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/dev/ukb-d-import/processed/ukb-d-40001_C349/ukb-d-40001_C349.vcf.gz \
--ref-ld-chr /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-40001_C349/ldsc.txt \
--w-ld-chr /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/reference/eur_w_ld_chr/ 

Beginning analysis at Mon Nov 25 15:01:44 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-40001_C349/ukb-d-40001_C349.vcf.gz ...
Read summary statistics for 9452277 SNPs.
Dropped 6986 SNPs with duplicated rs numbers.
Reading reference panel LD Score from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/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 /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/reference/eur_w_ld_chr/[1-22] ...
Read regression weight LD Scores for 1290028 SNPs.
After merging with reference panel LD, 1272273 SNPs remain.
After merging with regression SNP LD, 1272273 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.1005 (0.0478)
Lambda GC: 1.0086
Mean Chi^2: 1.0151
Intercept: 0.997 (0.0061)
Ratio < 0 (usually indicates GC correction).
Analysis finished at Mon Nov 25 15:03:21 2019
Total time elapsed: 1.0m:36.55s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9385,
    "inflation_factor": 1.0107,
    "mean_EFFECT": -0,
    "n": 9092,
    "n_snps": 9452277,
    "n_clumped_hits": 0,
    "n_p_sig": 0,
    "n_mono": 0,
    "n_ns": 1047321,
    "n_mac": 0,
    "is_snpid_unique": false,
    "n_miss_EFFECT": 0,
    "n_miss_SE": 0,
    "n_miss_PVAL": 0,
    "n_miss_AF": 0,
    "n_miss_AF_reference": 189405,
    "n_est": 9134.2892,
    "ratio_se_n": 1.0023,
    "mean_diff": -0,
    "ratio_diff": 7.3656,
    "sd_y_est1": 0.3265,
    "sd_y_est2": 0.3273,
    "r2_sum1": 0,
    "r2_sum2": 0,
    "r2_sum3": 0,
    "r2_sum4": 0,
    "ldsc_nsnp_merge_refpanel_ld": 1272273,
    "ldsc_nsnp_merge_regression_ld": 1272273,
    "ldsc_observed_scale_h2_beta": 0.1005,
    "ldsc_observed_scale_h2_se": 0.0478,
    "ldsc_intercept_beta": 0.997,
    "ldsc_intercept_se": 0.0061,
    "ldsc_lambda_gc": 1.0086,
    "ldsc_mean_chisq": 1.0151,
    "ldsc_ratio": -0.1987
}

Flags

name value
af_correlation FALSE
inflation_factor FALSE
n TRUE
is_snpid_non_unique TRUE
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 numeric.mean numeric.sd numeric.p0 numeric.p25 numeric.p50 numeric.p75 numeric.p100 numeric.hist
character ID 0 1.000000 3 94 0 9445830 0 NA NA NA NA NA NA NA NA
character REF 0 1.000000 1 98 0 46199 0 NA NA NA NA NA NA NA NA
character ALT 0 1.000000 1 342 0 29348 0 NA NA NA NA NA NA NA NA
numeric CHROM 0 1.000000 NA NA NA NA NA 9.079237e+00 6.173714e+00 1.0000000 4.000000e+00 8.000000e+00 1.300000e+01 2.300000e+01 ▇▅▅▂▂
numeric POS 0 1.000000 NA NA NA NA NA 7.870132e+07 5.611299e+07 302.0000000 3.241302e+07 6.956882e+07 1.147166e+08 2.492297e+08 ▇▆▅▂▁
numeric EFFECT 0 1.000000 NA NA NA NA NA -1.190000e-05 1.038530e-02 -0.1046300 -5.197300e-03 -6.180000e-05 5.072800e-03 1.170120e-01 ▁▁▇▁▁
numeric SE 0 1.000000 NA NA NA NA NA 9.096500e-03 4.932300e-03 0.0037810 5.281100e-03 6.935200e-03 1.153370e-02 2.870130e-02 ▇▂▂▁▁
numeric PVAL 0 1.000000 NA NA NA NA NA 4.979498e-01 2.891438e-01 0.0000002 2.467982e-01 4.977222e-01 7.484555e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.000000 NA NA NA NA NA 4.979322e-01 2.891544e-01 0.0000002 2.467676e-01 4.977049e-01 7.484490e-01 1.000000e+00 ▇▇▇▇▇
numeric AF 0 1.000000 NA NA NA NA NA 2.677322e-01 2.626981e-01 0.0113638 4.910390e-02 1.681850e-01 4.251730e-01 9.886360e-01 ▇▂▂▁▁
numeric AF_reference 189405 0.979962 NA NA NA NA NA 2.670357e-01 2.534754e-01 0.0000000 5.630990e-02 1.827080e-01 4.199280e-01 1.000000e+00 ▇▃▂▂▁
numeric N 0 1.000000 NA NA NA NA NA 9.092000e+03 0.000000e+00 9092.0000000 9.092000e+03 9.092000e+03 9.092000e+03 9.092000e+03 ▁▁▇▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 692794 rs530212009 CA C -0.0024808 0.0083944 0.7675965 0.7675891 0.1133500 0.1894970 9092
1 693731 rs12238997 A G -0.0023859 0.0079332 0.7636107 0.7636043 0.1192700 0.1417730 9092
1 707522 rs371890604 G C -0.0011281 0.0087688 0.8976410 0.8976382 0.1026080 0.1293930 9092
1 717587 rs144155419 G A 0.0112283 0.0224403 0.6168307 0.6168194 0.0145590 0.0045926 9092
1 730087 rs148120343 T C -0.0029763 0.0108264 0.7833900 0.7833851 0.0597649 0.0127796 9092
1 731718 rs142557973 T C -0.0020264 0.0074711 0.7862235 0.7862174 0.1262940 0.1543530 9092
1 732032 rs61770163 A C -0.0019928 0.0079320 0.8016319 0.8016269 0.1263420 0.1555510 9092
1 734349 rs141242758 T C -0.0021563 0.0074717 0.7728923 0.7728861 0.1256230 0.1525560 9092
1 749963 rs529266287 T TAA 0.0033358 0.0073598 0.6503782 0.6503664 0.8647550 0.7641770 9092
1 751343 rs28544273 T A -0.0018887 0.0072758 0.7951931 0.7951873 0.1278750 0.2426120 9092
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
23 154923311 rs141127553 C T -0.0061657 0.0082284 0.4536835 0.4536640 0.0570394 0.0309934 9092
23 154923374 rs111332691 T A -0.0181107 0.0090456 0.0452981 0.0452687 0.0454795 0.0116556 9092
23 154925045 rs509981 C T -0.0031714 0.0044633 0.4773853 0.4773654 0.2406280 0.3634440 9092
23 154925895 rs538470 C T -0.0035130 0.0045678 0.4418674 0.4418462 0.2368780 0.3634440 9092
23 154927581 rs644138 G A -0.0043687 0.0041784 0.2957903 0.2957626 0.2979560 0.4635760 9092
23 154929412 rs557132 C T -0.0031185 0.0044637 0.4847915 0.4847721 0.2405170 0.3568210 9092
23 154929637 rs35185538 CT C -0.0057256 0.0046463 0.2178678 0.2178355 0.2266580 0.3011920 9092
23 154929952 rs4012982 CAA C -0.0027541 0.0046758 0.5558735 0.5558590 0.2355220 0.3165560 9092
23 154930230 rs781880 A G -0.0030110 0.0044676 0.5003582 0.5003406 0.2406200 0.3618540 9092
23 154930487 rs781879 T A -0.0003774 0.0154462 0.9805070 0.9805066 0.0188345 0.1263580 9092

bcf preview

1   692794  rs530212009 CA  C   .   PASS    AF=0.11335  ES:SE:LP:AF:SS:ID   -0.00248079:0.00839438:0.114867:0.11335:9092:1_692794_CA_C
1   693731  rs12238997  A   G   .   PASS    AF=0.11927  ES:SE:LP:AF:SS:ID   -0.00238591:0.00793317:0.117128:0.11927:9092:rs12238997
1   707522  rs371890604 G   C   .   PASS    AF=0.102608 ES:SE:LP:AF:SS:ID   -0.00112806:0.00876875:0.0468973:0.102608:9092:rs371890604
1   717587  rs144155419 G   A   .   PASS    AF=0.014559 ES:SE:LP:AF:SS:ID   0.0112283:0.0224403:0.209834:0.014559:9092:rs144155419
1   730087  rs148120343 T   C   .   PASS    AF=0.0597649    ES:SE:LP:AF:SS:ID   -0.00297629:0.0108264:0.106022:0.0597649:9092:rs148120343
1   731718  rs58276399  T   C   .   PASS    AF=0.126294 ES:SE:LP:AF:SS:ID   -0.00202636:0.00747112:0.104454:0.126294:9092:rs58276399
1   732032  rs61770163  A   C   .   PASS    AF=0.126342 ES:SE:LP:AF:SS:ID   -0.00199285:0.00793199:0.096025:0.126342:9092:rs61770163
1   734349  rs141242758 T   C   .   PASS    AF=0.125623 ES:SE:LP:AF:SS:ID   -0.00215634:0.00747168:0.111881:0.125623:9092:rs141242758
1   749963  rs529266287 T   TAA .   PASS    AF=0.864755 ES:SE:LP:AF:SS:ID   0.00333584:0.00735977:0.186834:0.864755:9092:rs529266287
1   751343  rs28544273  T   A   .   PASS    AF=0.127875 ES:SE:LP:AF:SS:ID   -0.00188867:0.00727585:0.0995274:0.127875:9092:rs28544273
1   751488  rs200141114 G   GA  .   PASS    AF=0.146966 ES:SE:LP:AF:SS:ID   -0.000918377:0.00721637:0.0463683:0.146966:9092:rs200141114
1   751756  rs28527770  T   C   .   PASS    AF=0.127954 ES:SE:LP:AF:SS:ID   -0.00176267:0.00726528:0.0924231:0.127954:9092:rs28527770
1   753405  rs3115860   C   A   .   PASS    AF=0.86603  ES:SE:LP:AF:SS:ID   0.00265736:0.00709855:0.149874:0.86603:9092:rs3115860
1   753425  rs3131970   T   C   .   PASS    AF=0.870519 ES:SE:LP:AF:SS:ID   0.00229286:0.00720401:0.124775:0.870519:9092:rs3131970
1   753541  rs2073813   G   A   .   PASS    AF=0.133468 ES:SE:LP:AF:SS:ID   -0.00205703:0.00711091:0.112172:0.133468:9092:rs2073813
1   754105  rs12184325  C   T   .   PASS    AF=0.0349758    ES:SE:LP:AF:SS:ID   0.00835572:0.0134059:0.273182:0.0349758:9092:rs12184325
1   754182  rs3131969   A   G   .   PASS    AF=0.865646 ES:SE:LP:AF:SS:ID   0.00253772:0.00709477:0.142315:0.865646:9092:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.865694 ES:SE:LP:AF:SS:ID   0.00246916:0.00709594:0.137945:0.865694:9092:rs3131968
1   754334  rs3131967   T   C   .   PASS    AF=0.865644 ES:SE:LP:AF:SS:ID   0.00254817:0.0070944:0.142989:0.865644:9092:rs3131967
1   755890  rs3115858   A   T   .   PASS    AF=0.865718 ES:SE:LP:AF:SS:ID   0.00343621:0.00708156:0.202371:0.865718:9092:rs3115858
1   756434  rs61768170  G   C   .   PASS    AF=0.131086 ES:SE:LP:AF:SS:ID   -0.00317815:0.00720096:0.181135:0.131086:9092:rs61768170
1   756604  rs3131962   A   G   .   PASS    AF=0.865211 ES:SE:LP:AF:SS:ID   0.0035547:0.00706192:0.211321:0.865211:9092:rs3131962
1   757640  rs3115853   G   A   .   PASS    AF=0.864463 ES:SE:LP:AF:SS:ID   0.00314748:0.00705466:0.18343:0.864463:9092:rs3115853
1   757734  rs4951929   C   T   .   PASS    AF=0.865378 ES:SE:LP:AF:SS:ID   0.00369537:0.00706783:0.221056:0.865378:9092:rs4951929
1   757936  rs4951862   C   A   .   PASS    AF=0.865386 ES:SE:LP:AF:SS:ID   0.00368278:0.00706842:0.220139:0.865386:9092:rs4951862
1   758144  rs3131956   A   G   .   PASS    AF=0.865388 ES:SE:LP:AF:SS:ID   0.00367653:0.00706851:0.219692:0.865388:9092:rs3131956
1   758626  rs3131954   C   T   .   PASS    AF=0.865778 ES:SE:LP:AF:SS:ID   0.0034134:0.00708622:0.200637:0.865778:9092:rs3131954
1   759293  rs10157329  T   A   .   PASS    AF=0.10461  ES:SE:LP:AF:SS:ID   -0.00408961:0.00813654:0.210954:0.10461:9092:rs10157329
1   759837  rs3115851   T   A   .   PASS    AF=0.869947 ES:SE:LP:AF:SS:ID   0.00223171:0.00718632:0.121392:0.869947:9092:rs3115851
1   761732  rs2286139   C   T   .   PASS    AF=0.859132 ES:SE:LP:AF:SS:ID   0.00259724:0.00704979:0.147171:0.859132:9092:rs2286139
1   761752  rs1057213   C   T   .   PASS    AF=0.864751 ES:SE:LP:AF:SS:ID   0.00315747:0.00712331:0.182045:0.864751:9092:rs1057213
1   762273  rs3115849   G   A   .   PASS    AF=0.861759 ES:SE:LP:AF:SS:ID   0.00173354:0.00711574:0.0928413:0.861759:9092:rs3115849
1   762485  rs12095200  C   A   .   PASS    AF=0.102465 ES:SE:LP:AF:SS:ID   -0.00245235:0.0085092:0.111708:0.102465:9092:rs12095200
1   762589  rs3115848   G   C   .   PASS    AF=0.866688 ES:SE:LP:AF:SS:ID   0.00129996:0.00718753:0.0672833:0.866688:9092:rs3115848
1   762592  rs3131950   C   G   .   PASS    AF=0.866688 ES:SE:LP:AF:SS:ID   0.00129996:0.00718753:0.0672833:0.866688:9092:rs3131950
1   762601  rs3131949   T   C   .   PASS    AF=0.866685 ES:SE:LP:AF:SS:ID   0.00130378:0.00718754:0.0674953:0.866685:9092:rs3131949
1   762632  rs3131948   T   A   .   PASS    AF=0.867114 ES:SE:LP:AF:SS:ID   0.00196044:0.0071904:0.105058:0.867114:9092:rs3131948
1   764191  rs7515915   T   G   .   PASS    AF=0.130237 ES:SE:LP:AF:SS:ID   -0.00217413:0.00720319:0.117595:0.130237:9092:rs7515915
1   766007  rs61768174  A   C   .   PASS    AF=0.111374 ES:SE:LP:AF:SS:ID   -0.00645357:0.00781266:0.388486:0.111374:9092:rs61768174
1   766105  rs2519015   T   A   .   PASS    AF=0.849744 ES:SE:LP:AF:SS:ID   0.00357555:0.00703297:0.213827:0.849744:9092:rs2519015
1   768116  rs376645387 A   AGTTTT  .   PASS    AF=0.835493 ES:SE:LP:AF:SS:ID   -0.00619771:0.00698381:0.426124:0.835493:9092:rs376645387
1   768253  rs2977608   A   C   .   PASS    AF=0.756281 ES:SE:LP:AF:SS:ID   -0.00162402:0.00560493:0.112374:0.756281:9092:rs2977608
1   768448  rs12562034  G   A   .   PASS    AF=0.107952 ES:SE:LP:AF:SS:ID   0.00569121:0.00774235:0.335064:0.107952:9092:rs12562034
1   769138  rs59306077  CAT C   .   PASS    AF=0.133865 ES:SE:LP:AF:SS:ID   -0.00244191:0.00710067:0.136124:0.133865:9092:rs762168062
1   769223  rs60320384  C   G   .   PASS    AF=0.133523 ES:SE:LP:AF:SS:ID   -0.0029432:0.00709835:0.168501:0.133523:9092:rs60320384
1   769963  rs7518545   G   A   .   PASS    AF=0.107483 ES:SE:LP:AF:SS:ID   0.00515476:0.00779411:0.293799:0.107483:9092:rs7518545
1   770886  rs371458725 G   A   .   PASS    AF=0.106577 ES:SE:LP:AF:SS:ID   0.00452015:0.00785017:0.248134:0.106577:9092:rs371458725
1   771410  rs2519006   C   T   .   PASS    AF=0.824603 ES:SE:LP:AF:SS:ID   0.00322429:0.00695183:0.191925:0.824603:9092:rs2519006
1   771823  rs2977605   T   C   .   PASS    AF=0.865052 ES:SE:LP:AF:SS:ID   0.0027127:0.00706985:0.154152:0.865052:9092:rs2977605
1   771967  rs59066358  G   A   .   PASS    AF=0.133652 ES:SE:LP:AF:SS:ID   -0.00291866:0.00709134:0.167072:0.133652:9092:rs59066358