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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    "FORMAT.1": "<ID=SE,Number=A,Type=Float,Description=\"Standard error of effect size estimate\">",
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    "FORMAT.5": "<ID=EZ,Number=A,Type=Float,Description=\"Z-score provided if it was used to derive the EFFECT and SE fields\">",
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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-11312/UKB-b-11312_data.vcf.gz \
--ref-ld-chr ../reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-11312/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-11312/UKB-b-11312_data.vcf.gz ...
Read summary statistics for 9851866 SNPs.
Dropped 14738 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, 1289166 SNPs remain.
After merging with regression SNP LD, 1289166 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0121 (0.0015)
Lambda GC: 1.2579
Mean Chi^2: 1.2699
Intercept: 1.1701 (0.0073)
Ratio: 0.6304 (0.0271)
Analysis finished at Thu Oct 17 14:42:07 2019
Total time elapsed: 1.0m:49.23s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9499,
    "inflation_factor": 1.2544,
    "mean_EFFECT": 0.0004,
    "n": "-Inf",
    "n_snps": 9851866,
    "n_clumped_hits": 5,
    "n_p_sig": 20,
    "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": 184849,
    "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": 1289166,
    "ldsc_nsnp_merge_regression_ld": 1289166,
    "ldsc_observed_scale_h2_beta": 0.0121,
    "ldsc_observed_scale_h2_se": 0.0015,
    "ldsc_intercept_beta": 1.1701,
    "ldsc_intercept_se": 0.0073,
    "ldsc_lambda_gc": 1.2579,
    "ldsc_mean_chisq": 1.2699,
    "ldsc_ratio": 0.6302
}

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 FALSE
n_p_sig FALSE
miss_EFFECT FALSE
miss_SE FALSE
miss_PVAL FALSE
ldsc_ratio TRUE
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 9837196 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 9851866 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 8.622825e+00 5.748290e+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 7.886027e+07 5.628334e+07 828.0000000 3.259061e+07 6.948835e+07 1.145912e+08 2.492385e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA NA NA 3.943000e-04 1.101490e-02 -0.2446850 -3.215600e-03 8.170000e-05 3.500700e-03 1.806700e-01 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA NA NA 7.342800e-03 6.939100e-03 0.0020565 2.517500e-03 4.220900e-03 9.737100e-03 1.081400e-01 ▇▁▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA NA NA 4.660183e-01 2.969969e-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 4.660222e-01 2.969735e-01 0.0000000 2.003214e-01 4.533583e-01 7.229626e-01 9.999999e-01 ▇▆▆▆▆
numeric AF 0 1.0000000 NA NA NA NA NA NA NA 2.035097e-01 2.568524e-01 0.0008670 1.317700e-02 7.792300e-02 3.164240e-01 9.990500e-01 ▇▂▁▁▁
numeric AF_reference 184849 0.9812372 NA NA NA NA NA NA NA 2.068392e-01 2.482924e-01 0.0000000 1.198080e-02 9.984030e-02 3.202880e-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 -0.0028451 0.0037871 0.4500005 0.4524921 0.623965 0.7821490 NA
1 54676 rs2462492 C T -0.0035802 0.0037504 0.3400001 0.3397746 0.400253 NA NA
1 86028 rs114608975 T C 0.0047799 0.0060093 0.4299995 0.4263705 0.103396 0.0277556 NA
1 91536 rs6702460 G T 0.0010504 0.0036922 0.7800007 0.7760310 0.456774 0.4207270 NA
1 234313 rs8179466 C T -0.0032616 0.0072748 0.6499995 0.6539048 0.074661 NA NA
1 534192 rs6680723 C T -0.0001752 0.0042219 0.9699999 0.9669074 0.240786 NA NA
1 546697 rs12025928 A G 0.0085272 0.0052545 0.1000000 0.1046242 0.913314 NA NA
1 693731 rs12238997 A G 0.0031497 0.0035252 0.3700002 0.3716010 0.116854 0.1417730 NA
1 705882 rs72631875 G A 0.0012159 0.0051800 0.8100000 0.8144203 0.067315 0.0315495 NA
1 706368 rs55727773 A G -0.0010459 0.0026178 0.6899999 0.6895099 0.515551 0.2751600 NA
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51219704 rs147475742 G A 0.0025468 0.0055012 0.6400000 0.6433959 0.041870 0.0473243 NA
22 51219766 rs182321900 C T 0.0419693 0.0253024 0.0969996 0.0971746 0.001982 NA NA
22 51220146 rs868950473 C T 0.0433011 0.0250610 0.0840001 0.0840190 0.002031 NA NA
22 51221190 rs369304721 G A 0.0051138 0.0054929 0.3500000 0.3518604 0.049576 NA NA
22 51221731 rs115055839 T C 0.0025995 0.0041099 0.5300002 0.5270683 0.072969 0.0625000 NA
22 51222100 rs114553188 G T 0.0040250 0.0048205 0.4000000 0.4037273 0.054648 0.0880591 NA
22 51223637 rs375798137 G A 0.0037925 0.0048439 0.4299995 0.4336670 0.054274 0.0788738 NA
22 51229805 rs9616985 T C 0.0020782 0.0041248 0.6100002 0.6143796 0.072809 0.0730831 NA
22 51232488 rs376461333 A G 0.0110732 0.0097051 0.2500000 0.2538851 0.020068 NA NA
22 51237063 rs3896457 T C -0.0031396 0.0025181 0.2099999 0.2124704 0.297729 0.2050720 NA

bcf preview

1   49298   rs10399793  T   C   .   PASS    AF=0.623965 ES:SE:LP:AF:ID  -0.0028451:0.00378707:0.346787:0.623965:rs10399793
1   54676   rs2462492   C   T   .   PASS    AF=0.400253 ES:SE:LP:AF:ID  -0.00358022:0.00375045:0.468521:0.400253:rs2462492
1   86028   rs114608975 T   C   .   PASS    AF=0.103396 ES:SE:LP:AF:ID  0.00477992:0.00600932:0.366532:0.103396:rs114608975
1   91536   rs6702460   G   T   .   PASS    AF=0.456774 ES:SE:LP:AF:ID  0.00105041:0.00369219:0.107905:0.456774:rs6702460
1   234313  rs8179466   C   T   .   PASS    AF=0.074661 ES:SE:LP:AF:ID  -0.00326161:0.00727479:0.187087:0.074661:rs8179466
1   534192  rs6680723   C   T   .   PASS    AF=0.240786 ES:SE:LP:AF:ID  -0.000175157:0.00422194:0.0132283:0.240786:rs6680723
1   546697  rs12025928  A   G   .   PASS    AF=0.913314 ES:SE:LP:AF:ID  0.00852723:0.00525452:1:0.913314:rs12025928
1   693731  rs12238997  A   G   .   PASS    AF=0.116854 ES:SE:LP:AF:ID  0.00314969:0.0035252:0.431798:0.116854:rs12238997
1   705882  rs72631875  G   A   .   PASS    AF=0.067315 ES:SE:LP:AF:ID  0.0012159:0.00518005:0.091515:0.067315:rs72631875
1   706368  rs12029736  A   G   .   PASS    AF=0.515551 ES:SE:LP:AF:ID  -0.00104588:0.00261784:0.161151:0.515551:rs12029736
1   714596  rs149887893 T   C   .   PASS    AF=0.033064 ES:SE:LP:AF:ID  0.00612212:0.00659297:0.455932:0.033064:rs149887893
1   715265  rs12184267  C   T   .   PASS    AF=0.036686 ES:SE:LP:AF:ID  0.00525172:0.00598798:0.420216:0.036686:rs12184267
1   715367  rs12184277  A   G   .   PASS    AF=0.036808 ES:SE:LP:AF:ID  0.00507919:0.00596442:0.408935:0.036808:rs12184277
1   717485  rs12184279  C   A   .   PASS    AF=0.036496 ES:SE:LP:AF:ID  0.00463647:0.00600853:0.356547:0.036496:rs12184279
1   717587  rs144155419 G   A   .   PASS    AF=0.016498 ES:SE:LP:AF:ID  -0.00872706:0.00923021:0.468521:0.016498:rs144155419
1   720381  rs116801199 G   T   .   PASS    AF=0.037045 ES:SE:LP:AF:ID  0.00501263:0.00594131:0.39794:0.037045:rs116801199
1   721290  rs12565286  G   C   .   PASS    AF=0.037143 ES:SE:LP:AF:ID  0.00438462:0.00592083:0.337242:0.037143:rs12565286
1   722670  rs116030099 T   C   .   PASS    AF=0.101564 ES:SE:LP:AF:ID  -0.00740496:0.00431077:1.0655:0.101564:rs116030099
1   723891  rs2977670   G   C   .   PASS    AF=0.958946 ES:SE:LP:AF:ID  -0.00954959:0.00570587:1.02687:0.958946:rs2977670
1   724849  rs12126395  C   A   .   PASS    AF=0.031611 ES:SE:LP:AF:ID  -0.00501053:0.0103325:0.200659:0.031611:rs12126395
1   725060  rs865924913 A   T   .   PASS    AF=0.053093 ES:SE:LP:AF:ID  -0.0139453:0.00828268:1.03621:0.053093:rs865924913
1   726794  rs28454925  C   G   .   PASS    AF=0.036662 ES:SE:LP:AF:ID  0.00438639:0.00595842:0.337242:0.036662:rs28454925
1   729632  rs116720794 C   T   .   PASS    AF=0.036978 ES:SE:LP:AF:ID  0.00531066:0.00590498:0.431798:0.036978:rs116720794
1   729679  rs4951859   C   G   .   PASS    AF=0.842588 ES:SE:LP:AF:ID  -0.00483361:0.00305655:0.958607:0.842588:rs4951859
1   730087  rs148120343 T   C   .   PASS    AF=0.056119 ES:SE:LP:AF:ID  0.00131614:0.00494967:0.102373:0.056119:rs148120343
1   731718  rs58276399  T   C   .   PASS    AF=0.122837 ES:SE:LP:AF:ID  0.00178222:0.00334463:0.229148:0.122837:rs58276399
1   732989  rs369030935 C   T   .   PASS    AF=0.02572  ES:SE:LP:AF:ID  0.00066768:0.00824201:0.0268721:0.02572:rs369030935
1   734349  rs141242758 T   C   .   PASS    AF=0.122077 ES:SE:LP:AF:ID  0.00202255:0.00334595:0.259637:0.122077:rs141242758
1   736289  rs79010578  T   A   .   PASS    AF=0.132784 ES:SE:LP:AF:ID  0.00519464:0.00329939:0.920819:0.132784:rs79010578
1   736689  rs181876450 T   C   .   PASS    AF=0.011024 ES:SE:LP:AF:ID  0.0171302:0.0120892:0.79588:0.011024:rs181876450
1   740284  rs61770167  C   T   .   PASS    AF=0.005795 ES:SE:LP:AF:ID  -0.00888724:0.0153665:0.251812:0.005795:rs61770167
1   742813  rs112573343 C   T   .   PASS    AF=0.002315 ES:SE:LP:AF:ID  0.0470137:0.0257771:1.16749:0.002315:rs112573343
1   746189  rs139221807 A   G   .   PASS    AF=0.001038 ES:SE:LP:AF:ID  0.0819739:0.0425453:1.26761:0.001038:rs139221807
1   752478  rs146277091 G   A   .   PASS    AF=0.036894 ES:SE:LP:AF:ID  0.00506773:0.00584488:0.408935:0.036894:rs146277091
1   752566  rs3094315   G   A   .   PASS    AF=0.838313 ES:SE:LP:AF:ID  -0.00608989:0.00295978:1.39794:0.838313:rs3094315
1   752721  rs3131972   A   G   .   PASS    AF=0.837932 ES:SE:LP:AF:ID  -0.00619995:0.00295656:1.4437:0.837932:rs3131972
1   753405  rs3115860   C   A   .   PASS    AF=0.869174 ES:SE:LP:AF:ID  -0.00462445:0.00317111:0.853872:0.869174:rs3115860
1   753541  rs2073813   G   A   .   PASS    AF=0.130463 ES:SE:LP:AF:ID  0.00476267:0.00317774:0.886057:0.130463:rs2073813
1   754063  rs12184312  G   T   .   PASS    AF=0.037404 ES:SE:LP:AF:ID  0.00376809:0.0057454:0.29243:0.037404:rs12184312
1   754105  rs12184325  C   T   .   PASS    AF=0.037649 ES:SE:LP:AF:ID  0.0036095:0.00570896:0.275724:0.037649:rs12184325
1   754182  rs3131969   A   G   .   PASS    AF=0.868497 ES:SE:LP:AF:ID  -0.00480331:0.00316477:0.886057:0.868497:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.868594 ES:SE:LP:AF:ID  -0.00475569:0.003166:0.886057:0.868594:rs3131968
1   754211  rs12184313  G   A   .   PASS    AF=0.037611 ES:SE:LP:AF:ID  0.00379744:0.00573365:0.29243:0.037611:rs12184313
1   754334  rs3131967   T   C   .   PASS    AF=0.8685   ES:SE:LP:AF:ID  -0.00477922:0.00316469:0.886057:0.8685:rs3131967
1   754433  rs150578204 G   A   .   PASS    AF=0.005188 ES:SE:LP:AF:ID  0.0212168:0.0161744:0.721246:0.005188:rs150578204
1   754458  rs142682604 G   T   .   PASS    AF=0.005154 ES:SE:LP:AF:ID  0.0203581:0.0162166:0.677781:0.005154:rs142682604
1   754503  rs3115859   G   A   .   PASS    AF=0.837376 ES:SE:LP:AF:ID  -0.00586101:0.0029482:1.3279:0.837376:rs3115859
1   754629  rs10454459  A   G   .   PASS    AF=0.037624 ES:SE:LP:AF:ID  0.00373163:0.00574187:0.283997:0.037624:rs10454459
1   754964  rs3131966   C   T   .   PASS    AF=0.838009 ES:SE:LP:AF:ID  -0.00583254:0.00295649:1.3098:0.838009:rs3131966
1   755240  rs181660517 T   G   .   PASS    AF=0.013551 ES:SE:LP:AF:ID  -0.0227381:0.0104306:1.5376:0.013551:rs181660517