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-5495/UKB-b-5495_data.vcf.gz \
--ref-ld-chr ../reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-5495/ldsc.txt \
--w-ld-chr ../reference/eur_w_ld_chr/ 

Beginning analysis at Thu Oct 17 14:45:22 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-5495/UKB-b-5495_data.vcf.gz ...
Read summary statistics for 8903755 SNPs.
Dropped 8307 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, 1286802 SNPs remain.
After merging with regression SNP LD, 1286802 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0434 (0.0019)
Lambda GC: 1.3351
Mean Chi^2: 1.4133
Intercept: 1.0204 (0.0082)
Ratio: 0.0494 (0.0198)
Analysis finished at Thu Oct 17 14:46:48 2019
Total time elapsed: 1.0m:25.78s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9473,
    "inflation_factor": 1.2544,
    "mean_EFFECT": -1.7711e-06,
    "n": "-Inf",
    "n_snps": 9851866,
    "n_clumped_hits": 22,
    "n_p_sig": 1181,
    "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": 89888,
    "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": 1286802,
    "ldsc_nsnp_merge_regression_ld": 1286802,
    "ldsc_observed_scale_h2_beta": 0.0434,
    "ldsc_observed_scale_h2_se": 0.0019,
    "ldsc_intercept_beta": 1.0204,
    "ldsc_intercept_se": 0.0082,
    "ldsc_lambda_gc": 1.3351,
    "ldsc_mean_chisq": 1.4133,
    "ldsc_ratio": 0.0494
}

Flags

name value
af_correlation FALSE
inflation_factor TRUE
n TRUE
is_snpid_non_unique FALSE
mean_EFFECT_nonfinite FALSE
mean_EFFECT_05 FALSE
mean_EFFECT_01 FALSE
mean_chisq TRUE
n_p_sig TRUE
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 1.0000000 3 58 0 8895487 0 NA NA NA NA NA NA NA NA NA NA
character REF 0 1.0000000 1 1 0 4 0 NA NA NA NA NA NA NA NA NA NA
character ALT 0 1.0000000 1 1 0 4 0 NA NA NA NA NA NA NA NA NA NA
logical N 8903755 0.0000000 NA NA NA NA NA NaN : NA NA NA NA NA NA NA NA
numeric CHROM 0 1.0000000 NA NA NA NA NA NA NA 8.646183e+00 5.759501e+00 1.0000000 4.000000e+00 8.000000e+00 1.300000e+01 2.200000e+01 ▇▅▃▂▂
numeric POS 0 1.0000000 NA NA NA NA NA NA NA 7.878667e+07 5.634193e+07 828.0000000 3.242359e+07 6.934605e+07 1.145609e+08 2.492385e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA NA NA -1.800000e-06 2.731900e-03 -0.0283209 -1.170300e-03 -3.700000e-06 1.166900e-03 3.267450e-02 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA NA NA 2.104000e-03 1.510200e-03 0.0007837 9.312000e-04 1.411400e-03 2.878200e-03 1.816370e-02 ▇▁▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA NA NA 4.632517e-01 2.987491e-01 0.0000000 2.000000e-01 4.500005e-01 7.199992e-01 1.000000e+00 ▇▆▆▆▆
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA NA NA 4.632523e-01 2.987248e-01 0.0000000 1.953211e-01 4.507025e-01 7.215489e-01 1.000000e+00 ▇▆▆▆▆
numeric AF 0 1.0000000 NA NA NA NA NA NA NA 2.225012e-01 2.588015e-01 0.0040400 2.166300e-02 1.047530e-01 3.512500e-01 9.959590e-01 ▇▂▁▁▁
numeric AF_reference 89888 0.9899045 NA NA NA NA NA NA NA 2.226051e-01 2.507277e-01 0.0000000 1.896960e-02 1.220050e-01 3.492410e-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 0.0019771 0.0014418 0.1700000 0.1702886 0.623754 0.7821490 NA
1 54676 rs2462492 C T 0.0031008 0.0014284 0.0299999 0.0299432 0.400423 NA NA
1 86028 rs114608975 T C -0.0025492 0.0022830 0.2599998 0.2641640 0.103567 0.0277556 NA
1 91536 rs6702460 G T 0.0015367 0.0014064 0.2700001 0.2745527 0.456847 0.4207270 NA
1 234313 rs8179466 C T -0.0030090 0.0027726 0.2800000 0.2778024 0.074513 NA NA
1 534192 rs6680723 C T 0.0017455 0.0016067 0.2800000 0.2772873 0.240946 NA NA
1 546697 rs12025928 A G 0.0006319 0.0020041 0.7499995 0.7525198 0.913464 NA NA
1 693731 rs12238997 A G -0.0016587 0.0013462 0.2200002 0.2178987 0.116324 0.1417730 NA
1 705882 rs72631875 G A 0.0020185 0.0019730 0.3100002 0.3062765 0.067282 0.0315495 NA
1 706368 rs55727773 A G 0.0011412 0.0009973 0.2500000 0.2525263 0.515607 0.2751600 NA
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51219006 rs28729663 G A -0.0000811 0.0012038 0.9500000 0.9462601 0.137915 0.2052720 NA
22 51219387 rs9616832 T C 0.0020478 0.0015627 0.1900002 0.1900557 0.073703 0.0654952 NA
22 51219704 rs147475742 G A 0.0008587 0.0020944 0.6800001 0.6818148 0.041919 0.0473243 NA
22 51221190 rs369304721 G A 0.0033490 0.0020909 0.1100001 0.1092290 0.049696 NA NA
22 51221731 rs115055839 T C 0.0021157 0.0015637 0.1800002 0.1760529 0.073194 0.0625000 NA
22 51222100 rs114553188 G T -0.0029356 0.0018405 0.1100001 0.1107095 0.054459 0.0880591 NA
22 51223637 rs375798137 G A -0.0028640 0.0018494 0.1199999 0.1214787 0.054088 0.0788738 NA
22 51229805 rs9616985 T C 0.0021620 0.0015694 0.1700000 0.1683212 0.073030 0.0730831 NA
22 51232488 rs376461333 A G -0.0034434 0.0036948 0.3500000 0.3513622 0.020053 NA NA
22 51237063 rs3896457 T C 0.0001798 0.0009596 0.8499999 0.8513490 0.297994 0.2050720 NA

bcf preview

1   49298   rs10399793  T   C   .   PASS    AF=0.623754 ES:SE:LP:AF:ID  0.00197708:0.00144178:0.769551:0.623754:rs10399793
1   54676   rs2462492   C   T   .   PASS    AF=0.400423 ES:SE:LP:AF:ID  0.00310083:0.0014284:1.52288:0.400423:rs2462492
1   86028   rs114608975 T   C   .   PASS    AF=0.103567 ES:SE:LP:AF:ID  -0.00254925:0.00228304:0.585027:0.103567:rs114608975
1   91536   rs6702460   G   T   .   PASS    AF=0.456847 ES:SE:LP:AF:ID  0.00153673:0.00140644:0.568636:0.456847:rs6702460
1   234313  rs8179466   C   T   .   PASS    AF=0.074513 ES:SE:LP:AF:ID  -0.00300905:0.00277263:0.552842:0.074513:rs8179466
1   534192  rs6680723   C   T   .   PASS    AF=0.240946 ES:SE:LP:AF:ID  0.00174554:0.00160667:0.552842:0.240946:rs6680723
1   546697  rs12025928  A   G   .   PASS    AF=0.913464 ES:SE:LP:AF:ID  0.00063193:0.0020041:0.124939:0.913464:rs12025928
1   693731  rs12238997  A   G   .   PASS    AF=0.116324 ES:SE:LP:AF:ID  -0.0016587:0.0013462:0.657577:0.116324:rs12238997
1   705882  rs72631875  G   A   .   PASS    AF=0.067282 ES:SE:LP:AF:ID  0.00201851:0.001973:0.508638:0.067282:rs72631875
1   706368  rs12029736  A   G   .   PASS    AF=0.515607 ES:SE:LP:AF:ID  0.00114115:0.000997304:0.60206:0.515607:rs12029736
1   714596  rs149887893 T   C   .   PASS    AF=0.033001 ES:SE:LP:AF:ID  0.000938073:0.00251425:0.148742:0.033001:rs149887893
1   715265  rs12184267  C   T   .   PASS    AF=0.036615 ES:SE:LP:AF:ID  0.000989171:0.00228387:0.180456:0.036615:rs12184267
1   715367  rs12184277  A   G   .   PASS    AF=0.036732 ES:SE:LP:AF:ID  0.00108713:0.0022752:0.200659:0.036732:rs12184277
1   717485  rs12184279  C   A   .   PASS    AF=0.036432 ES:SE:LP:AF:ID  0.000556368:0.00229158:0.091515:0.036432:rs12184279
1   717587  rs144155419 G   A   .   PASS    AF=0.016392 ES:SE:LP:AF:ID  0.000649312:0.00353012:0.0705811:0.016392:rs144155419
1   720381  rs116801199 G   T   .   PASS    AF=0.036971 ES:SE:LP:AF:ID  0.00101498:0.00226621:0.187087:0.036971:rs116801199
1   721290  rs12565286  G   C   .   PASS    AF=0.037068 ES:SE:LP:AF:ID  0.000879959:0.00225843:0.154902:0.037068:rs12565286
1   722670  rs116030099 T   C   .   PASS    AF=0.101233 ES:SE:LP:AF:ID  -0.00147622:0.00164493:0.431798:0.101233:rs116030099
1   723891  rs2977670   G   C   .   PASS    AF=0.959111 ES:SE:LP:AF:ID  0.000164017:0.00217844:0.0268721:0.959111:rs2977670
1   724849  rs12126395  C   A   .   PASS    AF=0.031453 ES:SE:LP:AF:ID  2.99983e-05:0.00395338:0.00436481:0.031453:rs12126395
1   725060  rs865924913 A   T   .   PASS    AF=0.05326  ES:SE:LP:AF:ID  -0.00308587:0.00314432:0.481486:0.05326:rs865924913
1   726794  rs28454925  C   G   .   PASS    AF=0.036584 ES:SE:LP:AF:ID  0.000805049:0.00227311:0.142668:0.036584:rs28454925
1   729632  rs116720794 C   T   .   PASS    AF=0.0369   ES:SE:LP:AF:ID  0.0012238:0.0022524:0.229148:0.0369:rs116720794
1   729679  rs4951859   C   G   .   PASS    AF=0.84323  ES:SE:LP:AF:ID  0.0013199:0.00116677:0.585027:0.84323:rs4951859
1   730087  rs148120343 T   C   .   PASS    AF=0.055925 ES:SE:LP:AF:ID  -0.00528581:0.00188886:2.29243:0.055925:rs148120343
1   731718  rs58276399  T   C   .   PASS    AF=0.122303 ES:SE:LP:AF:ID  -0.0017052:0.00127701:0.744727:0.122303:rs58276399
1   732989  rs369030935 C   T   .   PASS    AF=0.025694 ES:SE:LP:AF:ID  0.00370034:0.00314244:0.619789:0.025694:rs369030935
1   734349  rs141242758 T   C   .   PASS    AF=0.121548 ES:SE:LP:AF:ID  -0.00156523:0.00127754:0.657577:0.121548:rs141242758
1   736289  rs79010578  T   A   .   PASS    AF=0.132339 ES:SE:LP:AF:ID  -0.000985647:0.00125917:0.366532:0.132339:rs79010578
1   736689  rs181876450 T   C   .   PASS    AF=0.011141 ES:SE:LP:AF:ID  0.00184297:0.00457693:0.161151:0.011141:rs181876450
1   740284  rs61770167  C   T   .   PASS    AF=0.005709 ES:SE:LP:AF:ID  0.00294595:0.00590533:0.207608:0.005709:rs61770167
1   752478  rs146277091 G   A   .   PASS    AF=0.036813 ES:SE:LP:AF:ID  0.00135707:0.00222972:0.267606:0.036813:rs146277091
1   752566  rs3094315   G   A   .   PASS    AF=0.838968 ES:SE:LP:AF:ID  0.00141721:0.00112995:0.677781:0.838968:rs3094315
1   752721  rs3131972   A   G   .   PASS    AF=0.838599 ES:SE:LP:AF:ID  0.00134558:0.00112875:0.638272:0.838599:rs3131972
1   753405  rs3115860   C   A   .   PASS    AF=0.869791 ES:SE:LP:AF:ID  0.00211228:0.00121119:1.09151:0.869791:rs3115860
1   753541  rs2073813   G   A   .   PASS    AF=0.129856 ES:SE:LP:AF:ID  -0.00188164:0.00121367:0.920819:0.129856:rs2073813
1   754063  rs12184312  G   T   .   PASS    AF=0.037324 ES:SE:LP:AF:ID  0.00139857:0.00219194:0.283997:0.037324:rs12184312
1   754105  rs12184325  C   T   .   PASS    AF=0.037566 ES:SE:LP:AF:ID  0.0014512:0.00217813:0.29243:0.037566:rs12184325
1   754182  rs3131969   A   G   .   PASS    AF=0.869137 ES:SE:LP:AF:ID  0.00208634:0.00120885:1.07572:0.869137:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.869234 ES:SE:LP:AF:ID  0.00210136:0.00120933:1.08619:0.869234:rs3131968
1   754211  rs12184313  G   A   .   PASS    AF=0.037524 ES:SE:LP:AF:ID  0.00120056:0.00218755:0.236572:0.037524:rs12184313
1   754334  rs3131967   T   C   .   PASS    AF=0.869139 ES:SE:LP:AF:ID  0.00210088:0.00120882:1.08619:0.869139:rs3131967
1   754433  rs150578204 G   A   .   PASS    AF=0.005121 ES:SE:LP:AF:ID  -0.00800805:0.00620621:0.69897:0.005121:rs150578204
1   754458  rs142682604 G   T   .   PASS    AF=0.005087 ES:SE:LP:AF:ID  -0.00812955:0.00622246:0.721246:0.005087:rs142682604
1   754503  rs3115859   G   A   .   PASS    AF=0.838051 ES:SE:LP:AF:ID  0.00143297:0.00112561:0.69897:0.838051:rs3115859
1   754629  rs10454459  A   G   .   PASS    AF=0.037537 ES:SE:LP:AF:ID  0.00108772:0.00219063:0.207608:0.037537:rs10454459
1   754964  rs3131966   C   T   .   PASS    AF=0.838681 ES:SE:LP:AF:ID  0.00143429:0.00112877:0.69897:0.838681:rs3131966
1   755240  rs181660517 T   G   .   PASS    AF=0.013777 ES:SE:LP:AF:ID  0.00213133:0.00393917:0.229148:0.013777:rs181660517
1   755435  rs184270342 T   G   .   PASS    AF=0.005545 ES:SE:LP:AF:ID  -0.00224954:0.00607992:0.148742:0.005545:rs184270342
1   755775  rs3131965   A   G   .   PASS    AF=0.839791 ES:SE:LP:AF:ID  0.00149751:0.00114402:0.721246:0.839791:rs3131965