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-5610_2/ukb-d-5610_2.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-5610_2/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 16:50:37 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-5610_2/ukb-d-5610_2.vcf.gz ...
Read summary statistics for 10226766 SNPs.
Dropped 8011 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, 1279552 SNPs remain.
After merging with regression SNP LD, 1279552 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0112 (0.0137)
Lambda GC: 1.0117
Mean Chi^2: 1.0097
Intercept: 1.0027 (0.0061)
Ratio: 0.2768 (0.6328)
Analysis finished at Mon Nov 25 16:52:18 2019
Total time elapsed: 1.0m:41.1s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9427,
    "inflation_factor": 1.006,
    "mean_EFFECT": 0,
    "n": 31494,
    "n_snps": 10226766,
    "n_clumped_hits": 0,
    "n_p_sig": 0,
    "n_mono": 0,
    "n_ns": 1096556,
    "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": 201396,
    "n_est": 31549.0231,
    "ratio_se_n": 1.0009,
    "mean_diff": 0.0001,
    "ratio_diff": 192.6391,
    "sd_y_est1": 0.2296,
    "sd_y_est2": 0.2298,
    "r2_sum1": 0,
    "r2_sum2": 0,
    "r2_sum3": 0,
    "r2_sum4": 0,
    "ldsc_nsnp_merge_refpanel_ld": 1279552,
    "ldsc_nsnp_merge_regression_ld": 1279552,
    "ldsc_observed_scale_h2_beta": 0.0112,
    "ldsc_observed_scale_h2_se": 0.0137,
    "ldsc_intercept_beta": 1.0027,
    "ldsc_intercept_se": 0.0061,
    "ldsc_lambda_gc": 1.0117,
    "ldsc_mean_chisq": 1.0097,
    "ldsc_ratio": 0.2784
}

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 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 10219315 0 NA NA NA NA NA NA NA NA
character REF 0 1.000000 1 100 0 48937 0 NA NA NA NA NA NA NA NA
character ALT 0 1.000000 1 342 0 30434 0 NA NA NA NA NA NA NA NA
numeric CHROM 0 1.000000 NA NA NA NA NA 9.078452e+00 6.178263e+00 1.00000e+00 4.000000e+00 8.000000e+00 1.300000e+01 2.300000e+01 ▇▅▅▂▂
numeric POS 0 1.000000 NA NA NA NA NA 7.877249e+07 5.606155e+07 3.02000e+02 3.252752e+07 6.968769e+07 1.147231e+08 2.492297e+08 ▇▆▅▂▁
numeric EFFECT 0 1.000000 NA NA NA NA NA 2.030000e-05 4.646500e-03 -4.32968e-02 -2.081100e-03 -3.100000e-06 2.070500e-03 5.545100e-02 ▁▁▇▁▁
numeric SE 0 1.000000 NA NA NA NA NA 3.930200e-03 2.493300e-03 1.50610e-03 2.024400e-03 2.796900e-03 5.120700e-03 1.417170e-02 ▇▂▁▁▁
numeric PVAL 0 1.000000 NA NA NA NA NA 4.987582e-01 2.886561e-01 5.00000e-07 2.487929e-01 4.987116e-01 7.486434e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.000000 NA NA NA NA NA 4.987531e-01 2.886591e-01 5.00000e-07 2.487840e-01 4.987065e-01 7.486407e-01 1.000000e+00 ▇▇▇▇▇
numeric AF 0 1.000000 NA NA NA NA NA 2.494352e-01 2.628711e-01 7.14290e-03 3.477590e-02 1.418560e-01 3.986160e-01 9.928560e-01 ▇▂▂▁▁
numeric AF_reference 201396 0.980307 NA NA NA NA NA 2.491827e-01 2.537474e-01 0.00000e+00 3.773960e-02 1.583470e-01 3.951680e-01 1.000000e+00 ▇▃▂▁▁
numeric N 0 1.000000 NA NA NA NA NA 3.149400e+04 0.000000e+00 3.14940e+04 3.149400e+04 3.149400e+04 3.149400e+04 3.149400e+04 ▁▁▇▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 692794 rs530212009 CA C 0.0008768 0.0032022 0.7842310 0.7842291 0.1116860 0.1894970 31494
1 693731 rs12238997 A G 0.0020658 0.0030271 0.4949793 0.4949743 0.1175430 0.1417730 31494
1 707522 rs371890604 G C 0.0005847 0.0034057 0.8636831 0.8636820 0.0978470 0.1293930 31494
1 717587 rs144155419 G A 0.0058515 0.0081231 0.4713180 0.4713129 0.0158964 0.0045926 31494
1 730087 rs148120343 T C -0.0036701 0.0042006 0.3822813 0.3822743 0.0574672 0.0127796 31494
1 731718 rs142557973 T C 0.0020792 0.0028679 0.4684497 0.4684453 0.1232790 0.1543530 31494
1 732032 rs61770163 A C 0.0020948 0.0030537 0.4927164 0.4927106 0.1228850 0.1555510 31494
1 734349 rs141242758 T C 0.0020538 0.0028706 0.4743195 0.4743152 0.1224210 0.1525560 31494
1 749963 rs529266287 T TAA -0.0012729 0.0028316 0.6530584 0.6530545 0.8686160 0.7641770 31494
1 751343 rs28544273 T A 0.0014127 0.0028071 0.6147988 0.6147943 0.1237510 0.2426120 31494
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
23 154923311 rs141127553 C T 0.0010787 0.0033274 0.7457993 0.7457978 0.0562109 0.0309934 31494
23 154923374 rs111332691 T A 0.0019472 0.0036623 0.5949466 0.5949425 0.0442783 0.0116556 31494
23 154925045 rs509981 C T 0.0005676 0.0017659 0.7478819 0.7478793 0.2440420 0.3634440 31494
23 154925895 rs538470 C T 0.0001985 0.0018060 0.9124610 0.9124601 0.2407340 0.3634440 31494
23 154927581 rs644138 G A 0.0006786 0.0016562 0.6819884 0.6819848 0.3007300 0.4635760 31494
23 154929412 rs557132 C T 0.0005103 0.0017666 0.7727002 0.7726993 0.2439040 0.3568210 31494
23 154929637 rs35185538 CT C 0.0018032 0.0018407 0.3272962 0.3272888 0.2286140 0.3011920 31494
23 154929952 rs4012982 CAA C 0.0010752 0.0018584 0.5628958 0.5628915 0.2378770 0.3165560 31494
23 154930230 rs781880 A G 0.0005728 0.0017663 0.7457152 0.7457135 0.2443960 0.3618540 31494
23 154930487 rs781879 T A -0.0048842 0.0062710 0.4360648 0.4360596 0.0182666 0.1263580 31494

bcf preview

1   692794  rs530212009 CA  C   .   PASS    AF=0.111686 ES:SE:LP:AF:SS:ID   0.000876787:0.00320215:0.105556:0.111686:31494:1_692794_CA_C
1   693731  rs12238997  A   G   .   PASS    AF=0.117543 ES:SE:LP:AF:SS:ID   0.00206577:0.00302713:0.305413:0.117543:31494:rs12238997
1   707522  rs371890604 G   C   .   PASS    AF=0.097847 ES:SE:LP:AF:SS:ID   0.000584723:0.00340571:0.0636456:0.097847:31494:rs371890604
1   717587  rs144155419 G   A   .   PASS    AF=0.0158964    ES:SE:LP:AF:SS:ID   0.00585146:0.00812314:0.326686:0.0158964:31494:rs144155419
1   730087  rs148120343 T   C   .   PASS    AF=0.0574672    ES:SE:LP:AF:SS:ID   -0.00367013:0.00420061:0.417617:0.0574672:31494:rs148120343
1   731718  rs58276399  T   C   .   PASS    AF=0.123279 ES:SE:LP:AF:SS:ID   0.00207923:0.00286786:0.329337:0.123279:31494:rs58276399
1   732032  rs61770163  A   C   .   PASS    AF=0.122885 ES:SE:LP:AF:SS:ID   0.00209483:0.00305367:0.307403:0.122885:31494:rs61770163
1   734349  rs141242758 T   C   .   PASS    AF=0.122421 ES:SE:LP:AF:SS:ID   0.00205383:0.00287058:0.323929:0.122421:31494:rs141242758
1   749963  rs529266287 T   TAA .   PASS    AF=0.868616 ES:SE:LP:AF:SS:ID   -0.00127286:0.00283158:0.185048:0.868616:31494:rs529266287
1   751343  rs28544273  T   A   .   PASS    AF=0.123751 ES:SE:LP:AF:SS:ID   0.00141267:0.00280714:0.211267:0.123751:31494:rs28544273
1   751488  rs200141114 G   GA  .   PASS    AF=0.142984 ES:SE:LP:AF:SS:ID   0.000524788:0.00278688:0.0702557:0.142984:31494:rs200141114
1   751756  rs28527770  T   C   .   PASS    AF=0.12384  ES:SE:LP:AF:SS:ID   0.00149329:0.00280303:0.226056:0.12384:31494:rs28527770
1   753405  rs3115860   C   A   .   PASS    AF=0.869898 ES:SE:LP:AF:SS:ID   -0.00101776:0.00273003:0.149171:0.869898:31494:rs3115860
1   753425  rs3131970   T   C   .   PASS    AF=0.874802 ES:SE:LP:AF:SS:ID   -0.00094757:0.002777:0.134932:0.874802:31494:rs3131970
1   753541  rs2073813   G   A   .   PASS    AF=0.129805 ES:SE:LP:AF:SS:ID   0.00141376:0.00273565:0.218025:0.129805:31494:rs2073813
1   754105  rs12184325  C   T   .   PASS    AF=0.0363244    ES:SE:LP:AF:SS:ID   0.00404332:0.0049691:0.381086:0.0363244:31494:rs12184325
1   754182  rs3131969   A   G   .   PASS    AF=0.869435 ES:SE:LP:AF:SS:ID   -0.00107045:0.00272699:0.158226:0.869435:31494:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.869579 ES:SE:LP:AF:SS:ID   -0.00114336:0.00272954:0.170501:0.869579:31494:rs3131968
1   754334  rs3131967   T   C   .   PASS    AF=0.869431 ES:SE:LP:AF:SS:ID   -0.00107294:0.0027269:0.158654:0.869431:31494:rs3131967
1   755890  rs3115858   A   T   .   PASS    AF=0.869571 ES:SE:LP:AF:SS:ID   -0.00134035:0.00272173:0.205933:0.869571:31494:rs3115858
1   756434  rs61768170  G   C   .   PASS    AF=0.126925 ES:SE:LP:AF:SS:ID   0.00183148:0.00277942:0.292483:0.126925:31494:rs61768170
1   756604  rs3131962   A   G   .   PASS    AF=0.869197 ES:SE:LP:AF:SS:ID   -0.00143969:0.00271594:0.224715:0.869197:31494:rs3131962
1   757640  rs3115853   G   A   .   PASS    AF=0.868317 ES:SE:LP:AF:SS:ID   -0.00146753:0.00271209:0.230299:0.868317:31494:rs3115853
1   757734  rs4951929   C   T   .   PASS    AF=0.869302 ES:SE:LP:AF:SS:ID   -0.0014969:0.00271743:0.23527:0.869302:31494:rs4951929
1   757936  rs4951862   C   A   .   PASS    AF=0.869309 ES:SE:LP:AF:SS:ID   -0.00149871:0.00271762:0.235591:0.869309:31494:rs4951862
1   758144  rs3131956   A   G   .   PASS    AF=0.869319 ES:SE:LP:AF:SS:ID   -0.00150274:0.00271773:0.236341:0.869319:31494:rs3131956
1   758626  rs3131954   C   T   .   PASS    AF=0.869749 ES:SE:LP:AF:SS:ID   -0.00124389:0.0027252:0.188373:0.869749:31494:rs3131954
1   759293  rs10157329  T   A   .   PASS    AF=0.0993643    ES:SE:LP:AF:SS:ID   0.000944699:0.00317213:0.115857:0.0993643:31494:rs10157329
1   759837  rs3115851   T   A   .   PASS    AF=0.873989 ES:SE:LP:AF:SS:ID   -0.00098808:0.0027687:0.141952:0.873989:31494:rs3115851
1   761732  rs2286139   C   T   .   PASS    AF=0.862883 ES:SE:LP:AF:SS:ID   -0.00173796:0.00271077:0.282795:0.862883:31494:rs2286139
1   761752  rs1057213   C   T   .   PASS    AF=0.868517 ES:SE:LP:AF:SS:ID   -0.00170364:0.00273925:0.272469:0.868517:31494:rs1057213
1   762273  rs3115849   G   A   .   PASS    AF=0.86524  ES:SE:LP:AF:SS:ID   -0.0018939:0.0027383:0.310538:0.86524:31494:rs3115849
1   762485  rs12095200  C   A   .   PASS    AF=0.0996428    ES:SE:LP:AF:SS:ID   0.000414728:0.00328776:0.0459414:0.0996428:31494:rs12095200
1   762589  rs3115848   G   C   .   PASS    AF=0.870703 ES:SE:LP:AF:SS:ID   -0.00125096:0.00277224:0.185875:0.870703:31494:rs3115848
1   762592  rs3131950   C   G   .   PASS    AF=0.870703 ES:SE:LP:AF:SS:ID   -0.00125099:0.00277224:0.18588:0.870703:31494:rs3131950
1   762601  rs3131949   T   C   .   PASS    AF=0.870699 ES:SE:LP:AF:SS:ID   -0.00125091:0.00277226:0.185866:0.870699:31494:rs3131949
1   762632  rs3131948   T   A   .   PASS    AF=0.871086 ES:SE:LP:AF:SS:ID   -0.00120579:0.00277351:0.177999:0.871086:31494:rs3131948
1   764191  rs7515915   T   G   .   PASS    AF=0.126451 ES:SE:LP:AF:SS:ID   0.00189266:0.00277559:0.305121:0.126451:31494:rs7515915
1   766007  rs61768174  A   C   .   PASS    AF=0.106419 ES:SE:LP:AF:SS:ID   0.000897443:0.00301735:0.115691:0.106419:31494:rs61768174
1   766105  rs2519015   T   A   .   PASS    AF=0.854426 ES:SE:LP:AF:SS:ID   -0.00127546:0.00271303:0.194996:0.854426:31494:rs2519015
1   768116  rs376645387 A   AGTTTT  .   PASS    AF=0.838692 ES:SE:LP:AF:SS:ID   0.000536914:0.00267734:0.075173:0.838692:31494:rs376645387
1   768253  rs2977608   A   C   .   PASS    AF=0.763349 ES:SE:LP:AF:SS:ID   -0.000249852:0.00215456:0.0420668:0.763349:31494:rs2977608
1   768448  rs12562034  G   A   .   PASS    AF=0.104925 ES:SE:LP:AF:SS:ID   -0.00185665:0.00296769:0.274441:0.104925:31494:rs12562034
1   768819  rs12562811  C   T   .   PASS    AF=0.00731736   ES:SE:LP:AF:SS:ID   -0.00216753:0.0113304:0.0714557:0.00731736:31494:rs12562811
1   769138  rs59306077  CAT C   .   PASS    AF=0.12989  ES:SE:LP:AF:SS:ID   0.00218104:0.00273418:0.371556:0.12989:31494:rs762168062
1   769223  rs60320384  C   G   .   PASS    AF=0.12956  ES:SE:LP:AF:SS:ID   0.00199952:0.00273345:0.333035:0.12956:31494:rs60320384
1   769963  rs7518545   G   A   .   PASS    AF=0.104208 ES:SE:LP:AF:SS:ID   -0.0018021:0.00299112:0.262126:0.104208:31494:rs7518545
1   770181  rs146076599 A   G   .   PASS    AF=0.00978338   ES:SE:LP:AF:SS:ID   0.0110333:0.0101336:0.558691:0.00978338:31494:rs146076599
1   770377  rs112563271 A   T   .   PASS    AF=0.00731593   ES:SE:LP:AF:SS:ID   -0.00175725:0.0113919:0.0567974:0.00731593:31494:rs112563271
1   770886  rs371458725 G   A   .   PASS    AF=0.103241 ES:SE:LP:AF:SS:ID   -0.00173842:0.00301565:0.248488:0.103241:31494:rs371458725