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-22617_8139/ukb-d-22617_8139.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-22617_8139/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 15:00:42 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-22617_8139/ukb-d-22617_8139.vcf.gz ...
Read summary statistics for 9637881 SNPs.
Dropped 7251 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, 1274836 SNPs remain.
After merging with regression SNP LD, 1274836 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: -0.0017 (0.0051)
Lambda GC: 1.0002
Mean Chi^2: 1.005
Intercept: 1.0081 (0.0062)
Ratio: 1.6035 (1.2342)
Analysis finished at Mon Nov 25 15:02:10 2019
Total time elapsed: 1.0m:27.7s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9397,
    "inflation_factor": 1.0057,
    "mean_EFFECT": 3.2932e-06,
    "n": 91149,
    "n_snps": 9637881,
    "n_clumped_hits": 0,
    "n_p_sig": 0,
    "n_mono": 0,
    "n_ns": 1059979,
    "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": 192220,
    "n_est": 91154.7493,
    "ratio_se_n": 1,
    "mean_diff": 0,
    "ratio_diff": 27.3133,
    "sd_y_est1": 0.1156,
    "sd_y_est2": 0.1156,
    "r2_sum1": 0,
    "r2_sum2": 0,
    "r2_sum3": 0,
    "r2_sum4": 0,
    "ldsc_nsnp_merge_refpanel_ld": 1274836,
    "ldsc_nsnp_merge_regression_ld": 1274836,
    "ldsc_observed_scale_h2_beta": "NA",
    "ldsc_observed_scale_h2_se": "NA",
    "ldsc_intercept_beta": 1.0081,
    "ldsc_intercept_se": 0.0062,
    "ldsc_lambda_gc": 1.0002,
    "ldsc_mean_chisq": 1.005,
    "ldsc_ratio": 1.62
}

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 9631178 0 NA NA NA NA NA NA NA NA
character REF 0 1.0000000 1 98 0 46924 0 NA NA NA NA NA NA NA NA
character ALT 0 1.0000000 1 342 0 29623 0 NA NA NA NA NA NA NA NA
numeric CHROM 0 1.0000000 NA NA NA NA NA 9.079591e+00 6.175378e+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 7.873411e+07 5.611670e+07 3.02000e+02 3.242810e+07 6.961581e+07 1.147434e+08 2.492297e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA 3.300000e-06 1.210500e-03 -1.07684e-02 -5.885000e-04 -5.600000e-06 5.752000e-04 1.451560e-02 ▁▂▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 1.049700e-03 5.920000e-04 4.47600e-04 5.925000e-04 7.878000e-04 1.340900e-03 3.309200e-03 ▇▂▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.991745e-01 2.891568e-01 1.00000e-07 2.489218e-01 4.987846e-01 7.497975e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.991728e-01 2.891579e-01 1.00000e-07 2.489195e-01 4.987837e-01 7.497971e-01 1.000000e+00 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA 2.631342e-01 2.628494e-01 1.01626e-02 4.526740e-02 1.616490e-01 4.185320e-01 9.898370e-01 ▇▂▂▁▁
numeric AF_reference 192220 0.9800558 NA NA NA NA NA 2.625882e-01 2.536538e-01 0.00000e+00 5.151760e-02 1.767170e-01 4.139380e-01 1.000000e+00 ▇▃▂▁▁
numeric N 0 1.0000000 NA NA NA NA NA 9.114900e+04 0.000000e+00 9.11490e+04 9.114900e+04 9.114900e+04 9.114900e+04 9.114900e+04 ▁▁▇▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 692794 rs530212009 CA C -0.0008862 0.0009468 0.3492714 0.3492676 0.1114870 0.1894970 91149
1 693731 rs12238997 A G -0.0015955 0.0008967 0.0751813 0.0751783 0.1164590 0.1417730 91149
1 707522 rs371890604 G C -0.0009775 0.0010076 0.3320137 0.3320096 0.0978765 0.1293930 91149
1 717587 rs144155419 G A -0.0017159 0.0024020 0.4750015 0.4749998 0.0157837 0.0045926 91149
1 730087 rs148120343 T C -0.0003700 0.0012429 0.7659105 0.7659097 0.0569973 0.0127796 91149
1 731718 rs142557973 T C -0.0015017 0.0008509 0.0775818 0.0775775 0.1223590 0.1543530 91149
1 732032 rs61770163 A C -0.0012936 0.0009072 0.1538952 0.1538924 0.1220470 0.1555510 91149
1 734349 rs141242758 T C -0.0015542 0.0008515 0.0679798 0.0679758 0.1215880 0.1525560 91149
1 749963 rs529266287 T TAA 0.0014870 0.0008376 0.0758595 0.0758578 0.8689170 0.7641770 91149
1 751343 rs28544273 T A -0.0013986 0.0008304 0.0921467 0.0921442 0.1236990 0.2426120 91149
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
23 154923311 rs141127553 C T 0.0002320 0.0009961 0.8158229 0.8158230 0.0552869 0.0309934 91149
23 154923374 rs111332691 T A 0.0006643 0.0010840 0.5399866 0.5399855 0.0448387 0.0116556 91149
23 154925045 rs509981 C T -0.0002351 0.0005224 0.6527246 0.6527236 0.2444670 0.3634440 91149
23 154925895 rs538470 C T -0.0002627 0.0005341 0.6228493 0.6228476 0.2409490 0.3634440 91149
23 154927581 rs644138 G A -0.0001516 0.0004913 0.7576280 0.7576281 0.3001640 0.4635760 91149
23 154929412 rs557132 C T -0.0002272 0.0005226 0.6637125 0.6637104 0.2443160 0.3568210 91149
23 154929637 rs35185538 CT C 0.0000031 0.0005456 0.9954780 0.9954779 0.2286640 0.3011920 91149
23 154929952 rs4012982 CAA C -0.0001963 0.0005500 0.7211390 0.7211384 0.2382530 0.3165560 91149
23 154930230 rs781880 A G -0.0002298 0.0005224 0.6599424 0.6599417 0.2447660 0.3618540 91149
23 154930487 rs781879 T A -0.0029325 0.0017716 0.0978723 0.0978701 0.0196632 0.1263580 91149

bcf preview

1   692794  rs530212009 CA  C   .   PASS    AF=0.111487 ES:SE:LP:AF:SS:ID   -0.000886171:0.000946753:0.456837:0.111487:91149:1_692794_CA_C
1   693731  rs12238997  A   G   .   PASS    AF=0.116459 ES:SE:LP:AF:SS:ID   -0.0015955:0.000896663:1.12389:0.116459:91149:rs12238997
1   707522  rs371890604 G   C   .   PASS    AF=0.0978765    ES:SE:LP:AF:SS:ID   -0.000977495:0.00100765:0.478844:0.0978765:91149:rs371890604
1   717587  rs144155419 G   A   .   PASS    AF=0.0157837    ES:SE:LP:AF:SS:ID   -0.00171594:0.00240204:0.323305:0.0157837:91149:rs144155419
1   730087  rs148120343 T   C   .   PASS    AF=0.0569973    ES:SE:LP:AF:SS:ID   -0.000370036:0.00124286:0.115822:0.0569973:91149:rs148120343
1   731718  rs58276399  T   C   .   PASS    AF=0.122359 ES:SE:LP:AF:SS:ID   -0.00150173:0.000850878:1.11024:0.122359:91149:rs58276399
1   732032  rs61770163  A   C   .   PASS    AF=0.122047 ES:SE:LP:AF:SS:ID   -0.00129365:0.000907241:0.812775:0.122047:91149:rs61770163
1   734349  rs141242758 T   C   .   PASS    AF=0.121588 ES:SE:LP:AF:SS:ID   -0.00155417:0.000851522:1.16762:0.121588:91149:rs141242758
1   749963  rs529266287 T   TAA .   PASS    AF=0.868917 ES:SE:LP:AF:SS:ID   0.00148697:0.000837615:1.11999:0.868917:91149:rs529266287
1   751343  rs28544273  T   A   .   PASS    AF=0.123699 ES:SE:LP:AF:SS:ID   -0.00139861:0.000830433:1.03552:0.123699:91149:rs28544273
1   751488  rs200141114 G   GA  .   PASS    AF=0.143202 ES:SE:LP:AF:SS:ID   -0.00188591:0.000822125:1.66163:0.143202:91149:rs200141114
1   751756  rs28527770  T   C   .   PASS    AF=0.123834 ES:SE:LP:AF:SS:ID   -0.00138004:0.000829232:1.01742:0.123834:91149:rs28527770
1   753405  rs3115860   C   A   .   PASS    AF=0.869892 ES:SE:LP:AF:SS:ID   0.00142294:0.000808005:1.10661:0.869892:91149:rs3115860
1   753425  rs3131970   T   C   .   PASS    AF=0.874553 ES:SE:LP:AF:SS:ID   0.00138674:0.00082111:1.03977:0.874553:91149:rs3131970
1   753541  rs2073813   G   A   .   PASS    AF=0.129529 ES:SE:LP:AF:SS:ID   -0.00135556:0.000810542:1.02481:0.129529:91149:rs2073813
1   754105  rs12184325  C   T   .   PASS    AF=0.0358205    ES:SE:LP:AF:SS:ID   -0.00082594:0.0014808:0.238821:0.0358205:91149:rs12184325
1   754182  rs3131969   A   G   .   PASS    AF=0.869539 ES:SE:LP:AF:SS:ID   0.00140271:0.00080733:1.08456:0.869539:91149:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.869616 ES:SE:LP:AF:SS:ID   0.00144715:0.000807682:1.13561:0.869616:91149:rs3131968
1   754334  rs3131967   T   C   .   PASS    AF=0.869535 ES:SE:LP:AF:SS:ID   0.00140395:0.000807297:1.08605:0.869535:91149:rs3131967
1   755890  rs3115858   A   T   .   PASS    AF=0.86952  ES:SE:LP:AF:SS:ID   0.00142266:0.000805633:1.11116:0.86952:91149:rs3115858
1   756434  rs61768170  G   C   .   PASS    AF=0.126911 ES:SE:LP:AF:SS:ID   -0.00142026:0.000822411:1.07479:0.126911:91149:rs61768170
1   756604  rs3131962   A   G   .   PASS    AF=0.86905  ES:SE:LP:AF:SS:ID   0.00144372:0.000803547:1.14033:0.86905:91149:rs3131962
1   757640  rs3115853   G   A   .   PASS    AF=0.868436 ES:SE:LP:AF:SS:ID   0.00140849:0.000803038:1.09995:0.868436:91149:rs3115853
1   757734  rs4951929   C   T   .   PASS    AF=0.869199 ES:SE:LP:AF:SS:ID   0.00142715:0.000804276:1.11924:0.869199:91149:rs4951929
1   757936  rs4951862   C   A   .   PASS    AF=0.869205 ES:SE:LP:AF:SS:ID   0.0014265:0.000804328:1.11836:0.869205:91149:rs4951862
1   758144  rs3131956   A   G   .   PASS    AF=0.869207 ES:SE:LP:AF:SS:ID   0.00142647:0.000804335:1.11832:0.869207:91149:rs3131956
1   758626  rs3131954   C   T   .   PASS    AF=0.869687 ES:SE:LP:AF:SS:ID   0.00142435:0.000806488:1.11137:0.869687:91149:rs3131954
1   759293  rs10157329  T   A   .   PASS    AF=0.0991787    ES:SE:LP:AF:SS:ID   -0.0012964:0.000938561:0.776761:0.0991787:91149:rs10157329
1   759837  rs3115851   T   A   .   PASS    AF=0.873682 ES:SE:LP:AF:SS:ID   0.00149377:0.000818431:1.16762:0.873682:91149:rs3115851
1   761732  rs2286139   C   T   .   PASS    AF=0.863058 ES:SE:LP:AF:SS:ID   0.00133399:0.000802817:1.01508:0.863058:91149:rs2286139
1   761752  rs1057213   C   T   .   PASS    AF=0.868472 ES:SE:LP:AF:SS:ID   0.00146599:0.00081078:1.15125:0.868472:91149:rs1057213
1   762273  rs3115849   G   A   .   PASS    AF=0.865369 ES:SE:LP:AF:SS:ID   0.00132302:0.000810935:0.988036:0.865369:91149:rs3115849
1   762485  rs12095200  C   A   .   PASS    AF=0.0995228    ES:SE:LP:AF:SS:ID   -0.00174087:0.000970534:1.13751:0.0995228:91149:rs12095200
1   762589  rs3115848   G   C   .   PASS    AF=0.870657 ES:SE:LP:AF:SS:ID   0.00146916:0.000820171:1.13519:0.870657:91149:rs3115848
1   762592  rs3131950   C   G   .   PASS    AF=0.870657 ES:SE:LP:AF:SS:ID   0.00146916:0.00082017:1.13519:0.870657:91149:rs3131950
1   762601  rs3131949   T   C   .   PASS    AF=0.870654 ES:SE:LP:AF:SS:ID   0.00146935:0.000820173:1.1354:0.870654:91149:rs3131949
1   762632  rs3131948   T   A   .   PASS    AF=0.871019 ES:SE:LP:AF:SS:ID   0.00149681:0.000820553:1.16664:0.871019:91149:rs3131948
1   764191  rs7515915   T   G   .   PASS    AF=0.126515 ES:SE:LP:AF:SS:ID   -0.00138774:0.000821468:1.04021:0.126515:91149:rs7515915
1   766007  rs61768174  A   C   .   PASS    AF=0.106037 ES:SE:LP:AF:SS:ID   -0.00139621:0.000892944:0.928431:0.106037:91149:rs61768174
1   766105  rs2519015   T   A   .   PASS    AF=0.85438  ES:SE:LP:AF:SS:ID   0.00114855:0.000802514:0.817075:0.85438:91149:rs2519015
1   768116  rs376645387 A   AGTTTT  .   PASS    AF=0.839153 ES:SE:LP:AF:SS:ID   1.64329e-05:0.000792927:0.00724065:0.839153:91149:rs376645387
1   768253  rs2977608   A   C   .   PASS    AF=0.763195 ES:SE:LP:AF:SS:ID   0.000522967:0.000637553:0.385036:0.763195:91149:rs2977608
1   768448  rs12562034  G   A   .   PASS    AF=0.105092 ES:SE:LP:AF:SS:ID   0.000710288:0.000878554:0.377973:0.105092:91149:rs12562034
1   769138  rs59306077  CAT C   .   PASS    AF=0.129904 ES:SE:LP:AF:SS:ID   -0.00129361:0.000809996:0.957598:0.129904:91149:rs762168062
1   769223  rs60320384  C   G   .   PASS    AF=0.129636 ES:SE:LP:AF:SS:ID   -0.0013003:0.00080893:0.966721:0.129636:91149:rs60320384
1   769963  rs7518545   G   A   .   PASS    AF=0.104365 ES:SE:LP:AF:SS:ID   0.000661967:0.000885375:0.342311:0.104365:91149:rs7518545
1   770886  rs371458725 G   A   .   PASS    AF=0.103379 ES:SE:LP:AF:SS:ID   0.000662331:0.000893032:0.338858:0.103379:91149:rs371458725
1   771410  rs2519006   C   T   .   PASS    AF=0.829291 ES:SE:LP:AF:SS:ID   0.000772534:0.000789219:0.484587:0.829291:91149:rs2519006
1   771823  rs2977605   T   C   .   PASS    AF=0.869067 ES:SE:LP:AF:SS:ID   0.00142432:0.000805028:1.11435:0.869067:91149:rs2977605
1   771967  rs59066358  G   A   .   PASS    AF=0.129741 ES:SE:LP:AF:SS:ID   -0.00136422:0.000808487:1.03842:0.129741:91149:rs59066358