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-20531/ukb-d-20531.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-20531/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 17:17:10 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-20531/ukb-d-20531.vcf.gz ...
Read summary statistics for 13571440 SNPs.
Dropped 12692 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, 1283502 SNPs remain.
After merging with regression SNP LD, 1283502 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0391 (0.0048)
Lambda GC: 1.0683
Mean Chi^2: 1.0836
Intercept: 0.9954 (0.0064)
Ratio < 0 (usually indicates GC correction).
Analysis finished at Mon Nov 25 17:19:30 2019
Total time elapsed: 2.0m:20.29s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9521,
    "inflation_factor": 1.0422,
    "mean_EFFECT": 0,
    "n": 116671,
    "n_snps": 13571440,
    "n_clumped_hits": 1,
    "n_p_sig": 3,
    "n_mono": 0,
    "n_ns": 1251336,
    "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": 564553,
    "n_est": 117096.1576,
    "ratio_se_n": 1.0018,
    "mean_diff": 0,
    "ratio_diff": 43.7162,
    "sd_y_est1": 0.3494,
    "sd_y_est2": 0.3501,
    "r2_sum1": 0,
    "r2_sum2": 0.0003,
    "r2_sum3": 0.0003,
    "r2_sum4": 0.0003,
    "ldsc_nsnp_merge_refpanel_ld": 1283502,
    "ldsc_nsnp_merge_regression_ld": 1283502,
    "ldsc_observed_scale_h2_beta": 0.0391,
    "ldsc_observed_scale_h2_se": 0.0048,
    "ldsc_intercept_beta": 0.9954,
    "ldsc_intercept_se": 0.0064,
    "ldsc_lambda_gc": 1.0683,
    "ldsc_mean_chisq": 1.0836,
    "ldsc_ratio": -0.055
}

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 1.0000000 3 94 0 13559412 0 NA NA NA NA NA NA NA NA
character REF 0 1.0000000 1 100 0 57054 0 NA NA NA NA NA NA NA NA
character ALT 0 1.0000000 1 342 0 33331 0 NA NA NA NA NA NA NA NA
numeric CHROM 0 1.0000000 NA NA NA NA NA 9.051431e+00 6.185060e+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 7.902502e+07 5.591566e+07 3.02000e+02 3.292807e+07 7.013925e+07 1.148583e+08 2.492309e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA 2.450000e-05 8.454100e-03 -9.66979e-02 -2.293200e-03 -3.500000e-06 2.281500e-03 1.103800e-01 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 6.060800e-03 5.842200e-03 1.19690e-03 1.729900e-03 3.183600e-03 8.702300e-03 2.908860e-02 ▇▂▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.931082e-01 2.904611e-01 0.00000e+00 2.401638e-01 4.910989e-01 7.445781e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.931068e-01 2.904619e-01 0.00000e+00 2.401613e-01 4.910975e-01 7.445776e-01 9.999998e-01 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA 1.909995e-01 2.544497e-01 1.00000e-03 7.483200e-03 6.026700e-02 2.956792e-01 9.990000e-01 ▇▂▁▁▁
numeric AF_reference 564553 0.9584014 NA NA NA NA NA 1.964743e-01 2.471295e-01 0.00000e+00 5.790700e-03 8.446490e-02 3.083070e-01 1.000000e+00 ▇▂▁▁▁
numeric N 0 1.0000000 NA NA NA NA NA 1.166710e+05 0.000000e+00 1.16671e+05 1.166710e+05 1.166710e+05 1.166710e+05 1.166710e+05 ▁▁▇▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 692794 rs530212009 CA C 0.0058156 0.0025183 0.0209247 0.0209226 0.1117640 0.1894970 116671
1 693731 rs12238997 A G 0.0056749 0.0023848 0.0173325 0.0173307 0.1167870 0.1417730 116671
1 707522 rs371890604 G C 0.0062717 0.0026756 0.0190801 0.0190784 0.0984045 0.1293930 116671
1 717587 rs144155419 G A 0.0022287 0.0064033 0.7277982 0.7277978 0.0158098 0.0045926 116671
1 723329 rs189787166 A T 0.0143586 0.0187298 0.4433125 0.4433087 0.0017688 0.0003994 116671
1 730087 rs148120343 T C 0.0083217 0.0033178 0.0121361 0.0121346 0.0569652 0.0127796 116671
1 731718 rs142557973 T C 0.0048133 0.0022629 0.0334164 0.0334144 0.1227110 0.1543530 116671
1 732032 rs61770163 A C 0.0046893 0.0024114 0.0518239 0.0518220 0.1223360 0.1555510 116671
1 734349 rs141242758 T C 0.0048456 0.0022641 0.0323415 0.0323393 0.1219640 0.1525560 116671
1 740284 rs61770167 C T 0.0055912 0.0103665 0.5896401 0.5896402 0.0058416 0.0023962 116671
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
23 154923311 rs141127553 C T 0.0009777 0.0026603 0.7132372 0.7132371 0.0553982 0.0309934 116671
23 154923374 rs111332691 T A -0.0043412 0.0028998 0.1343869 0.1343848 0.0447326 0.0116556 116671
23 154925045 rs509981 C T 0.0022757 0.0013955 0.1029480 0.1029437 0.2447630 0.3634440 116671
23 154925895 rs538470 C T 0.0021054 0.0014270 0.1400990 0.1400968 0.2411910 0.3634440 116671
23 154927581 rs644138 G A 0.0023413 0.0013133 0.0746277 0.0746250 0.3005140 0.4635760 116671
23 154929412 rs557132 C T 0.0022723 0.0013959 0.1035481 0.1035456 0.2446370 0.3568210 116671
23 154929637 rs35185538 CT C 0.0029743 0.0014582 0.0413800 0.0413774 0.2288170 0.3011920 116671
23 154929952 rs4012982 CAA C 0.0025954 0.0014692 0.0773108 0.0773083 0.2386790 0.3165560 116671
23 154930230 rs781880 A G 0.0021788 0.0013954 0.1184459 0.1184422 0.2450490 0.3618540 116671
23 154930487 rs781879 T A -0.0021523 0.0047466 0.6502285 0.6502264 0.0196771 0.1263580 116671

bcf preview

1   692794  rs530212009 CA  C   .   PASS    AF=0.111764 ES:SE:LP:AF:SS:ID   0.00581564:0.00251827:1.67934:0.111764:116671:1_692794_CA_C
1   693731  rs12238997  A   G   .   PASS    AF=0.116787 ES:SE:LP:AF:SS:ID   0.00567493:0.00238481:1.76114:0.116787:116671:rs12238997
1   707522  rs371890604 G   C   .   PASS    AF=0.0984045    ES:SE:LP:AF:SS:ID   0.00627169:0.00267564:1.71942:0.0984045:116671:rs371890604
1   717587  rs144155419 G   A   .   PASS    AF=0.0158098    ES:SE:LP:AF:SS:ID   0.00222871:0.0064033:0.137989:0.0158098:116671:rs144155419
1   723329  rs189787166 A   T   .   PASS    AF=0.00176879   ES:SE:LP:AF:SS:ID   0.0143586:0.0187298:0.35329:0.00176879:116671:rs189787166
1   730087  rs148120343 T   C   .   PASS    AF=0.0569652    ES:SE:LP:AF:SS:ID   0.0083217:0.00331779:1.91592:0.0569652:116671:rs148120343
1   731718  rs58276399  T   C   .   PASS    AF=0.122711 ES:SE:LP:AF:SS:ID   0.00481328:0.00226287:1.47604:0.122711:116671:rs58276399
1   732032  rs61770163  A   C   .   PASS    AF=0.122336 ES:SE:LP:AF:SS:ID   0.00468929:0.00241143:1.28547:0.122336:116671:rs61770163
1   734349  rs141242758 T   C   .   PASS    AF=0.121964 ES:SE:LP:AF:SS:ID   0.00484565:0.00226412:1.49024:0.121964:116671:rs141242758
1   740284  rs61770167  C   T   .   PASS    AF=0.00584163   ES:SE:LP:AF:SS:ID   0.00559125:0.0103665:0.229413:0.00584163:116671:rs61770167
1   742813  rs112573343 C   T   .   PASS    AF=0.00184013   ES:SE:LP:AF:SS:ID   0.012509:0.0197882:0.277946:0.00184013:116671:rs112573343
1   749963  rs529266287 T   TAA .   PASS    AF=0.868961 ES:SE:LP:AF:SS:ID   -0.00535937:0.00223067:1.78831:0.868961:116671:rs529266287
1   750230  rs190826124 G   C   .   PASS    AF=0.00159334   ES:SE:LP:AF:SS:ID   -0.020068:0.0197884:0.507906:0.00159334:116671:rs190826124
1   751343  rs28544273  T   A   .   PASS    AF=0.12375  ES:SE:LP:AF:SS:ID   0.00615349:0.00221015:2.27027:0.12375:116671:rs28544273
1   751488  rs200141114 G   GA  .   PASS    AF=0.143417 ES:SE:LP:AF:SS:ID   0.00706:0.00218556:2.90765:0.143417:116671:rs200141114
1   751756  rs28527770  T   C   .   PASS    AF=0.123871 ES:SE:LP:AF:SS:ID   0.00616343:0.00220709:2.28148:0.123871:116671:rs28527770
1   753405  rs3115860   C   A   .   PASS    AF=0.869725 ES:SE:LP:AF:SS:ID   -0.00584619:0.00214954:2.1848:0.869725:116671:rs3115860
1   753425  rs3131970   T   C   .   PASS    AF=0.874521 ES:SE:LP:AF:SS:ID   -0.00587852:0.00218564:2.14541:0.874521:116671:rs3131970
1   753541  rs2073813   G   A   .   PASS    AF=0.129734 ES:SE:LP:AF:SS:ID   0.00601575:0.00215552:2.27921:0.129734:116671:rs2073813
1   754105  rs12184325  C   T   .   PASS    AF=0.0365044    ES:SE:LP:AF:SS:ID   0.00223284:0.00391676:0.245171:0.0365044:116671:rs12184325
1   754182  rs3131969   A   G   .   PASS    AF=0.86932  ES:SE:LP:AF:SS:ID   -0.00585852:0.00214747:2.1958:0.86932:116671:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.869388 ES:SE:LP:AF:SS:ID   -0.00575331:0.00214826:2.13049:0.869388:116671:rs3131968
1   754334  rs3131967   T   C   .   PASS    AF=0.86932  ES:SE:LP:AF:SS:ID   -0.00586379:0.00214742:2.19912:0.86932:116671:rs3131967
1   754433  rs150578204 G   A   .   PASS    AF=0.00511436   ES:SE:LP:AF:SS:ID   0.0232865:0.010986:1.46804:0.00511436:116671:rs150578204
1   754458  rs142682604 G   T   .   PASS    AF=0.00508319   ES:SE:LP:AF:SS:ID   0.0229991:0.0110104:1.43507:0.00508319:116671:rs142682604
1   755435  rs184270342 T   G   .   PASS    AF=0.00567226   ES:SE:LP:AF:SS:ID   -0.00823176:0.0106069:0.358819:0.00567226:116671:rs184270342
1   755890  rs3115858   A   T   .   PASS    AF=0.869393 ES:SE:LP:AF:SS:ID   -0.0057355:0.0021435:2.12744:0.869393:116671:rs3115858
1   756434  rs61768170  G   C   .   PASS    AF=0.127006 ES:SE:LP:AF:SS:ID   0.00623828:0.00218805:2.36072:0.127006:116671:rs61768170
1   756604  rs3131962   A   G   .   PASS    AF=0.868922 ES:SE:LP:AF:SS:ID   -0.0058002:0.00213794:2.17594:0.868922:116671:rs3131962
1   757640  rs3115853   G   A   .   PASS    AF=0.868312 ES:SE:LP:AF:SS:ID   -0.00591398:0.00213703:2.24782:0.868312:116671:rs3115853
1   757734  rs4951929   C   T   .   PASS    AF=0.869102 ES:SE:LP:AF:SS:ID   -0.00573499:0.00213999:2.13282:0.869102:116671:rs4951929
1   757936  rs4951862   C   A   .   PASS    AF=0.869109 ES:SE:LP:AF:SS:ID   -0.00574066:0.00214014:2.13601:0.869109:116671:rs4951862
1   758144  rs3131956   A   G   .   PASS    AF=0.869111 ES:SE:LP:AF:SS:ID   -0.00573747:0.00214015:2.13406:0.869111:116671:rs3131956
1   758626  rs3131954   C   T   .   PASS    AF=0.869547 ES:SE:LP:AF:SS:ID   -0.00576359:0.00214561:2.14101:0.869547:116671:rs3131954
1   759293  rs10157329  T   A   .   PASS    AF=0.0996286    ES:SE:LP:AF:SS:ID   0.00544401:0.00249419:1.53668:0.0996286:116671:rs10157329
1   759600  rs545998451 AGT A   .   PASS    AF=0.00653587   ES:SE:LP:AF:SS:ID   -0.00502195:0.00962283:0.22058:0.00653587:116671:1_759600_AGT_A
1   759837  rs3115851   T   A   .   PASS    AF=0.873604 ES:SE:LP:AF:SS:ID   -0.00596735:0.00217843:2.21056:0.873604:116671:rs3115851
1   761732  rs2286139   C   T   .   PASS    AF=0.862894 ES:SE:LP:AF:SS:ID   -0.00664321:0.0021366:2.72673:0.862894:116671:rs2286139
1   761752  rs1057213   C   T   .   PASS    AF=0.868289 ES:SE:LP:AF:SS:ID   -0.00593035:0.00215713:2.22364:0.868289:116671:rs1057213
1   762273  rs3115849   G   A   .   PASS    AF=0.865301 ES:SE:LP:AF:SS:ID   -0.00571926:0.00215739:2.0955:0.865301:116671:rs3115849
1   762485  rs12095200  C   A   .   PASS    AF=0.0998268    ES:SE:LP:AF:SS:ID   0.00699855:0.00257709:2.17947:0.0998268:116671:rs12095200
1   762589  rs3115848   G   C   .   PASS    AF=0.87059  ES:SE:LP:AF:SS:ID   -0.00585303:0.00218275:2.13487:0.87059:116671:rs3115848
1   762592  rs3131950   C   G   .   PASS    AF=0.87059  ES:SE:LP:AF:SS:ID   -0.00585315:0.00218275:2.13494:0.87059:116671:rs3131950
1   762601  rs3131949   T   C   .   PASS    AF=0.870588 ES:SE:LP:AF:SS:ID   -0.00585493:0.00218275:2.136:0.870588:116671:rs3131949
1   762632  rs3131948   T   A   .   PASS    AF=0.870908 ES:SE:LP:AF:SS:ID   -0.00587892:0.00218364:2.14886:0.870908:116671:rs3131948
1   764191  rs7515915   T   G   .   PASS    AF=0.126614 ES:SE:LP:AF:SS:ID   0.00616506:0.00218544:2.31977:0.126614:116671:rs7515915
1   766007  rs61768174  A   C   .   PASS    AF=0.106349 ES:SE:LP:AF:SS:ID   0.00573575:0.0023757:1.8023:0.106349:116671:rs61768174
1   766105  rs2519015   T   A   .   PASS    AF=0.854325 ES:SE:LP:AF:SS:ID   -0.00587441:0.00213598:2.22501:0.854325:116671:rs2519015
1   767393  rs538667473 A   C   .   PASS    AF=0.00168058   ES:SE:LP:AF:SS:ID   0.0112587:0.0188138:0.259988:0.00168058:116671:rs538667473
1   768116  rs376645387 A   AGTTTT  .   PASS    AF=0.839027 ES:SE:LP:AF:SS:ID   0.00091161:0.00211679:0.176058:0.839027:116671:rs376645387