT   vs   YRI   22   39144446   130.914   0.871847
CHB+JPT   vs   YRI   22   40684335   106.033   0.840158
CHB+JPT   vs   YRI   22   44880019   157.294   0.923577
CHB+JPT   vs   YRI   22   45022832   147.687   0.824496
CHB+JPT   vs   YRI   22   45031623   164.361   0.908163
CHB+JPT   vs   YRI   22   45140161   154.244   0.852405
CHB+JPT   vs   YRI   22   48683439   120.775   0.800125
      GENE     FUNCTION
EDAR         nonsynonymous
RAB3GAP1     synonymous
MYH15        nonsynonymous
MYLK         synonymous
TLR1         nonsynonymous
ADH1B        nonsynonymous
SLC45A2      nonsynonymous
PCDH15       synonymous
PCDH15       nonsynonymous
IFITM2       nonsynonymous
OAF          nonsynonymous
SLC24A5      nonsynonymous
HERC1        nonsynonymous
ABCC11       nonsynonymous
FANCA        nonsynonymous
AC007952.8   nonsynonymous
B9D1         nonsynonymous
SRMS         synonymous
SRMS         synonymous
BMP8A        nonsynonymous
COLEC11      nonsynonymous
C2orf81      synonymous
WBP1         synonymous
MOGS         nonsynonymous
TTC31        nonsynonymous
RAB3GAP1     synonymous
LRIG1        nonsynonymous
LRIG1        nonsynonymous
BTLA         nonsynonymous
MYLK         synonymous
FAIM         nonsynonymous
LPP          nonsynonymous
TLR1         nonsynonymous
SLC45A2      nonsynonymous
PSMG4        nonsynonymous
ENPP1        nonsynonymous
CPSF4        synonymous
RP1L1        nonsynonymous
TEX15        nonsynonymous
TEX15        nonsynonymous
MAPK15       synonymous
AF205589.2   nonsynonymous
NR5A1        nonsynonymous
TBC1D13      nonsynonymous
C10orf108    nonsynonymous
AL117340.3   synonymous
ADRBK1       synonymous
RAD9A        synonymous
TBC1D10C     synonymous
PAWR         nonsynonymous
DHRS4        synonymous
TDP1         synonymous
STARD9       nonsynonymous
TGM7         synonymous
DUOX2        nonsynonymous
SLC24A5      nonsynonymous
CES8         nonsynonymous
PLEKHG4      nonsynonymous
PLEKHG4      nonsynonymous
KCTD19       synonymous
RNF135       nonsynonymous
C17orf64     synonymous
BCAS3        nonsynonymous
SCN4A        synonymous
AC103810.1   nonsynonymous
AC087749.2   synonymous
RTTN         nonsynonymous
AC011472.2   synonymous
LILRA3       nonsynonymous
SRMS         synonymous
MTOR         synonymous
SEPN1        nonsynonymous
PBXIP1       nonsynonymous
DARC         nonsynonymous
TNN          nonsynonymous
ASPM         synonymous
COLEC11      nonsynonymous
ASAP2        nonsynonymous
GEN1         synonymous
EXOC6B       synonymous
ALMS1        nonsynonymous
ALMS1        synonymous
ALMS1        nonsynonymous
ALMS1        nonsynonymous
ALMS1        nonsynonymous
ALMS1        nonsynonymous
ALMS1        nonsynonymous
ALMS1        nonsynonymous
ALMS1        synonymous
SMYD1        synonymous
SULT1C4      nonsynonymous
EDAR         nonsynonymous
TTLL4        synonymous
TTLL4        synonymous
RESP18       nonsynonymous
SETMAR       synonymous
MKRN2        synonymous
ZNF35        nonsynonymous
LRIG1        nonsynonymous
LRIG1        nonsynonymous
FAIM         nonsynonymous
BCL6         synonymous
LPP          nonsynonymous
SPON2        nonsynonymous
WFS1         nonsynonymous
WDR21B       synonymous
SLC30A9      nonsynonymous
ADH1B        nonsynonymous
ETFDH        nonsynonymous
NUP155       synonymous
ATG10        nonsynonymous
ATG10        nonsynonymous
PCDHB12      nonsynonymous
C6orf52      nonsynonymous
PREP         synonymous
ENPP1        nonsynonymous
RPS6KA2      nonsynonymous
DGKB         synonymous
SEMA3E       synonymous
WNT16        nonsynonymous
WNT16        nonsynonymous
KIAA1549     nonsynonymous
FBXO25       nonsynonymous
AC068020.2   nonsynonymous
AC068020.3   nonsynonymous
RP1L1        nonsynonymous
TNFRSF10A    nonsynonymous
TEX15        nonsynonymous
TEX15        nonsynonymous
TEX15        nonsynonymous
NRG1         nonsynonymous
TOP1MT       nonsynonymous
PLEC1        synonymous
PLEC1        synonymous
PLEC1        synonymous
PLEC1        synonymous
PLEC1        synonymous
PLEC1        nonsynonymous
AF205589.2   nonsynonymous
CER1         nonsynonymous
VAV2         nonsynonymous
RPP38        nonsynonymous
CH25H        synonymous
AFAP1L2      synonymous
AL157888.1   nonsynonymous
OR56B4       nonsynonymous
DGKZ         nonsynonymous
AP000872.1   synonymous
AP000872.1   synonymous
AP000872.1   nonsynonymous
FAM90A1      nonsynonymous
TAS2R43      nonsynonymous
NAP1L1       synonymous
C12orf50     nonsynonymous
PAH          synonymous
MPHOSPH9     synonymous
TCTN2        synonymous
AL391152.1   nonsynonymous
EXOC5        synonymous
MUDENG       synonymous
EXD2         synonymous
C14orf174    nonsynonymous
C14orf174    nonsynonymous
C14orf174    nonsynonymous
AHSA1        synonymous
AHSA1        synonymous
ISM2         nonsynonymous
TDP1         synonymous
SPTBN5       nonsynonymous
SPTBN5       nonsynonymous
DUOX2        nonsynonymous
CSNK1G1      synonymous
ZNF768       synonymous
ZNF668       synonymous
ZNF646       synonymous
ZNF646       nonsynonymous
BCKDK        synonymous
PRSS36       synonymous
ABCC12       nonsynonymous
ABCC11       nonsynonymous
PLEKHG4      nonsynonymous
PLEKHG4      nonsynonymous
KCTD19       synonymous
ACD          nonsynonymous
RNF135       nonsynonymous
GPR179       synonymous
CACNA1G      synonymous
C17orf64     synonymous
SCN4A        synonymous
AC103810.1   nonsynonymous
SLC25A19     synonymous
AC087749.2   synonymous
AC087749.2        synonymous
RTTN              nonsynonymous
C19orf71          nonsynonymous
PIAS4             synonymous
NDUFA11           synonymous
IL29              nonsynonymous
SERTAD1           nonsynonymous
TMEM150B          nonsynonymous
IL11              synonymous
AC020922.1        nonsynonymous
ID1               synonymous
DUSP15            nonsynonymous
SRMS              synonymous
SRMS              synonymous
SRMS              synonymous
SRMS              synonymous
POM121L1P         synonymous
MKL1              nonsynonymous
CTA-250D10.1      nonsynonymous
RP4-695O20__B.1   nonsynonymous
C22orf40          nonsynonymous
PKDREJ            synonymous
CELSR1            nonsynonymous
ALG12             nonsynonymous
Colours
Gene appears   in   both CEU vs CHB+JPT, and CHB+JPT vs YRI
Gene appears   in   both CEU vs CHB+JPT, and CEU vs YRI
Gene appears   in   both CEU vs YRI, and CHB+JPT vs YRI
Gene appears   in   all three pairwise comparisons
1000 Genomes Samples for the Full-Scale Project

                                                           Populations in the 1000 Genomes Project
                                                                                                                            Number of Samples
      Full Population Name                                                    Short Population NameAbbreviationTrio Pilot LowCov PilotExon Pilot Full Project
      Han Chinese in Beijing, China                                           Han Chinese          CHB                            30       109           100
      Han Chinese South                                                       Southern Han Chinese CHS                                                   100
      Chinese Dai in Xishuangbanna, China                                     Dai Chinese           CDX                                                 100
      Chinese in Denver, Colorado                                             Denver Chinese        CHD                                      107
      Japanese in Tokyo, Japan                                                Japanese              JPT                             30       105        100
      Kinh in Ho Chi Minh City, Vietnam                                       Kinh Vietnamese       KHV                                                 100


      Utah residents (CEPH) with Northern and Western European
                                                                              CEPH                  CEU                 3           60        90        100
      ancestry
      Toscani in Italia                                                       Tuscan                TSI                                       66        100
      British in England and Scotland                                         British               GBR                                                 100
      Finnish in Finland                                                      Finnish               FIN                                                 100
      Iberian populations in Spain                                            Spanish               IBS                                                 100


      Yoruba in Ibadan, Nigeria                                               Yoruba                YRI                 3           59       112        100
      Luhya in Webuye, Kenya                                                  Luhya                 LWK                                      108        100
      Gambian in Western Division, The Gambia                                                                                                                1
                                                                              Gambian               GWD                                            2 x 100
      (possibly two populations)
      Malawian in Blantyre, Malawi                                            Malawian              MAB                                                      1
                                                                                                                                                       100


      African Ancestry in Southwest US                                        African-American SW   ASW                                                  61
      African American in Jackson, Mississippi                                African-American MS   AJM                                                  80
      African Caribbean in Barbados                                           Barbadian             ACB                                                  79
      Mexican Ancestry in Los Angeles, California                             Mexican-American      MXL                                                  70
      Colombian in Medellin, Colombia                                         Colombian             CLM                                                  70
      Peruvian in Lima, Peru                                                  Peruvian              PEL                                                  70
      Puerto Rican in Puerto Rico                                             Puerto Rican          PUR                                                  70


                                                                              Ahom                  AHD                                                      1
      Ahom in Dibrugarh, India                                                                                                                         100
                                                                              Kayastha              KAK                                                      1
      Kayastha in Kolkata, India                                                                                                                       100
                                                                              Reddy                 RDH                                                      1
      Reddy in Hyderabad, India                                                                                                                        100
                                                                              Maratha               MRM                                                      1
      Maratha in Mumbai, India                                                                                                                         100
      Punjabi in Lahore, Pakistan                                             Punjabi               PJL                                                 100

                                                                                                    Totals              6          179       697       2500

      Note 1: the use of these populations in the full project has not been finalised
mtDNA Heteroplasmy in the Low-Coverage Project (n=163)


   No. of Samples with heteroplasmy
                                         140      85.9
      (with length heteroplasmy)
     No. of heteroplasmy per locus
                   93                    1        0.6
                   63                    1        0.6
                   43                    1        0.6
                    6                    1        0.6
                    3                    2        1.2
                    2                    2        1.2
                    1                    94       57.7
       No. of heteroplasmy per
               individual
                    5                    4        2.5
                    4                    16       9.8
                    3                    30       18.4
                    2                    49       30.1
                    1                    41       25.2


   No. of Samples with heteroplasmy
                                         74       45.4
    (without length heteroplasmy)
     No. of heteroplasmy per locus
                    6                    1        0.6
                    3                    1        0.6
                    2                    2        1.2
                    1                    94       57.7
       No. of heteroplasmy per
               individual
                    3                    9        5.5
                    2                    17       10.4
                    1                    48       29.4

      Coding region heteroplasmy
                                          8       4.9
     (without length heteroplsmy)
     No. of heteroplasmy per locus
                     1                    9       5.5
        No. of heteroplasmy per
                individual
                     2                    1       0.6
                     1                    7       4.3

       No. of length heteroplasmy     Frequency    %
           HVSI (16188~16192)             63      38.7
             HVSII (303~309)              93      57.1
             HVIII (522~523)              43      26.4
              HVIII (568-573)             3       1.8
Numbers of coding functional variants per individual in the LC and HCT projects, broken down by po

                  Pop    Project        syn          non-syn       stop   splice      FS
                                                                                    indel
            CEU         LC         10,533-        9,690-9,776    74-78    34-38    217-
                                   10,652                                          223
            CHB+JPT     LC         10,357-        9,932-10,115 102-   53-58        226-
                                   10,471                      108                 230
            YRI         LC         12,334-        11,048-      93-100 41-47        247-
                                   12,591         11,422                           255
            CEU         HCT        9,193-9,414    8,299-11,122 55-69  21-35        192-
                                                                                   211
            YRI         HCT        11,508-        10,349-        78-84    35-37    254-
                                   12,500         11,122                           280

            Numbers of coding functional variants per individual in the LC and Trio (HCT)
            Projects, broken down by population. Numbers shown are interquartile range
            (rounded to nearest whole number) for the LC project and minimum to
            maximum in the HCT project. Abbreviations: non-syn, non-synonymous;
            splice, splice-disrupting SNP; stop, stop codon-introducing SNP; FS indel,
            small frameshift insertion/deletion; SV, gene-disrupting large deletion.
ojects, broken down by population.

           SV

          34-37

          33-37

          32-35

          36-49

          33-40
Summary statistics of low-coverage project SNP calls




                                                     #dbSNPs
              Pop       Dataset        #SNPs        (build129)       %dbSNP

            CEU       Consensus        7,724,854       5,202,345           67.3
            CEU       Sanger            9,536,615       6,196,816          65.0
            CEU       Michigan          9,158,226       5,813,294          63.5
            CEU       Broad             9,264,373       6,034,253          65.1

            CHBJPT    Consensus        6,107,825       4,443,547           72.8
            CHBJPT    Sanger            7,503,638       5,246,527          69.9
            CHBJPT    Michigan          6,419,971       4,440,712          69.2
            CHB       Broad             6,687,855       4,696,311          70.2
            JPT       Broad             6,232,300       4,520,570          72.5

            YRI       Consensus      10,556,156        5,650,026           53.5
            YRI       Sanger          12,062,137        6,553,310          54.3
            YRI       Michigan        10,682,823        5,804,195          54.3
            YRI       Broad           14,469,954        6,602,526          45.6

            Numbers of SNPs called by each group and their consensus call across autosomal chromosomes.
            compared to evaluate the overlap with each set. HapMap II r23a SNPs with MAF > 0.01 for overl
            selected for evaluating discovery rate after excluding HapMap 3 sites, which were used to improv
            subset of SNP calls. Known and Novel Ts/Tv ratio represents transition/tranversion ratio among d
            sites, respectively.




Genotype concordance of low-coverage calls with HapMap data


                                    # HOM-REF         #HET          #HOM-ALT
                                    HM2(-HM3)       HM2(-HM3)       HM2(-HM3)
              Pop       Dataset     genotypes       genotypes       genotypes

            CEU       Consensus      22,327,356      14,364,108      9,711,756
            CEU       Sanger          22,536,903      14,482,704      9,814,131
            CEU       Michigan        22,211,026      14,442,106      9,726,914
            CEU       Broad           22,368,145      14,433,726      9,781,905

            CHBJPT    Consensus      25,775,363      18,615,172 13,725,094
            CHBJPT    Sanger          26,222,753      18,803,200 13,896,631
            CHBJPT    Michigan        24,435,802      18,119,614 13,293,183
            CHB       Broad           10,972,979       8,799,959  6,546,018
            JPT       Broad           11,562,600       9,236,410  6,930,129
YRI       Consensus      26,260,853      15,608,415 10,924,030
YRI       Sanger          26,380,162      15,734,018 11,060,715
YRI       Michigan        25,076,136      15,230,502 10,601,163
YRI       Broad           27,069,772      15,740,985 10,919,389

Genotype concordance between HapMap II genotypes and each of low coverage calls were evalua
between each pair of call sets, after excluding HapMap 3 SNPs which was used for improving call
call sets. 41 CEU, 59 CHBJPT (29 CHB, 30 JPT), 41 YRI HapMap II individuals overlapping with 1
project data was evaluated. Genotype concordance per each of HapMap II genotype category is p
overcall genotype concordance
                             %HapMap
             #HapMap2            2
             (excluding      Discovery    Known        Novel       Overall
               HM3)            Rate       Ts/Tv        Ts/Tv       Ts/Tv

                1,144,644          93.1       2.07          1.94       2.03
                 1,156,533         94.1       2.08          1.91       2.02
                 1,143,423         93.0       2.03          1.62       1.86
                 1,149,367         93.5       2.08          1.67       1.92

                  992,698          90.1       2.15          1.71       2.02
                 1,006,624         91.4       2.13          1.51       1.92
                   953,962         86.6       2.06          1.30       1.78
                   915,988         83.2       2.10          1.48       1.88
                   931,966         84.6       2.07          1.60       1.92

                1,302,431          90.9       2.09          2.02       2.06
                 1,312,777         91.6       2.10          2.02       2.07
                 1,254,561         87.6       2.07          1.85       1.96
                 1,328,360         92.7       2.04          1.70       1.84

s call across autosomal chromosomes. dbSNP build 129 is
 I r23a SNPs with MAF > 0.01 for overlapping individuals, is
Map 3 sites, which were used to improve genotype calling in a
 ts transition/tranversion ratio among dbSNP and non-dbSNP




              # TOTAL         %HOM-
             HM2(-HM3)          REF        %HET      %HOMALT %TOTAL
             genotypes        concord     concord     concord concord

              46,403,220          99.55      97.95        97.79      98.69
               46,833,738         98.73      96.57        97.40      97.78
               46,380,046         99.32      96.74        96.94      98.01
               46,583,776         99.34      95.71        96.20      97.56

              58,115,629          99.12      95.88        98.61      97.96
               58,922,584         98.12      95.35        97.13      97.00
               55,848,599         98.53      95.15        97.90      97.28
               26,318,956         98.30      84.96        97.10      93.54
               27,729,139         98.27      84.30        96.73      93.23
              52,793,298          99.20      95.09        98.03     97.74
               53,174,895         97.19      91.98        94.89     95.17
               50,907,801         98.14      94.27        96.61     96.66
               53,730,146         98.85      87.34        96.64     95.03

  each of low coverage calls were evaluated on overlapping SNPs
SNPs which was used for improving calling accuracy in a subset of
 pMap II individuals overlapping with 1000 genomes low-coverage
 ch of HapMap II genotype category is presented, as well as the
Heterozygote Call Accuracy in Simulated Data, with and without panel of genotyped tag SNPs


                                  MAF 2-5%                            MAF > 5%
         Sequencing         Sequence     Sequence              Sequence      Sequence
           Depth           w/Tag SNPs      Only               w/Tag SNPs       Only

             1x               84.88%          83.08%                 91.67%        90.56%
             2x               92.92%          92.62%                 97.48%        97.29%
             4x               97.81%          97.78%                 99.44%        99.43%
             8x               99.56%          99.56%                 99.89%        99.89%
             16x              99.98%          99.97%                 99.98%        99.98%


        In a panel of 100 sequenced individuals, the table shows predicted heterozygote call accuracy, as a f
        Results are tabulated separately for markers with allele frequency >5% and for markers with frequen
        using the coalescent model proposed by Schaffner et al (2005) for European ancestry samples. For e
        combination, the results of two analyses are shown. The first analysis uses only sequence data. The s
        genotyped tag SNPs to aid genotype calling. Simulations assumed no mapping error and per base err
 yped tag SNPs




ote call accuracy, as a function of sequencing depth.
or markers with frequency 2-5%. Data were simulated
ancestry samples. For each depth and allele frequency
 ly sequence data. The second analysis also uses a panel of
g error and per base error rate of 1% in sequence reads.

				
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