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-6541/UKB-b-6541_data.vcf.gz \
--ref-ld-chr ../reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-6541/ldsc.txt \
--w-ld-chr ../reference/eur_w_ld_chr/ 

Beginning analysis at Thu Oct 17 14:40:18 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-6541/UKB-b-6541_data.vcf.gz ...
Read summary statistics for 9081141 SNPs.
Dropped 9093 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, 1287373 SNPs remain.
After merging with regression SNP LD, 1287373 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0187 (0.0016)
Lambda GC: 1.2597
Mean Chi^2: 1.2764
Intercept: 1.1071 (0.0072)
Ratio: 0.3876 (0.0259)
Analysis finished at Thu Oct 17 14:42:01 2019
Total time elapsed: 1.0m:42.87s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9479,
    "inflation_factor": 1.1999,
    "mean_EFFECT": 0,
    "n": "-Inf",
    "n_snps": 9851866,
    "n_clumped_hits": 6,
    "n_p_sig": 221,
    "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": 97270,
    "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": 1287373,
    "ldsc_nsnp_merge_regression_ld": 1287373,
    "ldsc_observed_scale_h2_beta": 0.0187,
    "ldsc_observed_scale_h2_se": 0.0016,
    "ldsc_intercept_beta": 1.1071,
    "ldsc_intercept_se": 0.0072,
    "ldsc_lambda_gc": 1.2597,
    "ldsc_mean_chisq": 1.2764,
    "ldsc_ratio": 0.3875
}

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 1.0000000 3 58 0 9072091 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 9081141 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 8.641388e+00 5.757525e+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 7.879352e+07 5.633112e+07 828.0000000 3.244811e+07 6.936241e+07 1.145304e+08 2.492385e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA NA NA 1.440000e-05 3.163900e-03 -0.0358008 -1.247900e-03 5.800000e-06 1.264100e-03 3.598000e-02 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA NA NA 2.381100e-03 1.775600e-03 0.0008488 1.014000e-03 1.564800e-03 3.267200e-03 1.966820e-02 ▇▂▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA NA NA 4.691989e-01 2.964961e-01 0.0000000 2.000000e-01 4.600002e-01 7.300002e-01 1.000000e+00 ▇▆▆▆▆
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA NA NA 4.692001e-01 2.964709e-01 0.0000000 2.046068e-01 4.578508e-01 7.259104e-01 9.999998e-01 ▇▆▆▆▆
numeric AF 0 1.0000000 NA NA NA NA NA NA NA 2.185412e-01 2.583652e-01 0.0032230 1.967900e-02 9.915600e-02 3.444140e-01 9.967770e-01 ▇▂▁▁▁
numeric AF_reference 97270 0.9892888 NA NA NA NA NA NA NA 2.189698e-01 2.502402e-01 0.0000000 1.697280e-02 1.168130e-01 3.430510e-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 0.0003233 0.0015615 0.8400000 0.8359940 0.623782 0.7821490 NA
1 54676 rs2462492 C T 0.0007917 0.0015471 0.6100002 0.6088463 0.400391 NA NA
1 86028 rs114608975 T C 0.0021573 0.0024733 0.3800004 0.3830964 0.103561 0.0277556 NA
1 91536 rs6702460 G T 0.0002877 0.0015232 0.8499999 0.8501751 0.456851 0.4207270 NA
1 234313 rs8179466 C T -0.0000398 0.0030034 0.9900000 0.9894370 0.074513 NA NA
1 534192 rs6680723 C T -0.0014477 0.0017398 0.4100001 0.4053555 0.240954 NA NA
1 546697 rs12025928 A G 0.0010445 0.0021705 0.6300007 0.6303646 0.913461 NA NA
1 693731 rs12238997 A G 0.0003460 0.0014581 0.8100000 0.8124330 0.116332 0.1417730 NA
1 705882 rs72631875 G A -0.0039764 0.0021366 0.0629999 0.0627339 0.067301 0.0315495 NA
1 706368 rs55727773 A G -0.0013482 0.0010802 0.2099999 0.2119860 0.515673 0.2751600 NA
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51219006 rs28729663 G A 0.0025344 0.0013036 0.0519996 0.0518750 0.137974 0.2052720 NA
22 51219387 rs9616832 T C 0.0039520 0.0016920 0.0200000 0.0195056 0.073758 0.0654952 NA
22 51219704 rs147475742 G A 0.0047882 0.0022672 0.0350002 0.0346947 0.041966 0.0473243 NA
22 51221190 rs369304721 G A 0.0044053 0.0022635 0.0519996 0.0516246 0.049742 NA NA
22 51221731 rs115055839 T C 0.0039963 0.0016930 0.0179999 0.0182538 0.073249 0.0625000 NA
22 51222100 rs114553188 G T 0.0018353 0.0019933 0.3599996 0.3571945 0.054471 0.0880591 NA
22 51223637 rs375798137 G A 0.0017720 0.0020030 0.3800004 0.3763292 0.054100 0.0788738 NA
22 51229805 rs9616985 T C 0.0039037 0.0016992 0.0219999 0.0215944 0.073085 0.0730831 NA
22 51232488 rs376461333 A G 0.0021587 0.0040023 0.5900000 0.5896370 0.020051 NA NA
22 51237063 rs3896457 T C 0.0005057 0.0010394 0.6300007 0.6265706 0.297961 0.2050720 NA

bcf preview

1   49298   rs10399793  T   C   .   PASS    AF=0.623782 ES:SE:LP:AF:ID  0.000323258:0.00156148:0.0757207:0.623782:rs10399793
1   54676   rs2462492   C   T   .   PASS    AF=0.400391 ES:SE:LP:AF:ID  0.000791704:0.00154714:0.21467:0.400391:rs2462492
1   86028   rs114608975 T   C   .   PASS    AF=0.103561 ES:SE:LP:AF:ID  0.00215726:0.00247334:0.420216:0.103561:rs114608975
1   91536   rs6702460   G   T   .   PASS    AF=0.456851 ES:SE:LP:AF:ID  0.000287723:0.00152319:0.0705811:0.456851:rs6702460
1   234313  rs8179466   C   T   .   PASS    AF=0.074513 ES:SE:LP:AF:ID  -3.97622e-05:0.00300337:0.00436481:0.074513:rs8179466
1   534192  rs6680723   C   T   .   PASS    AF=0.240954 ES:SE:LP:AF:ID  -0.00144772:0.00173985:0.387216:0.240954:rs6680723
1   546697  rs12025928  A   G   .   PASS    AF=0.913461 ES:SE:LP:AF:ID  0.00104446:0.00217047:0.200659:0.913461:rs12025928
1   693731  rs12238997  A   G   .   PASS    AF=0.116332 ES:SE:LP:AF:ID  0.000345995:0.00145812:0.091515:0.116332:rs12238997
1   705882  rs72631875  G   A   .   PASS    AF=0.067301 ES:SE:LP:AF:ID  -0.00397635:0.00213659:1.20066:0.067301:rs72631875
1   706368  rs12029736  A   G   .   PASS    AF=0.515673 ES:SE:LP:AF:ID  -0.00134816:0.00108015:0.677781:0.515673:rs12029736
1   714596  rs149887893 T   C   .   PASS    AF=0.033019 ES:SE:LP:AF:ID  -0.00590977:0.00272251:1.52288:0.033019:rs149887893
1   715265  rs12184267  C   T   .   PASS    AF=0.036636 ES:SE:LP:AF:ID  -0.00543009:0.00247299:1.55284:0.036636:rs12184267
1   715367  rs12184277  A   G   .   PASS    AF=0.036752 ES:SE:LP:AF:ID  -0.00575012:0.00246364:1.69897:0.036752:rs12184277
1   717485  rs12184279  C   A   .   PASS    AF=0.036451 ES:SE:LP:AF:ID  -0.00558089:0.00248141:1.60206:0.036451:rs12184279
1   717587  rs144155419 G   A   .   PASS    AF=0.016412 ES:SE:LP:AF:ID  0.000827378:0.00382073:0.0809219:0.016412:rs144155419
1   720381  rs116801199 G   T   .   PASS    AF=0.036991 ES:SE:LP:AF:ID  -0.00555949:0.00245389:1.63827:0.036991:rs116801199
1   721290  rs12565286  G   C   .   PASS    AF=0.037088 ES:SE:LP:AF:ID  -0.00552586:0.00244546:1.61979:0.037088:rs12565286
1   722670  rs116030099 T   C   .   PASS    AF=0.101224 ES:SE:LP:AF:ID  0.00138733:0.00178206:0.356547:0.101224:rs116030099
1   723891  rs2977670   G   C   .   PASS    AF=0.959082 ES:SE:LP:AF:ID  0.00670476:0.0023587:2.34679:0.959082:rs2977670
1   724849  rs12126395  C   A   .   PASS    AF=0.031449 ES:SE:LP:AF:ID  0.00100418:0.00428281:0.091515:0.031449:rs12126395
1   725060  rs865924913 A   T   .   PASS    AF=0.053257 ES:SE:LP:AF:ID  -0.00561716:0.00340651:1.00436:0.053257:rs865924913
1   726794  rs28454925  C   G   .   PASS    AF=0.036604 ES:SE:LP:AF:ID  -0.0055004:0.00246132:1.60206:0.036604:rs28454925
1   729632  rs116720794 C   T   .   PASS    AF=0.03692  ES:SE:LP:AF:ID  -0.00540273:0.00243895:1.56864:0.03692:rs116720794
1   729679  rs4951859   C   G   .   PASS    AF=0.843186 ES:SE:LP:AF:ID  0.00131067:0.00126366:0.522879:0.843186:rs4951859
1   730087  rs148120343 T   C   .   PASS    AF=0.055919 ES:SE:LP:AF:ID  0.00043531:0.00204601:0.0809219:0.055919:rs148120343
1   731718  rs58276399  T   C   .   PASS    AF=0.122319 ES:SE:LP:AF:ID  0.000500158:0.00138319:0.142668:0.122319:rs58276399
1   732989  rs369030935 C   T   .   PASS    AF=0.025709 ES:SE:LP:AF:ID  0.00289572:0.0034026:0.408935:0.025709:rs369030935
1   734349  rs141242758 T   C   .   PASS    AF=0.121561 ES:SE:LP:AF:ID  0.000492886:0.00138377:0.142668:0.121561:rs141242758
1   736289  rs79010578  T   A   .   PASS    AF=0.132351 ES:SE:LP:AF:ID  -0.00151052:0.00136382:0.568636:0.132351:rs79010578
1   736689  rs181876450 T   C   .   PASS    AF=0.01113  ES:SE:LP:AF:ID  -0.00341611:0.00495984:0.309804:0.01113:rs181876450
1   740284  rs61770167  C   T   .   PASS    AF=0.005702 ES:SE:LP:AF:ID  0.00156266:0.00639974:0.091515:0.005702:rs61770167
1   752478  rs146277091 G   A   .   PASS    AF=0.036836 ES:SE:LP:AF:ID  -0.00520324:0.00241426:1.50864:0.036836:rs146277091
1   752566  rs3094315   G   A   .   PASS    AF=0.838922 ES:SE:LP:AF:ID  0.00105032:0.00122374:0.408935:0.838922:rs3094315
1   752721  rs3131972   A   G   .   PASS    AF=0.83855  ES:SE:LP:AF:ID  0.00110774:0.00122242:0.443698:0.83855:rs3131972
1   753405  rs3115860   C   A   .   PASS    AF=0.869765 ES:SE:LP:AF:ID  -0.000165615:0.00131172:0.0457575:0.869765:rs3115860
1   753541  rs2073813   G   A   .   PASS    AF=0.129889 ES:SE:LP:AF:ID  0.000336675:0.00131438:0.09691:0.129889:rs2073813
1   754063  rs12184312  G   T   .   PASS    AF=0.037347 ES:SE:LP:AF:ID  -0.00562568:0.00237333:1.74473:0.037347:rs12184312
1   754105  rs12184325  C   T   .   PASS    AF=0.037591 ES:SE:LP:AF:ID  -0.00528479:0.00235832:1.60206:0.037591:rs12184325
1   754182  rs3131969   A   G   .   PASS    AF=0.869107 ES:SE:LP:AF:ID  -9.59161e-05:0.00130915:0.0268721:0.869107:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.869205 ES:SE:LP:AF:ID  -0.000102336:0.00130967:0.0268721:0.869205:rs3131968
1   754211  rs12184313  G   A   .   PASS    AF=0.037549 ES:SE:LP:AF:ID  -0.0054502:0.00236853:1.67778:0.037549:rs12184313
1   754334  rs3131967   T   C   .   PASS    AF=0.86911  ES:SE:LP:AF:ID  -9.68789e-05:0.00130913:0.0268721:0.86911:rs3131967
1   754433  rs150578204 G   A   .   PASS    AF=0.005123 ES:SE:LP:AF:ID  0.00799442:0.00672139:0.638272:0.005123:rs150578204
1   754458  rs142682604 G   T   .   PASS    AF=0.005089 ES:SE:LP:AF:ID  0.00804333:0.00673898:0.638272:0.005089:rs142682604
1   754503  rs3115859   G   A   .   PASS    AF=0.838003 ES:SE:LP:AF:ID  0.00122442:0.00121903:0.49485:0.838003:rs3115859
1   754629  rs10454459  A   G   .   PASS    AF=0.037562 ES:SE:LP:AF:ID  -0.00537983:0.00237188:1.63827:0.037562:rs10454459
1   754964  rs3131966   C   T   .   PASS    AF=0.838634 ES:SE:LP:AF:ID  0.00123147:0.00122246:0.508638:0.838634:rs3131966
1   755240  rs181660517 T   G   .   PASS    AF=0.013774 ES:SE:LP:AF:ID  -0.00335713:0.00426746:0.366532:0.013774:rs181660517
1   755435  rs184270342 T   G   .   PASS    AF=0.005542 ES:SE:LP:AF:ID  0.0009125:0.00658672:0.05061:0.005542:rs184270342
1   755775  rs3131965   A   G   .   PASS    AF=0.839751 ES:SE:LP:AF:ID  0.00113405:0.00123899:0.443698:0.839751:rs3131965