Summary

Summary {data-width=650}

Manhattan plot

manhattan_plot

manhattan_plot

QQ plot

qq_plot

qq_plot

AF plot

af_plot

af_plot

P-Z plot

pz_plot

pz_plot

beta_std plot

beta_std_plot

beta_std_plot

Metadata

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}

LDSC

*********************************************************************
* LD Score Regression (LDSC)
* Version 1.0.1
* (C) 2014-2019 Brendan Bulik-Sullivan and Hilary Finucane
* Broad Institute of MIT and Harvard / MIT Department of Mathematics
* GNU General Public License v3
*********************************************************************
Call: 
./ldsc.py \
--h2 /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-5115/UKB-b-5115_data.vcf.gz \
--ref-ld-chr ../reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-5115/ldsc.txt \
--w-ld-chr ../reference/eur_w_ld_chr/ 

Beginning analysis at Thu Oct 17 14:44:59 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-5115/UKB-b-5115_data.vcf.gz ...
Read summary statistics for 6368611 SNPs.
Dropped 3316 SNPs with duplicated rs numbers.
Reading reference panel LD Score from ../reference/eur_w_ld_chr/[1-22] ...
Read reference panel LD Scores for 1290028 SNPs.
Removing partitioned LD Scores with zero variance.
Reading regression weight LD Score from ../reference/eur_w_ld_chr/[1-22] ...
Read regression weight LD Scores for 1290028 SNPs.
After merging with reference panel LD, 1236719 SNPs remain.
After merging with regression SNP LD, 1236719 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0157 (0.0014)
Lambda GC: 1.1555
Mean Chi^2: 1.1829
Intercept: 1.0386 (0.008)
Ratio: 0.2108 (0.0439)
Analysis finished at Thu Oct 17 14:46:10 2019
Total time elapsed: 1.0m:10.68s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9293,
    "inflation_factor": 1.1474,
    "mean_EFFECT": 3.9769e-06,
    "n": "-Inf",
    "n_snps": 9851866,
    "n_clumped_hits": 3,
    "n_p_sig": 64,
    "n_mono": 0,
    "n_ns": 0,
    "n_mac": 0,
    "is_snpid_unique": true,
    "n_miss_EFFECT": 0,
    "n_miss_SE": 0,
    "n_miss_PVAL": 0,
    "n_miss_AF": 0,
    "n_miss_AF_reference": 58349,
    "n_est": "NA",
    "ratio_se_n": "NA",
    "mean_diff": "NaN",
    "ratio_diff": "NaN",
    "sd_y_est1": "NaN",
    "sd_y_est2": "NA",
    "r2_sum1": 0,
    "r2_sum2": 0,
    "r2_sum3": 0,
    "r2_sum4": 0,
    "ldsc_nsnp_merge_refpanel_ld": 1236719,
    "ldsc_nsnp_merge_regression_ld": 1236719,
    "ldsc_observed_scale_h2_beta": 0.0157,
    "ldsc_observed_scale_h2_se": 0.0014,
    "ldsc_intercept_beta": 1.0386,
    "ldsc_intercept_se": 0.008,
    "ldsc_lambda_gc": 1.1555,
    "ldsc_mean_chisq": 1.1829,
    "ldsc_ratio": 0.211
}

Flags

name value
af_correlation FALSE
inflation_factor FALSE
n TRUE
is_snpid_non_unique FALSE
mean_EFFECT_nonfinite FALSE
mean_EFFECT_05 FALSE
mean_EFFECT_01 FALSE
mean_chisq FALSE
n_p_sig FALSE
miss_EFFECT FALSE
miss_SE FALSE
miss_PVAL FALSE
ldsc_ratio FALSE
ldsc_intercept_beta FALSE
n_clumped_hits FALSE
r2_sum1 FALSE
r2_sum2 FALSE
r2_sum3 FALSE
r2_sum4 FALSE

Definitions

General metrics

  • af_correlation: Correlation coefficient between AF and AF_reference.
  • inflation_factor (lambda): Genomic inflation factor.
  • mean_EFFECT: Mean of EFFECT size.
  • n: Maximum value of reported sample size across all SNPs, \(n\).
  • n_clumped_hits: Number of clumped hits.
  • n_snps: Number of SNPs
  • n_p_sig: Number of SNPs with pvalue below 5e-8.
  • n_mono: Number of monomorphic (MAF == 1 or MAF == 0) SNPs.
  • n_ns: Number of SNPs with nonsense values:
    • alleles other than A, C, G or T.
    • P-values < 0 or > 1.
    • negative or infinite standard errors (<= 0 or = Infinity).
    • infinite beta estimates or allele frequencies < 0 or > 1.
  • n_mac: Number of cases where MAC (\(2 \times N \times MAF\)) is less than 6.
  • is_snpid_unique: true if the combination of ID REF ALT is unique and therefore no duplication in snpid.
  • n_miss_<*>: Number of NA observations for <*> column.

se_n metrics

  • n_est: Estimated sample size value, \(\widehat{n}\).
  • ratio_se_n: \(\texttt{ratio_se_n} = \frac{\sqrt{\widehat{n}}}{\sqrt{n}}\). We expect ratio_se_n to be 1. When it is not 1, it implies that the trait did not have a variance of 1, the reported sample size is wrong, or that the SNP-level effective sample sizes differ markedly from the reported sample size.
  • mean_diff: \(\texttt{mean_diff} = \sum_{j} \frac{\widehat{\beta_j^{std}} - \beta_j}{\texttt{n_snps}}\), mean difference between the standardised beta, predicted from P-values, and the observed beta. The difference should be very close to zero if trait has a variance of 1.
    • \(\widehat{\beta_j^{std}} = \sqrt{\frac{{z}_j^2 / ({z}_j^2 + n -2)}{2 \times {MAF}_j \times (1 - {MAF}_j)}} \times sign({z}_j)\),
    • \({z}_j = \frac{\beta_j}{{se}_j}\),
    • and \(\beta_j\) is the reported effect size.
  • ratio_diff: \(\texttt{ratio_diff} = |\frac{\texttt{mean_diff}}{\texttt{mean_diff2}}|\), absolute ratio between the mean of diff and the mean of diff2 (expected difference between the standardised beta predicted from P-values, and the standardised beta derived from the observed beta divided by the predicted SD; NOT reported). The ratio should be close to 1. If different from 1, then implies that the betas are not in a standard deviation scale.
    • \(\texttt{mean_diff2} = \sum_{j} \frac{\widehat{\beta_j^{std}} - \beta^{\prime}_j}{\texttt{n_snps}}\)
    • \(\beta^{\prime}_j = \frac{\beta_j}{\widehat{\texttt{sd2}}_{y}}\)
  • sd_y_est1: The standard deviation for the trait inferred from the reported sample size, median standard errors for the SNP-trait assocations and SNP variances.
    • \(\widehat{\texttt{sd1}}_{y} = \frac{\sqrt{n} \times median({se}_j)}{C}\),
    • \(C = median(\frac{1}{\sqrt{2 \times {MAF}_j \times (1 - {MAF}_j)}})\),
    • and \({se}_j\) is the reported standard error.
  • sd_y_est2: The standard deviation for the trait inferred from the reported sample size, Z statistics for the SNP-trait effects (beta/se) and allele frequency.
    • \(\widehat{\texttt{sd2}}_{y} = median(\widehat{sd_j})\),
    • \(\widehat{sd_j} = \frac{\beta_j}{\widehat{\beta_j^{std}}}\),

r2 metrics

Sum of variance explained, calculated from the clumped top hits sample.

  • r2_sum<*>: r2 statistics under various assumptions
    • 1: \(r^2 = \sum_j{\frac{2 \times \beta_j^2 \times {MAF}_j \times (1 - {MAF}_j)}{\texttt{var1}}}\), \(\texttt{var1} = 1\).
    • 2: \(r^2 = \sum_j{\frac{2 \times \beta_j^2 \times {MAF}_j \times (1 - {MAF}_j)}{\texttt{var2}}}\), \(\texttt{var2} = {\widehat{\texttt{sd1}}_{y}}^2\),
    • 3: \(r^2 = \sum_j{\frac{2 \times \beta_j^2 \times {MAF}_j \times (1 - {MAF}_j)}{\texttt{var3}}}\), \(\texttt{var3} = {\widehat{\texttt{sd2}}_{y}}^2\),
    • 4: \(r^2 = \sum_j{\frac{F_j}{F_j + n - 2}}\), \(F = \frac{\beta_j^2}{{se}_j^2}\).

LDSC metrics

Metrics from LD regression

  • ldsc_nsnp_merge_refpanel_ld: Number of remaining SNPs after merging with reference panel LD.
  • ldsc_nsnp_merge_regression_ld: Number of remaining SNPs after merging with regression SNP LD.
  • ldsc_observed_scale_h2_{beta,se} Coefficient value and SE for total observed scale h2.
  • ldsc_intercept_{beta,se}: Coefficient value and SE for intercept. Intercept is expected to be 1.
  • ldsc_lambda_gc: Lambda GC statistics.
  • ldsc_mean_chisq: Mean \(\chi^2\) statistics.
  • ldsc_ratio: \(\frac{\texttt{ldsc_intercept_beta} - 1}{\texttt{ldsc_mean_chisq} - 1}\), the proportion of the inflation in the mean \(\chi^2\) that the LD Score regression intercepts ascribes to causes other than polygenic heritability. The value of ratio should be close to zero, though in practice values of 0.1-0.2 are not uncommon, probably due to sample/reference LD Score mismatch or model misspecification (e.g., low LD variants have slightly higher \(h^2\) per SNP).

Flags

When a metric needs attention, the flag should return TRUE.

  • af_correlation: abs(af_correlation) < 0.7.
  • inflation_factor: inflation_factor > 1.2.
  • n: n (max reported sample size) < 10000.
  • is_snpid_non_unique: NOT is_snpid_unique.
  • mean_EFFECT_nonfinite: mean(EFFECT) is NA, NaN, or Inf.
  • mean_EFFECT_05: abs(mean(EFFECT)) > 0.5.
  • mean_EFFECT_01: abs(mean(EFFECT)) > 0.1.
  • mean_chisq: ldsc_mean_chisq > 1.3 or ldsc_mean_chisq < 0.7.
  • n_p_sig: n_p_sig > 1000.
  • miss_<*>: n_miss_<*> / n_snps > 0.01.
  • ldsc_ratio: ldsc_ratio > 0.5
  • ldsc_intercept_beta: ldsc_intercept_beta > 1.5
  • n_clumped_hits: n_clumped_hits > 1000
  • r2_sum<*>: r2_sum<*> > 0.5

Plots

  • Manhattan plot
    • Red line: \(-log_{10}^{5 \times 10^{-8}}\)
    • Blue line: \(-log_{10}^{5 \times 10^{-5}}\)
  • QQ plot
  • AF plot
  • P-Z plot
  • beta_std plot: Scatter plot between \(\widehat{\beta_j^{std}}\) and \(\beta_j\)

Diagnostics

Details

Summary stats

skim_type skim_variable n_missing complete_rate character.min character.max character.empty character.n_unique character.whitespace logical.mean logical.count numeric.mean numeric.sd numeric.p0 numeric.p25 numeric.p50 numeric.p75 numeric.p100 numeric.hist
character ID 0 1.000000 3 58 0 6365316 0 NA NA NA NA NA NA NA NA NA NA
character REF 0 1.000000 1 1 0 4 0 NA NA NA NA NA NA NA NA NA NA
character ALT 0 1.000000 1 1 0 4 0 NA NA NA NA NA NA NA NA NA NA
logical N 6368611 0.000000 NA NA NA NA NA NaN : NA NA NA NA NA NA NA NA
numeric CHROM 0 1.000000 NA NA NA NA NA NA NA 8.667476e+00 5.763517e+00 1.0000000 4.000000e+00 8.000000e+00 1.300000e+01 2.200000e+01 ▇▅▅▂▂
numeric POS 0 1.000000 NA NA NA NA NA NA NA 7.857646e+07 5.649955e+07 828.0000000 3.201266e+07 6.900898e+07 1.144914e+08 2.492385e+08 ▇▆▅▂▁
numeric EFFECT 0 1.000000 NA NA NA NA NA NA NA 4.000000e-06 6.175000e-04 -0.0050051 -3.557000e-04 1.000000e-06 3.594000e-04 5.090600e-03 ▁▁▇▁▁
numeric SE 0 1.000000 NA NA NA NA NA NA NA 5.424000e-04 2.072000e-04 0.0003354 3.735000e-04 4.592000e-04 6.609000e-04 2.907400e-03 ▇▁▁▁▁
numeric PVAL 0 1.000000 NA NA NA NA NA NA NA 4.773434e-01 2.951273e-01 0.0000000 2.200002e-01 4.700002e-01 7.300002e-01 1.000000e+00 ▇▇▇▆▇
numeric PVAL_ztest 0 1.000000 NA NA NA NA NA NA NA 4.773431e-01 2.951019e-01 0.0000000 2.155481e-01 4.697293e-01 7.327289e-01 9.999997e-01 ▇▇▆▆▆
numeric AF 0 1.000000 NA NA NA NA NA NA NA 2.978795e-01 2.565048e-01 0.0260790 8.159000e-02 2.104630e-01 4.605650e-01 9.739210e-01 ▇▃▂▂▁
numeric AF_reference 58349 0.990838 NA NA NA NA NA NA NA 2.951570e-01 2.490705e-01 0.0000000 9.085460e-02 2.194490e-01 4.522760e-01 1.000000e+00 ▇▅▂▂▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 49298 rs200943160 T C -0.0007288 0.0006172 0.2399999 0.2377000 0.623765 0.7821490 NA
1 54676 rs2462492 C T 0.0003905 0.0006115 0.5199996 0.5230985 0.400401 NA NA
1 86028 rs114608975 T C -0.0018898 0.0009776 0.0530005 0.0532328 0.103556 0.0277556 NA
1 91536 rs6702460 G T 0.0008359 0.0006021 0.1700000 0.1650389 0.456846 0.4207270 NA
1 234313 rs8179466 C T 0.0011586 0.0011872 0.3300000 0.3290930 0.074506 NA NA
1 534192 rs6680723 C T 0.0004611 0.0006877 0.5000000 0.5025885 0.240959 NA NA
1 546697 rs12025928 A G 0.0017744 0.0008580 0.0389996 0.0386329 0.913475 NA NA
1 693731 rs12238997 A G -0.0002299 0.0005763 0.6899999 0.6899158 0.116329 0.1417730 NA
1 705882 rs72631875 G A -0.0020960 0.0008446 0.0129999 0.0130730 0.067288 0.0315495 NA
1 706368 rs55727773 A G -0.0004033 0.0004269 0.3400001 0.3448752 0.515645 0.2751600 NA
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51218377 rs2519461 G C -0.0011748 0.0006673 0.0779992 0.0783263 0.073622 0.0826677 NA
22 51219006 rs28729663 G A -0.0005036 0.0005151 0.3300000 0.3282207 0.137950 0.2052720 NA
22 51219387 rs9616832 T C -0.0012425 0.0006686 0.0629999 0.0631316 0.073744 0.0654952 NA
22 51219704 rs147475742 G A -0.0003533 0.0008960 0.6899999 0.6933419 0.041954 0.0473243 NA
22 51221190 rs369304721 G A -0.0012758 0.0008945 0.1499999 0.1538033 0.049731 NA NA
22 51221731 rs115055839 T C -0.0011874 0.0006691 0.0759994 0.0759360 0.073235 0.0625000 NA
22 51222100 rs114553188 G T 0.0002546 0.0007877 0.7499995 0.7464978 0.054460 0.0880591 NA
22 51223637 rs375798137 G A 0.0001972 0.0007915 0.8000000 0.8032792 0.054089 0.0788738 NA
22 51229805 rs9616985 T C -0.0011676 0.0006715 0.0819993 0.0820720 0.073071 0.0730831 NA
22 51237063 rs3896457 T C 0.0006383 0.0004107 0.1199999 0.1201440 0.297974 0.2050720 NA

bcf preview

1   49298   rs10399793  T   C   .   PASS    AF=0.623765 ES:SE:LP:AF:ID  -0.000728794:0.000617227:0.619789:0.623765:rs10399793
1   54676   rs2462492   C   T   .   PASS    AF=0.400401 ES:SE:LP:AF:ID  0.000390478:0.000611482:0.283997:0.400401:rs2462492
1   86028   rs114608975 T   C   .   PASS    AF=0.103556 ES:SE:LP:AF:ID  -0.00188979:0.000977632:1.27572:0.103556:rs114608975
1   91536   rs6702460   G   T   .   PASS    AF=0.456846 ES:SE:LP:AF:ID  0.000835877:0.000602077:0.769551:0.456846:rs6702460
1   234313  rs8179466   C   T   .   PASS    AF=0.074506 ES:SE:LP:AF:ID  0.00115859:0.00118715:0.481486:0.074506:rs8179466
1   534192  rs6680723   C   T   .   PASS    AF=0.240959 ES:SE:LP:AF:ID  0.000461071:0.000687732:0.30103:0.240959:rs6680723
1   546697  rs12025928  A   G   .   PASS    AF=0.913475 ES:SE:LP:AF:ID  0.00177437:0.000857981:1.40894:0.913475:rs12025928
1   693731  rs12238997  A   G   .   PASS    AF=0.116329 ES:SE:LP:AF:ID  -0.000229942:0.00057634:0.161151:0.116329:rs12238997
1   705882  rs72631875  G   A   .   PASS    AF=0.067288 ES:SE:LP:AF:ID  -0.00209601:0.000844561:1.88606:0.067288:rs72631875
1   706368  rs12029736  A   G   .   PASS    AF=0.515645 ES:SE:LP:AF:ID  -0.000403268:0.00042693:0.468521:0.515645:rs12029736
1   714596  rs149887893 T   C   .   PASS    AF=0.033009 ES:SE:LP:AF:ID  0.000348724:0.00107625:0.124939:0.033009:rs149887893
1   715265  rs12184267  C   T   .   PASS    AF=0.036624 ES:SE:LP:AF:ID  0.000104603:0.000977611:0.0409586:0.036624:rs12184267
1   715367  rs12184277  A   G   .   PASS    AF=0.036741 ES:SE:LP:AF:ID  0.000198416:0.000973913:0.0757207:0.036741:rs12184277
1   717485  rs12184279  C   A   .   PASS    AF=0.036439 ES:SE:LP:AF:ID  4.57839e-05:0.00098094:0.0177288:0.036439:rs12184279
1   720381  rs116801199 G   T   .   PASS    AF=0.03698  ES:SE:LP:AF:ID  8.81554e-05:0.00097005:0.0315171:0.03698:rs116801199
1   721290  rs12565286  G   C   .   PASS    AF=0.037077 ES:SE:LP:AF:ID  0.000191229:0.000966728:0.0757207:0.037077:rs12565286
1   722670  rs116030099 T   C   .   PASS    AF=0.1012   ES:SE:LP:AF:ID  -0.00102786:0.000704409:0.853872:0.1012:rs116030099
1   723891  rs2977670   G   C   .   PASS    AF=0.959091 ES:SE:LP:AF:ID  -0.000225175:0.000932387:0.091515:0.959091:rs2977670
1   724849  rs12126395  C   A   .   PASS    AF=0.03145  ES:SE:LP:AF:ID  0.00147154:0.00169275:0.420216:0.03145:rs12126395
1   725060  rs865924913 A   T   .   PASS    AF=0.053255 ES:SE:LP:AF:ID  5.56061e-05:0.00134655:0.0132283:0.053255:rs865924913
1   726794  rs28454925  C   G   .   PASS    AF=0.036594 ES:SE:LP:AF:ID  0.000177029:0.000972999:0.0655015:0.036594:rs28454925
1   729632  rs116720794 C   T   .   PASS    AF=0.03691  ES:SE:LP:AF:ID  0.000164807:0.000964142:0.0655015:0.03691:rs116720794
1   729679  rs4951859   C   G   .   PASS    AF=0.843204 ES:SE:LP:AF:ID  0.000306562:0.000499473:0.267606:0.843204:rs4951859
1   730087  rs148120343 T   C   .   PASS    AF=0.055912 ES:SE:LP:AF:ID  -0.00134165:0.000808728:1.01323:0.055912:rs148120343
1   731718  rs58276399  T   C   .   PASS    AF=0.122312 ES:SE:LP:AF:ID  -0.000206785:0.000546716:0.148742:0.122312:rs58276399
1   734349  rs141242758 T   C   .   PASS    AF=0.121554 ES:SE:LP:AF:ID  -0.000198986:0.000546946:0.142668:0.121554:rs141242758
1   736289  rs79010578  T   A   .   PASS    AF=0.132335 ES:SE:LP:AF:ID  -0.000293763:0.00053907:0.229148:0.132335:rs79010578
1   752478  rs146277091 G   A   .   PASS    AF=0.036825 ES:SE:LP:AF:ID  0.000254369:0.000954389:0.102373:0.036825:rs146277091
1   752566  rs3094315   G   A   .   PASS    AF=0.838945 ES:SE:LP:AF:ID  0.00047583:0.000483706:0.481486:0.838945:rs3094315
1   752721  rs3131972   A   G   .   PASS    AF=0.838573 ES:SE:LP:AF:ID  0.0004521:0.000483186:0.455932:0.838573:rs3131972
1   753405  rs3115860   C   A   .   PASS    AF=0.869776 ES:SE:LP:AF:ID  0.000479877:0.000518475:0.455932:0.869776:rs3115860
1   753541  rs2073813   G   A   .   PASS    AF=0.129876 ES:SE:LP:AF:ID  -0.000441931:0.000519536:0.408935:0.129876:rs2073813
1   754063  rs12184312  G   T   .   PASS    AF=0.037336 ES:SE:LP:AF:ID  0.000106361:0.000938207:0.0409586:0.037336:rs12184312
1   754105  rs12184325  C   T   .   PASS    AF=0.03758  ES:SE:LP:AF:ID  0.000133307:0.000932279:0.05061:0.03758:rs12184325
1   754182  rs3131969   A   G   .   PASS    AF=0.869117 ES:SE:LP:AF:ID  0.00044811:0.000517459:0.408935:0.869117:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.869215 ES:SE:LP:AF:ID  0.000459829:0.000517665:0.431798:0.869215:rs3131968
1   754211  rs12184313  G   A   .   PASS    AF=0.037538 ES:SE:LP:AF:ID  0.000139849:0.000936311:0.0555173:0.037538:rs12184313
1   754334  rs3131967   T   C   .   PASS    AF=0.869121 ES:SE:LP:AF:ID  0.000451425:0.00051745:0.420216:0.869121:rs3131967
1   754503  rs3115859   G   A   .   PASS    AF=0.838026 ES:SE:LP:AF:ID  0.000503632:0.000481845:0.522879:0.838026:rs3115859
1   754629  rs10454459  A   G   .   PASS    AF=0.03755  ES:SE:LP:AF:ID  0.000181584:0.000937634:0.0705811:0.03755:rs10454459
1   754964  rs3131966   C   T   .   PASS    AF=0.838657 ES:SE:LP:AF:ID  0.000502929:0.000483199:0.522879:0.838657:rs3131966
1   755775  rs3131965   A   G   .   PASS    AF=0.83977  ES:SE:LP:AF:ID  0.000504844:0.000489734:0.522879:0.83977:rs3131965
1   755890  rs3115858   A   T   .   PASS    AF=0.8694   ES:SE:LP:AF:ID  0.000474208:0.000516851:0.443698:0.8694:rs3115858
1   756604  rs3131962   A   G   .   PASS    AF=0.868947 ES:SE:LP:AF:ID  0.000450524:0.000515551:0.420216:0.868947:rs3131962
1   757640  rs3115853   G   A   .   PASS    AF=0.867898 ES:SE:LP:AF:ID  0.000444019:0.000514562:0.408935:0.867898:rs3115853
1   757734  rs4951929   C   T   .   PASS    AF=0.86909  ES:SE:LP:AF:ID  0.000464723:0.000515972:0.431798:0.86909:rs4951929
1   757936  rs4951862   C   A   .   PASS    AF=0.869098 ES:SE:LP:AF:ID  0.000464823:0.000516012:0.431798:0.869098:rs4951862
1   758144  rs3131956   A   G   .   PASS    AF=0.869106 ES:SE:LP:AF:ID  0.000463379:0.000516024:0.431798:0.869106:rs3131956
1   758626  rs3131954   C   T   .   PASS    AF=0.869584 ES:SE:LP:AF:ID  0.000496209:0.000517441:0.468521:0.869584:rs3131954
1   759036  rs114525117 G   A   .   PASS    AF=0.037599 ES:SE:LP:AF:ID  0.000303661:0.000932144:0.130768:0.037599:rs114525117