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-20090_367/ukb-d-20090_367.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-20090_367/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 16:52:14 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-20090_367/ukb-d-20090_367.vcf.gz ...
Read summary statistics for 9527193 SNPs.
Dropped 7088 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, 1273515 SNPs remain.
After merging with regression SNP LD, 1273515 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: -0.0015 (0.0078)
Lambda GC: 0.9944
Mean Chi^2: 0.9965
Intercept: 0.998 (0.0056)
Ratio: NA (mean chi^2 < 1)
Analysis finished at Mon Nov 25 16:53:48 2019
Total time elapsed: 1.0m:33.97s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9391,
    "inflation_factor": 0.9975,
    "mean_EFFECT": -4.223e-06,
    "n": 51427,
    "n_snps": 9527193,
    "n_clumped_hits": 1,
    "n_p_sig": 5,
    "n_mono": 0,
    "n_ns": 1052550,
    "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": 190524,
    "n_est": 51430.3474,
    "ratio_se_n": 1,
    "mean_diff": -0,
    "ratio_diff": 28.7038,
    "sd_y_est1": 0.1483,
    "sd_y_est2": 0.1483,
    "r2_sum1": 0,
    "r2_sum2": 0.0007,
    "r2_sum3": 0.0007,
    "r2_sum4": 0.0007,
    "ldsc_nsnp_merge_refpanel_ld": 1273515,
    "ldsc_nsnp_merge_regression_ld": 1273515,
    "ldsc_observed_scale_h2_beta": "NA",
    "ldsc_observed_scale_h2_se": "NA",
    "ldsc_intercept_beta": 0.998,
    "ldsc_intercept_se": 0.0056,
    "ldsc_lambda_gc": 0.9944,
    "ldsc_mean_chisq": 0.9965,
    "ldsc_ratio": 0.5714
}

Flags

name value
af_correlation FALSE
inflation_factor FALSE
n FALSE
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 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 numeric.mean numeric.sd numeric.p0 numeric.p25 numeric.p50 numeric.p75 numeric.p100 numeric.hist
character ID 0 1.0000000 3 94 0 9520644 0 NA NA NA NA NA NA NA NA
character REF 0 1.0000000 1 98 0 46519 0 NA NA NA NA NA NA NA NA
character ALT 0 1.0000000 1 342 0 29458 0 NA NA NA NA NA NA NA NA
numeric CHROM 0 1.0000000 NA NA NA NA NA 9.080888e+00 6.174334e+00 1.00000e+00 4.000000e+00 8.000000e+00 1.300000e+01 2.300000e+01 ▇▅▅▂▂
numeric POS 0 1.0000000 NA NA NA NA NA 7.871082e+07 5.610846e+07 3.02000e+02 3.241786e+07 6.958921e+07 1.147230e+08 2.492297e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA -4.200000e-06 2.005000e-03 -1.60235e-02 -9.943000e-04 -1.250000e-05 9.669000e-04 2.634250e-02 ▁▇▃▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 1.759100e-03 9.685000e-04 7.61700e-04 1.009700e-03 1.332900e-03 2.238300e-03 5.591700e-03 ▇▂▂▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 5.002501e-01 2.881614e-01 0.00000e+00 2.515232e-01 5.005414e-01 7.496007e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 5.002470e-01 2.881633e-01 0.00000e+00 2.515175e-01 5.005378e-01 7.495993e-01 1.000000e+00 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA 2.658536e-01 2.627393e-01 1.08790e-02 4.754080e-02 1.655340e-01 4.225370e-01 9.891210e-01 ▇▂▂▁▁
numeric AF_reference 190524 0.9800021 NA NA NA NA NA 2.652390e-01 2.535469e-01 0.00000e+00 5.431310e-02 1.801320e-01 4.175320e-01 1.000000e+00 ▇▃▂▂▁
numeric N 0 1.0000000 NA NA NA NA NA 5.142700e+04 0.000000e+00 5.14270e+04 5.142700e+04 5.142700e+04 5.142700e+04 5.142700e+04 ▁▁▇▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 692794 rs530212009 CA C -0.0009502 0.0016108 0.5552710 0.5552684 0.1121000 0.1894970 51427
1 693731 rs12238997 A G -0.0015907 0.0015307 0.2987397 0.2987345 0.1168090 0.1417730 51427
1 707522 rs371890604 G C -0.0010080 0.0017168 0.5571331 0.5571314 0.0982930 0.1293930 51427
1 717587 rs144155419 G A -0.0007425 0.0041505 0.8580141 0.8580135 0.0154808 0.0045926 51427
1 730087 rs148120343 T C -0.0022819 0.0021317 0.2844199 0.2844166 0.0570822 0.0127796 51427
1 731718 rs142557973 T C -0.0013097 0.0014546 0.3679197 0.3679176 0.1225210 0.1543530 51427
1 732032 rs61770163 A C -0.0015629 0.0015506 0.3135011 0.3134963 0.1216510 0.1555510 51427
1 734349 rs141242758 T C -0.0012633 0.0014554 0.3853887 0.3853848 0.1217650 0.1525560 51427
1 749963 rs529266287 T TAA 0.0016694 0.0014327 0.2439400 0.2439344 0.8686130 0.7641770 51427
1 751343 rs28544273 T A -0.0019558 0.0014193 0.1682050 0.1681988 0.1239570 0.2426120 51427
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
23 154923311 rs141127553 C T -0.0022683 0.0017113 0.1850218 0.1850146 0.0542488 0.0309934 51427
23 154923374 rs111332691 T A -0.0038161 0.0018537 0.0395403 0.0395346 0.0445389 0.0116556 51427
23 154925045 rs509981 C T -0.0001096 0.0008912 0.9021171 0.9021168 0.2434190 0.3634440 51427
23 154925895 rs538470 C T -0.0001986 0.0009104 0.8272760 0.8272748 0.2401390 0.3634440 51427
23 154927581 rs644138 G A -0.0006072 0.0008383 0.4688652 0.4688619 0.2981050 0.4635760 51427
23 154929412 rs557132 C T -0.0000960 0.0008915 0.9142330 0.9142329 0.2432580 0.3568210 51427
23 154929637 rs35185538 CT C -0.0004853 0.0009289 0.6013953 0.6013933 0.2278210 0.3011920 51427
23 154929952 rs4012982 CAA C 0.0000331 0.0009380 0.9718499 0.9718500 0.2374290 0.3165560 51427
23 154930230 rs781880 A G -0.0001182 0.0008911 0.8944511 0.8944505 0.2438260 0.3618540 51427
23 154930487 rs781879 T A 0.0012130 0.0030987 0.6954517 0.6954490 0.0189843 0.1263580 51427

bcf preview

1   692794  rs530212009 CA  C   .   PASS    AF=0.1121   ES:SE:LP:AF:SS:ID   -0.000950203:0.00161083:0.255495:0.1121:51427:1_692794_CA_C
1   693731  rs12238997  A   G   .   PASS    AF=0.116809 ES:SE:LP:AF:SS:ID   -0.00159067:0.00153074:0.524707:0.116809:51427:rs12238997
1   707522  rs371890604 G   C   .   PASS    AF=0.098293 ES:SE:LP:AF:SS:ID   -0.00100797:0.00171684:0.254041:0.098293:51427:rs371890604
1   717587  rs144155419 G   A   .   PASS    AF=0.0154808    ES:SE:LP:AF:SS:ID   -0.000742539:0.0041505:0.0665056:0.0154808:51427:rs144155419
1   730087  rs148120343 T   C   .   PASS    AF=0.0570822    ES:SE:LP:AF:SS:ID   -0.00228189:0.00213171:0.54604:0.0570822:51427:rs148120343
1   731718  rs58276399  T   C   .   PASS    AF=0.122521 ES:SE:LP:AF:SS:ID   -0.00130973:0.00145464:0.434247:0.122521:51427:rs58276399
1   732032  rs61770163  A   C   .   PASS    AF=0.121651 ES:SE:LP:AF:SS:ID   -0.00156291:0.00155064:0.503761:0.121651:51427:rs61770163
1   734349  rs141242758 T   C   .   PASS    AF=0.121765 ES:SE:LP:AF:SS:ID   -0.00126333:0.00145542:0.414101:0.121765:51427:rs141242758
1   749963  rs529266287 T   TAA .   PASS    AF=0.868613 ES:SE:LP:AF:SS:ID   0.00166943:0.00143273:0.612717:0.868613:51427:rs529266287
1   751343  rs28544273  T   A   .   PASS    AF=0.123957 ES:SE:LP:AF:SS:ID   -0.00195583:0.00141931:0.774161:0.123957:51427:rs28544273
1   751488  rs200141114 G   GA  .   PASS    AF=0.143385 ES:SE:LP:AF:SS:ID   -0.00187171:0.00140817:0.735662:0.143385:51427:rs200141114
1   751756  rs28527770  T   C   .   PASS    AF=0.124126 ES:SE:LP:AF:SS:ID   -0.00186904:0.00141696:0.727792:0.124126:51427:rs28527770
1   753405  rs3115860   C   A   .   PASS    AF=0.869933 ES:SE:LP:AF:SS:ID   0.00197392:0.00138095:0.815595:0.869933:51427:rs3115860
1   753425  rs3131970   T   C   .   PASS    AF=0.874426 ES:SE:LP:AF:SS:ID   0.00190106:0.00140291:0.75598:0.874426:51427:rs3131970
1   753541  rs2073813   G   A   .   PASS    AF=0.129659 ES:SE:LP:AF:SS:ID   -0.00191826:0.00138436:0.780271:0.129659:51427:rs2073813
1   754105  rs12184325  C   T   .   PASS    AF=0.0369164    ES:SE:LP:AF:SS:ID   -0.000592692:0.00249345:0.0903819:0.0369164:51427:rs12184325
1   754182  rs3131969   A   G   .   PASS    AF=0.869554 ES:SE:LP:AF:SS:ID   0.00198409:0.00137966:0.822715:0.869554:51427:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.869648 ES:SE:LP:AF:SS:ID   0.00196996:0.00138038:0.813739:0.869648:51427:rs3131968
1   754334  rs3131967   T   C   .   PASS    AF=0.86957  ES:SE:LP:AF:SS:ID   0.00197425:0.00137966:0.816887:0.86957:51427:rs3131967
1   755890  rs3115858   A   T   .   PASS    AF=0.869706 ES:SE:LP:AF:SS:ID   0.00196654:0.00137758:0.814078:0.869706:51427:rs3115858
1   756434  rs61768170  G   C   .   PASS    AF=0.12702  ES:SE:LP:AF:SS:ID   -0.00182881:0.00140499:0.714355:0.12702:51427:rs61768170
1   756604  rs3131962   A   G   .   PASS    AF=0.869213 ES:SE:LP:AF:SS:ID   0.00202515:0.00137396:0.852324:0.869213:51427:rs3131962
1   757640  rs3115853   G   A   .   PASS    AF=0.868449 ES:SE:LP:AF:SS:ID   0.00189358:0.00137263:0.775366:0.868449:51427:rs3115853
1   757734  rs4951929   C   T   .   PASS    AF=0.869419 ES:SE:LP:AF:SS:ID   0.00198918:0.00137547:0.829348:0.869419:51427:rs4951929
1   757936  rs4951862   C   A   .   PASS    AF=0.869426 ES:SE:LP:AF:SS:ID   0.00198941:0.00137556:0.82941:0.869426:51427:rs4951862
1   758144  rs3131956   A   G   .   PASS    AF=0.869437 ES:SE:LP:AF:SS:ID   0.00198592:0.00137563:0.827269:0.869437:51427:rs3131956
1   758626  rs3131954   C   T   .   PASS    AF=0.869848 ES:SE:LP:AF:SS:ID   0.00192852:0.00137884:0.790689:0.869848:51427:rs3131954
1   759293  rs10157329  T   A   .   PASS    AF=0.0999077    ES:SE:LP:AF:SS:ID   -0.00145369:0.001599:0.439745:0.0999077:51427:rs10157329
1   759837  rs3115851   T   A   .   PASS    AF=0.87358  ES:SE:LP:AF:SS:ID   0.00164159:0.00139877:0.618773:0.87358:51427:rs3115851
1   761732  rs2286139   C   T   .   PASS    AF=0.86295  ES:SE:LP:AF:SS:ID   0.00174088:0.00137226:0.689133:0.86295:51427:rs2286139
1   761752  rs1057213   C   T   .   PASS    AF=0.868667 ES:SE:LP:AF:SS:ID   0.00192358:0.00138572:0.782258:0.868667:51427:rs1057213
1   762273  rs3115849   G   A   .   PASS    AF=0.8652   ES:SE:LP:AF:SS:ID   0.00187324:0.00138511:0.753876:0.8652:51427:rs3115849
1   762485  rs12095200  C   A   .   PASS    AF=0.0992889    ES:SE:LP:AF:SS:ID   -0.00263038:0.00166235:0.944694:0.0992889:51427:rs12095200
1   762589  rs3115848   G   C   .   PASS    AF=0.870459 ES:SE:LP:AF:SS:ID   0.0016131:0.00140068:0.602985:0.870459:51427:rs3115848
1   762592  rs3131950   C   G   .   PASS    AF=0.870459 ES:SE:LP:AF:SS:ID   0.00161311:0.00140068:0.60299:0.870459:51427:rs3131950
1   762601  rs3131949   T   C   .   PASS    AF=0.870456 ES:SE:LP:AF:SS:ID   0.0016123:0.00140069:0.602569:0.870456:51427:rs3131949
1   762632  rs3131948   T   A   .   PASS    AF=0.870829 ES:SE:LP:AF:SS:ID   0.00166997:0.00140148:0.631834:0.870829:51427:rs3131948
1   764191  rs7515915   T   G   .   PASS    AF=0.126636 ES:SE:LP:AF:SS:ID   -0.00168754:0.00140305:0.640026:0.126636:51427:rs7515915
1   766007  rs61768174  A   C   .   PASS    AF=0.106247 ES:SE:LP:AF:SS:ID   -0.00189052:0.00152794:0.665584:0.106247:51427:rs61768174
1   766105  rs2519015   T   A   .   PASS    AF=0.854084 ES:SE:LP:AF:SS:ID   0.00180235:0.00137212:0.723534:0.854084:51427:rs2519015
1   768116  rs376645387 A   AGTTTT  .   PASS    AF=0.836377 ES:SE:LP:AF:SS:ID   0.000333149:0.00134379:0.0946365:0.836377:51427:rs376645387
1   768253  rs2977608   A   C   .   PASS    AF=0.76015  ES:SE:LP:AF:SS:ID   0.0015577:0.00108028:0.825873:0.76015:51427:rs2977608
1   768448  rs12562034  G   A   .   PASS    AF=0.108173 ES:SE:LP:AF:SS:ID   -0.000594965:0.00148277:0.162263:0.108173:51427:rs12562034
1   769138  rs59306077  CAT C   .   PASS    AF=0.129757 ES:SE:LP:AF:SS:ID   -0.00200233:0.00138449:0.82941:0.129757:51427:rs762168062
1   769223  rs60320384  C   G   .   PASS    AF=0.129482 ES:SE:LP:AF:SS:ID   -0.00196804:0.00138335:0.810122:0.129482:51427:rs60320384
1   769963  rs7518545   G   A   .   PASS    AF=0.107436 ES:SE:LP:AF:SS:ID   -0.000622487:0.00149406:0.169449:0.107436:51427:rs7518545
1   770886  rs371458725 G   A   .   PASS    AF=0.106291 ES:SE:LP:AF:SS:ID   -0.00059464:0.00150782:0.159073:0.106291:51427:rs371458725
1   771410  rs2519006   C   T   .   PASS    AF=0.828506 ES:SE:LP:AF:SS:ID   0.00203122:0.00134718:0.880668:0.828506:51427:rs2519006
1   771823  rs2977605   T   C   .   PASS    AF=0.869399 ES:SE:LP:AF:SS:ID   0.00206146:0.00137751:0.871197:0.869399:51427:rs2977605
1   771967  rs59066358  G   A   .   PASS    AF=0.129528 ES:SE:LP:AF:SS:ID   -0.00196006:0.00138276:0.805916:0.129528:51427:rs59066358