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-22601_33123442/ukb-d-22601_33123442.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-22601_33123442/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 15:01:12 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-22601_33123442/ukb-d-22601_33123442.vcf.gz ...
Read summary statistics for 9514022 SNPs.
Dropped 7070 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, 1273333 SNPs remain.
After merging with regression SNP LD, 1273333 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0005 (0.0053)
Lambda GC: 1.0022
Mean Chi^2: 1.0055
Intercept: 1.0046 (0.0068)
Ratio: 0.8398 (1.2391)
Analysis finished at Mon Nov 25 15:02:30 2019
Total time elapsed: 1.0m:17.68s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9389,
    "inflation_factor": 1.0102,
    "mean_EFFECT": -1.969e-07,
    "n": 89866,
    "n_snps": 9514022,
    "n_clumped_hits": 0,
    "n_p_sig": 8,
    "n_mono": 0,
    "n_ns": 1051676,
    "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": 190320,
    "n_est": 89848.7825,
    "ratio_se_n": 0.9999,
    "mean_diff": -1.8453e-06,
    "ratio_diff": 6.4595,
    "sd_y_est1": 0.1121,
    "sd_y_est2": 0.1121,
    "r2_sum1": 0,
    "r2_sum2": 0,
    "r2_sum3": 0,
    "r2_sum4": 0,
    "ldsc_nsnp_merge_refpanel_ld": 1273333,
    "ldsc_nsnp_merge_regression_ld": 1273333,
    "ldsc_observed_scale_h2_beta": 0.0005,
    "ldsc_observed_scale_h2_se": 0.0053,
    "ldsc_intercept_beta": 1.0046,
    "ldsc_intercept_se": 0.0068,
    "ldsc_lambda_gc": 1.0022,
    "ldsc_mean_chisq": 1.0055,
    "ldsc_ratio": 0.8364
}

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 9507490 0 NA NA NA NA NA NA NA NA
character REF 0 1.0000000 1 98 0 46451 0 NA NA NA NA NA NA NA NA
character ALT 0 1.0000000 1 342 0 29451 0 NA NA NA NA NA NA NA NA
numeric CHROM 0 1.0000000 NA NA NA NA NA 9.080406e+00 6.174421e+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 7.870740e+07 5.611413e+07 3.02000e+02 3.241547e+07 6.957775e+07 1.147303e+08 2.492297e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA -2.000000e-07 1.149200e-03 -1.03644e-02 -5.700000e-04 -5.600000e-06 5.576000e-04 1.290750e-02 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 1.003700e-03 5.510000e-04 4.37300e-04 5.771000e-04 7.614000e-04 1.276500e-03 3.125400e-03 ▇▂▂▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.983233e-01 2.887896e-01 0.00000e+00 2.481993e-01 4.978208e-01 7.479955e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.983215e-01 2.887906e-01 0.00000e+00 2.481963e-01 4.978196e-01 7.479952e-01 9.999997e-01 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA 2.661863e-01 2.627503e-01 1.09457e-02 4.780370e-02 1.659390e-01 4.230398e-01 9.890540e-01 ▇▂▂▁▁
numeric AF_reference 190320 0.9799958 NA NA NA NA NA 2.655649e-01 2.535437e-01 0.00000e+00 5.471250e-02 1.807110e-01 4.179310e-01 1.000000e+00 ▇▃▂▂▁
numeric N 0 1.0000000 NA NA NA NA NA 8.986600e+04 0.000000e+00 8.98660e+04 8.986600e+04 8.986600e+04 8.986600e+04 8.986600e+04 ▁▁▇▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 692794 rs530212009 CA C -0.0003798 0.0009238 0.6809528 0.6809516 0.1114870 0.1894970 89866
1 693731 rs12238997 A G 0.0000794 0.0008751 0.9277311 0.9277310 0.1164980 0.1417730 89866
1 707522 rs371890604 G C -0.0002787 0.0009838 0.7769857 0.7769859 0.0978285 0.1293930 89866
1 717587 rs144155419 G A -0.0011580 0.0023433 0.6211965 0.6211948 0.0158090 0.0045926 89866
1 730087 rs148120343 T C -0.0002414 0.0012134 0.8423390 0.8423386 0.0569661 0.0127796 89866
1 731718 rs142557973 T C -0.0002672 0.0008304 0.7476150 0.7476143 0.1223780 0.1543530 89866
1 732032 rs61770163 A C -0.0002622 0.0008853 0.7671265 0.7671259 0.1220530 0.1555510 89866
1 734349 rs141242758 T C -0.0002869 0.0008310 0.7299212 0.7299202 0.1216170 0.1525560 89866
1 749963 rs529266287 T TAA 0.0003024 0.0008176 0.7114739 0.7114738 0.8689590 0.7641770 89866
1 751343 rs28544273 T A -0.0004438 0.0008105 0.5840056 0.5840044 0.1236780 0.2426120 89866
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
23 154923311 rs141127553 C T 0.0012324 0.0009720 0.2048330 0.2048298 0.0553576 0.0309934 89866
23 154923374 rs111332691 T A -0.0008745 0.0010581 0.4085639 0.4085622 0.0449113 0.0116556 89866
23 154925045 rs509981 C T -0.0000141 0.0005103 0.9779660 0.9779658 0.2444280 0.3634440 89866
23 154925895 rs538470 C T 0.0001680 0.0005218 0.7475324 0.7475323 0.2408760 0.3634440 89866
23 154927581 rs644138 G A 0.0003247 0.0004800 0.4988098 0.4988077 0.3001910 0.4635760 89866
23 154929412 rs557132 C T -0.0000077 0.0005105 0.9879830 0.9879829 0.2442750 0.3568210 89866
23 154929637 rs35185538 CT C 0.0004030 0.0005330 0.4495717 0.4495702 0.2286930 0.3011920 89866
23 154929952 rs4012982 CAA C 0.0001923 0.0005372 0.7204055 0.7204042 0.2381980 0.3165560 89866
23 154930230 rs781880 A G 0.0000698 0.0005103 0.8912571 0.8912564 0.2447120 0.3618540 89866
23 154930487 rs781879 T A 0.0000438 0.0017311 0.9798030 0.9798024 0.0196791 0.1263580 89866

bcf preview

1   692794  rs530212009 CA  C   .   PASS    AF=0.111487 ES:SE:LP:AF:SS:ID   -0.000379826:0.00092378:0.166883:0.111487:89866:1_692794_CA_C
1   693731  rs12238997  A   G   .   PASS    AF=0.116498 ES:SE:LP:AF:SS:ID   7.93689e-05:0.000875071:0.0325779:0.116498:89866:rs12238997
1   707522  rs371890604 G   C   .   PASS    AF=0.0978285    ES:SE:LP:AF:SS:ID   -0.000278652:0.00098377:0.109587:0.0978285:89866:rs371890604
1   717587  rs144155419 G   A   .   PASS    AF=0.015809 ES:SE:LP:AF:SS:ID   -0.00115795:0.00234328:0.206771:0.015809:89866:rs144155419
1   730087  rs148120343 T   C   .   PASS    AF=0.0569661    ES:SE:LP:AF:SS:ID   -0.000241351:0.00121341:0.0745131:0.0569661:89866:rs148120343
1   731718  rs58276399  T   C   .   PASS    AF=0.122378 ES:SE:LP:AF:SS:ID   -0.000267211:0.000830398:0.126322:0.122378:89866:rs58276399
1   732032  rs61770163  A   C   .   PASS    AF=0.122053 ES:SE:LP:AF:SS:ID   -0.000262169:0.000885298:0.115133:0.122053:89866:rs61770163
1   734349  rs141242758 T   C   .   PASS    AF=0.121617 ES:SE:LP:AF:SS:ID   -0.000286893:0.000831016:0.136724:0.121617:89866:rs141242758
1   749963  rs529266287 T   TAA .   PASS    AF=0.868959 ES:SE:LP:AF:SS:ID   0.00030241:0.000817595:0.147841:0.868959:89866:rs529266287
1   751343  rs28544273  T   A   .   PASS    AF=0.123678 ES:SE:LP:AF:SS:ID   -0.0004438:0.000810527:0.233583:0.123678:89866:rs28544273
1   751488  rs200141114 G   GA  .   PASS    AF=0.143191 ES:SE:LP:AF:SS:ID   -0.000223993:0.000802469:0.107824:0.143191:89866:rs200141114
1   751756  rs28527770  T   C   .   PASS    AF=0.123813 ES:SE:LP:AF:SS:ID   -0.000465752:0.000809358:0.247965:0.123813:89866:rs28527770
1   753405  rs3115860   C   A   .   PASS    AF=0.869927 ES:SE:LP:AF:SS:ID   0.000333814:0.000788604:0.172579:0.869927:89866:rs3115860
1   753425  rs3131970   T   C   .   PASS    AF=0.87461  ES:SE:LP:AF:SS:ID   0.000343993:0.000801461:0.17537:0.87461:89866:rs3131970
1   753541  rs2073813   G   A   .   PASS    AF=0.12951  ES:SE:LP:AF:SS:ID   -0.000251791:0.000791015:0.124796:0.12951:89866:rs2073813
1   754105  rs12184325  C   T   .   PASS    AF=0.0357365    ES:SE:LP:AF:SS:ID   0.000758135:0.00144717:0.221583:0.0357365:89866:rs12184325
1   754182  rs3131969   A   G   .   PASS    AF=0.869574 ES:SE:LP:AF:SS:ID   0.000235899:0.00078791:0.116545:0.869574:89866:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.869652 ES:SE:LP:AF:SS:ID   0.000230747:0.000788261:0.113662:0.869652:89866:rs3131968
1   754334  rs3131967   T   C   .   PASS    AF=0.86957  ES:SE:LP:AF:SS:ID   0.000239105:0.000787878:0.118316:0.86957:89866:rs3131967
1   755890  rs3115858   A   T   .   PASS    AF=0.869566 ES:SE:LP:AF:SS:ID   0.00037529:0.000786316:0.198482:0.869566:89866:rs3115858
1   756434  rs61768170  G   C   .   PASS    AF=0.126879 ES:SE:LP:AF:SS:ID   -0.00055684:0.000802704:0.311697:0.126879:89866:rs61768170
1   756604  rs3131962   A   G   .   PASS    AF=0.869094 ES:SE:LP:AF:SS:ID   0.000413463:0.000784277:0.223253:0.869094:89866:rs3131962
1   757640  rs3115853   G   A   .   PASS    AF=0.868498 ES:SE:LP:AF:SS:ID   0.000317941:0.000783798:0.164305:0.868498:89866:rs3115853
1   757734  rs4951929   C   T   .   PASS    AF=0.869245 ES:SE:LP:AF:SS:ID   0.0003918:0.000784993:0.209221:0.869245:89866:rs4951929
1   757936  rs4951862   C   A   .   PASS    AF=0.869251 ES:SE:LP:AF:SS:ID   0.000391608:0.000785047:0.209083:0.869251:89866:rs4951862
1   758144  rs3131956   A   G   .   PASS    AF=0.869252 ES:SE:LP:AF:SS:ID   0.000392647:0.000785052:0.209737:0.869252:89866:rs3131956
1   758626  rs3131954   C   T   .   PASS    AF=0.869724 ES:SE:LP:AF:SS:ID   0.000373539:0.00078714:0.197153:0.869724:89866:rs3131954
1   759293  rs10157329  T   A   .   PASS    AF=0.0991203    ES:SE:LP:AF:SS:ID   -0.000332504:0.000916362:0.144653:0.0991203:89866:rs10157329
1   759837  rs3115851   T   A   .   PASS    AF=0.873732 ES:SE:LP:AF:SS:ID   0.000421751:0.000798833:0.223641:0.873732:89866:rs3115851
1   761732  rs2286139   C   T   .   PASS    AF=0.863116 ES:SE:LP:AF:SS:ID   0.000339695:0.000783533:0.177426:0.863116:89866:rs2286139
1   761752  rs1057213   C   T   .   PASS    AF=0.868511 ES:SE:LP:AF:SS:ID   0.000499028:0.00079136:0.277114:0.868511:89866:rs1057213
1   762273  rs3115849   G   A   .   PASS    AF=0.86539  ES:SE:LP:AF:SS:ID   0.000361924:0.000791476:0.188778:0.86539:89866:rs3115849
1   762485  rs12095200  C   A   .   PASS    AF=0.0994301    ES:SE:LP:AF:SS:ID   -0.00043218:0.000947795:0.188156:0.0994301:89866:rs12095200
1   762589  rs3115848   G   C   .   PASS    AF=0.870696 ES:SE:LP:AF:SS:ID   0.000335404:0.000800581:0.170533:0.870696:89866:rs3115848
1   762592  rs3131950   C   G   .   PASS    AF=0.870695 ES:SE:LP:AF:SS:ID   0.000335402:0.000800581:0.170532:0.870695:89866:rs3131950
1   762601  rs3131949   T   C   .   PASS    AF=0.870693 ES:SE:LP:AF:SS:ID   0.000335551:0.000800584:0.170619:0.870693:89866:rs3131949
1   762632  rs3131948   T   A   .   PASS    AF=0.871061 ES:SE:LP:AF:SS:ID   0.000307505:0.000800962:0.154258:0.871061:89866:rs3131948
1   764191  rs7515915   T   G   .   PASS    AF=0.126484 ES:SE:LP:AF:SS:ID   -0.000480652:0.00080177:0.260548:0.126484:89866:rs7515915
1   766007  rs61768174  A   C   .   PASS    AF=0.106022 ES:SE:LP:AF:SS:ID   1.76865e-05:0.000871592:0.00708877:0.106022:89866:rs61768174
1   766105  rs2519015   T   A   .   PASS    AF=0.854451 ES:SE:LP:AF:SS:ID   0.00022668:0.000783347:0.112216:0.854451:89866:rs2519015
1   768116  rs376645387 A   AGTTTT  .   PASS    AF=0.839008 ES:SE:LP:AF:SS:ID   -0.00124941:0.000773854:0.972997:0.839008:89866:rs376645387
1   768253  rs2977608   A   C   .   PASS    AF=0.76317  ES:SE:LP:AF:SS:ID   -0.000763745:0.000622178:0.658318:0.76317:89866:rs2977608
1   768448  rs12562034  G   A   .   PASS    AF=0.10519  ES:SE:LP:AF:SS:ID   0.00194499:0.000857439:1.63247:0.10519:89866:rs12562034
1   769138  rs59306077  CAT C   .   PASS    AF=0.129876 ES:SE:LP:AF:SS:ID   -0.00055283:0.000790539:0.31483:0.129876:89866:rs762168062
1   769223  rs60320384  C   G   .   PASS    AF=0.129602 ES:SE:LP:AF:SS:ID   -0.000554552:0.000789505:0.316567:0.129602:89866:rs60320384
1   769963  rs7518545   G   A   .   PASS    AF=0.104469 ES:SE:LP:AF:SS:ID   0.00205293:0.000864049:1.75681:0.104469:89866:rs7518545
1   770886  rs371458725 G   A   .   PASS    AF=0.103468 ES:SE:LP:AF:SS:ID   0.00204158:0.000871547:1.71764:0.103468:89866:rs371458725
1   771410  rs2519006   C   T   .   PASS    AF=0.829371 ES:SE:LP:AF:SS:ID   1.62244e-05:0.000770618:0.0073568:0.829371:89866:rs2519006
1   771823  rs2977605   T   C   .   PASS    AF=0.869112 ES:SE:LP:AF:SS:ID   0.000503397:0.000785696:0.282564:0.869112:89866:rs2977605
1   771967  rs59066358  G   A   .   PASS    AF=0.129712 ES:SE:LP:AF:SS:ID   -0.000534683:0.000789052:0.302762:0.129712:89866:rs59066358