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-20543/ukb-d-20543.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-20543/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 17:17:54 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-20543/ukb-d-20543.vcf.gz ...
Read summary statistics for 13542967 SNPs.
Dropped 12660 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, 1283494 SNPs remain.
After merging with regression SNP LD, 1283494 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0345 (0.012)
Lambda GC: 1.018
Mean Chi^2: 1.0104
Intercept: 0.9865 (0.0062)
Ratio < 0 (usually indicates GC correction).
Analysis finished at Mon Nov 25 17:20:43 2019
Total time elapsed: 2.0m:48.72s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.952,
    "inflation_factor": 1.011,
    "mean_EFFECT": 0,
    "n": 35558,
    "n_snps": 13542967,
    "n_clumped_hits": 0,
    "n_p_sig": 0,
    "n_mono": 0,
    "n_ns": 1250276,
    "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": 557819,
    "n_est": 35667.4911,
    "ratio_se_n": 1.0015,
    "mean_diff": 0,
    "ratio_diff": 24.9659,
    "sd_y_est1": 0.4955,
    "sd_y_est2": 0.4963,
    "r2_sum1": 0,
    "r2_sum2": 0,
    "r2_sum3": 0,
    "r2_sum4": 0,
    "ldsc_nsnp_merge_refpanel_ld": 1283494,
    "ldsc_nsnp_merge_regression_ld": 1283494,
    "ldsc_observed_scale_h2_beta": 0.0345,
    "ldsc_observed_scale_h2_se": 0.012,
    "ldsc_intercept_beta": 0.9865,
    "ldsc_intercept_se": 0.0062,
    "ldsc_lambda_gc": 1.018,
    "ldsc_mean_chisq": 1.0104,
    "ldsc_ratio": -1.2981
}

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 13530971 0 NA NA NA NA NA NA NA NA
character REF 0 1.0000000 1 100 0 57007 0 NA NA NA NA NA NA NA NA
character ALT 0 1.0000000 1 342 0 33309 0 NA NA NA NA NA NA NA NA
numeric CHROM 0 1.0000000 NA NA NA NA NA 9.051425e+00 6.184942e+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 7.902350e+07 5.591536e+07 3.02000e+02 3.292489e+07 7.013954e+07 1.148560e+08 2.492309e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA 4.480000e-05 2.145690e-02 -2.99503e-01 -5.706400e-03 2.310000e-05 5.745000e-03 2.422670e-01 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 1.548510e-02 1.490680e-02 3.15840e-03 4.439100e-03 8.144600e-03 2.221360e-02 8.159030e-02 ▇▂▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.985928e-01 2.886917e-01 2.00000e-07 2.482813e-01 4.976523e-01 7.486279e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.985883e-01 2.886944e-01 2.00000e-07 2.482737e-01 4.976478e-01 7.486257e-01 1.000000e+00 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA 1.913816e-01 2.545448e-01 1.00000e-03 7.582900e-03 6.069560e-02 2.965130e-01 9.990000e-01 ▇▂▁▁▁
numeric AF_reference 557819 0.9588112 NA NA NA NA NA 1.967547e-01 2.471933e-01 0.00000e+00 5.790700e-03 8.486420e-02 3.089060e-01 1.000000e+00 ▇▂▁▁▁
numeric N 0 1.0000000 NA NA NA NA NA 3.555800e+04 0.000000e+00 3.55580e+04 3.555800e+04 3.555800e+04 3.555800e+04 3.555800e+04 ▁▁▇▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 692794 rs530212009 CA C -0.0064866 0.0064614 0.3154329 0.3154268 0.1122720 0.1894970 35558
1 693731 rs12238997 A G -0.0023544 0.0061030 0.6996615 0.6996584 0.1173980 0.1417730 35558
1 707522 rs371890604 G C -0.0031456 0.0068537 0.6462626 0.6462604 0.0990478 0.1293930 35558
1 717587 rs144155419 G A -0.0051561 0.0161077 0.7488934 0.7488913 0.0163583 0.0045926 35558
1 723329 rs189787166 A T -0.0594680 0.0477705 0.2131881 0.2131800 0.0018052 0.0003994 35558
1 730087 rs148120343 T C -0.0053675 0.0084784 0.5266875 0.5266829 0.0571760 0.0127796 35558
1 731718 rs142557973 T C -0.0046732 0.0057820 0.4189643 0.4189582 0.1239870 0.1543530 35558
1 732032 rs61770163 A C -0.0038415 0.0061661 0.5332870 0.5332823 0.1234660 0.1555510 35558
1 734349 rs141242758 T C -0.0043348 0.0057865 0.4537953 0.4537893 0.1231800 0.1525560 35558
1 740284 rs61770167 C T 0.0350321 0.0272413 0.1984541 0.1984458 0.0055840 0.0023962 35558
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
23 154923311 rs141127553 C T -0.0102528 0.0069410 0.1396449 0.1396364 0.0568025 0.0309934 35558
23 154923374 rs111332691 T A -0.0006519 0.0077460 0.9329350 0.9329349 0.0440267 0.0116556 35558
23 154925045 rs509981 C T -0.0018430 0.0037041 0.6187953 0.6187936 0.2427290 0.3634440 35558
23 154925895 rs538470 C T -0.0004583 0.0037878 0.9036890 0.9036881 0.2391410 0.3634440 35558
23 154927581 rs644138 G A -0.0043907 0.0034752 0.2064339 0.2064263 0.2999900 0.4635760 35558
23 154929412 rs557132 C T -0.0019204 0.0037052 0.6042644 0.6042614 0.2425630 0.3568210 35558
23 154929637 rs35185538 CT C 0.0006037 0.0038679 0.8759699 0.8759695 0.2272230 0.3011920 35558
23 154929952 rs4012982 CAA C -0.0015974 0.0039008 0.6821832 0.6821818 0.2371130 0.3165560 35558
23 154930230 rs781880 A G -0.0017246 0.0037043 0.6415300 0.6415271 0.2428810 0.3618540 35558
23 154930487 rs781879 T A -0.0293088 0.0122844 0.0170447 0.0170395 0.0202143 0.1263580 35558

bcf preview

1   692794  rs530212009 CA  C   .   PASS    AF=0.112272 ES:SE:LP:AF:SS:ID   -0.0064866:0.0064614:0.501093:0.112272:35558:1_692794_CA_C
1   693731  rs12238997  A   G   .   PASS    AF=0.117398 ES:SE:LP:AF:SS:ID   -0.00235441:0.00610296:0.155112:0.117398:35558:rs12238997
1   707522  rs371890604 G   C   .   PASS    AF=0.0990478    ES:SE:LP:AF:SS:ID   -0.00314558:0.00685366:0.189591:0.0990478:35558:rs371890604
1   717587  rs144155419 G   A   .   PASS    AF=0.0163583    ES:SE:LP:AF:SS:ID   -0.0051561:0.0161077:0.12558:0.0163583:35558:rs144155419
1   723329  rs189787166 A   T   .   PASS    AF=0.00180523   ES:SE:LP:AF:SS:ID   -0.059468:0.0477705:0.671237:0.00180523:35558:rs189787166
1   730087  rs148120343 T   C   .   PASS    AF=0.057176 ES:SE:LP:AF:SS:ID   -0.00536748:0.00847839:0.278447:0.057176:35558:rs148120343
1   731718  rs58276399  T   C   .   PASS    AF=0.123987 ES:SE:LP:AF:SS:ID   -0.00467317:0.00578198:0.377823:0.123987:35558:rs58276399
1   732032  rs61770163  A   C   .   PASS    AF=0.123466 ES:SE:LP:AF:SS:ID   -0.00384152:0.00616613:0.273039:0.123466:35558:rs61770163
1   734349  rs141242758 T   C   .   PASS    AF=0.12318  ES:SE:LP:AF:SS:ID   -0.00433477:0.00578654:0.34314:0.12318:35558:rs141242758
1   740284  rs61770167  C   T   .   PASS    AF=0.00558397   ES:SE:LP:AF:SS:ID   0.0350321:0.0272413:0.70234:0.00558397:35558:rs61770167
1   742813  rs112573343 C   T   .   PASS    AF=0.00202519   ES:SE:LP:AF:SS:ID   0.0482445:0.0478908:0.503408:0.00202519:35558:rs112573343
1   749963  rs529266287 T   TAA .   PASS    AF=0.867239 ES:SE:LP:AF:SS:ID   0.00323348:0.00568649:0.244419:0.867239:35558:rs529266287
1   750230  rs190826124 G   C   .   PASS    AF=0.00146179   ES:SE:LP:AF:SS:ID   0.0300514:0.0533705:0.24155:0.00146179:35558:rs190826124
1   751343  rs28544273  T   A   .   PASS    AF=0.125227 ES:SE:LP:AF:SS:ID   -0.00154105:0.00564196:0.105271:0.125227:35558:rs28544273
1   751488  rs200141114 G   GA  .   PASS    AF=0.14514  ES:SE:LP:AF:SS:ID   -0.00430148:0.00558028:0.35575:0.14514:35558:rs200141114
1   751756  rs28527770  T   C   .   PASS    AF=0.125303 ES:SE:LP:AF:SS:ID   -0.00139726:0.00563456:0.0946619:0.125303:35558:rs28527770
1   753405  rs3115860   C   A   .   PASS    AF=0.868028 ES:SE:LP:AF:SS:ID   0.000944615:0.00549266:0.0637598:0.868028:35558:rs3115860
1   753425  rs3131970   T   C   .   PASS    AF=0.873044 ES:SE:LP:AF:SS:ID   0.000891739:0.0055815:0.0589529:0.873044:35558:rs3131970
1   753541  rs2073813   G   A   .   PASS    AF=0.131406 ES:SE:LP:AF:SS:ID   -0.00138162:0.00550623:0.0958922:0.131406:35558:rs2073813
1   754105  rs12184325  C   T   .   PASS    AF=0.0363069    ES:SE:LP:AF:SS:ID   0.00632553:0.010082:0.2754:0.0363069:35558:rs12184325
1   754182  rs3131969   A   G   .   PASS    AF=0.867573 ES:SE:LP:AF:SS:ID   0.000861811:0.00548556:0.0579111:0.867573:35558:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.867646 ES:SE:LP:AF:SS:ID   0.000725417:0.00548672:0.0482663:0.867646:35558:rs3131968
1   754334  rs3131967   T   C   .   PASS    AF=0.867567 ES:SE:LP:AF:SS:ID   0.000876183:0.00548529:0.05894:0.867567:35558:rs3131967
1   754433  rs150578204 G   A   .   PASS    AF=0.00542819   ES:SE:LP:AF:SS:ID   0.0179748:0.0272918:0.292305:0.00542819:35558:rs150578204
1   754458  rs142682604 G   T   .   PASS    AF=0.00540211   ES:SE:LP:AF:SS:ID   0.0179713:0.0273477:0.291499:0.00540211:35558:rs142682604
1   755435  rs184270342 T   G   .   PASS    AF=0.00584745   ES:SE:LP:AF:SS:ID   0.0354583:0.0267203:0.733978:0.00584745:35558:rs184270342
1   755890  rs3115858   A   T   .   PASS    AF=0.867706 ES:SE:LP:AF:SS:ID   0.00119952:0.00547803:0.0826652:0.867706:35558:rs3115858
1   756434  rs61768170  G   C   .   PASS    AF=0.128675 ES:SE:LP:AF:SS:ID   -0.00139075:0.00558567:0.0950828:0.128675:35558:rs61768170
1   756604  rs3131962   A   G   .   PASS    AF=0.867189 ES:SE:LP:AF:SS:ID   0.00113891:0.00546329:0.0783832:0.867189:35558:rs3131962
1   757640  rs3115853   G   A   .   PASS    AF=0.866619 ES:SE:LP:AF:SS:ID   0.000657914:0.00545966:0.0437912:0.866619:35558:rs3115853
1   757734  rs4951929   C   T   .   PASS    AF=0.867383 ES:SE:LP:AF:SS:ID   0.000986159:0.00546883:0.0670699:0.867383:35558:rs4951929
1   757936  rs4951862   C   A   .   PASS    AF=0.86739  ES:SE:LP:AF:SS:ID   0.000998284:0.00546919:0.0679481:0.86739:35558:rs4951862
1   758144  rs3131956   A   G   .   PASS    AF=0.867392 ES:SE:LP:AF:SS:ID   0.000991829:0.00546921:0.0674775:0.867392:35558:rs3131956
1   758626  rs3131954   C   T   .   PASS    AF=0.867842 ES:SE:LP:AF:SS:ID   0.00119881:0.005483:0.0825313:0.867842:35558:rs3131954
1   759293  rs10157329  T   A   .   PASS    AF=0.100634 ES:SE:LP:AF:SS:ID   -0.00207836:0.00636692:0.128368:0.100634:35558:rs10157329
1   759600  rs545998451 AGT A   .   PASS    AF=0.00680595   ES:SE:LP:AF:SS:ID   0.0382676:0.0241606:0.946042:0.00680595:35558:1_759600_AGT_A
1   759837  rs3115851   T   A   .   PASS    AF=0.872119 ES:SE:LP:AF:SS:ID   0.00172173:0.00556576:0.120869:0.872119:35558:rs3115851
1   761732  rs2286139   C   T   .   PASS    AF=0.861036 ES:SE:LP:AF:SS:ID   0.00043635:0.00545276:0.0286225:0.861036:35558:rs2286139
1   761752  rs1057213   C   T   .   PASS    AF=0.866757 ES:SE:LP:AF:SS:ID   0.00121003:0.00551563:0.0828339:0.866757:35558:rs1057213
1   762273  rs3115849   G   A   .   PASS    AF=0.863799 ES:SE:LP:AF:SS:ID   0.00138019:0.00551391:0.0956367:0.863799:35558:rs3115849
1   762485  rs12095200  C   A   .   PASS    AF=0.101023 ES:SE:LP:AF:SS:ID   -9.68314e-06:0.00658099:0.000510161:0.101023:35558:rs12095200
1   762589  rs3115848   G   C   .   PASS    AF=0.868993 ES:SE:LP:AF:SS:ID   0.00199636:0.00557279:0.142564:0.868993:35558:rs3115848
1   762592  rs3131950   C   G   .   PASS    AF=0.868993 ES:SE:LP:AF:SS:ID   0.00199664:0.00557279:0.142587:0.868993:35558:rs3131950
1   762601  rs3131949   T   C   .   PASS    AF=0.86899  ES:SE:LP:AF:SS:ID   0.00199832:0.0055728:0.142723:0.86899:35558:rs3131949
1   762632  rs3131948   T   A   .   PASS    AF=0.869382 ES:SE:LP:AF:SS:ID   0.00222976:0.00557633:0.161616:0.869382:35558:rs3131948
1   764191  rs7515915   T   G   .   PASS    AF=0.12808  ES:SE:LP:AF:SS:ID   -0.00256538:0.0055839:0.189813:0.12808:35558:rs7515915
1   766007  rs61768174  A   C   .   PASS    AF=0.107018 ES:SE:LP:AF:SS:ID   -0.00373757:0.0060842:0.268398:0.107018:35558:rs61768174
1   766105  rs2519015   T   A   .   PASS    AF=0.852759 ES:SE:LP:AF:SS:ID   0.00311462:0.00545011:0.245897:0.852759:35558:rs2519015
1   767393  rs538667473 A   C   .   PASS    AF=0.00172477   ES:SE:LP:AF:SS:ID   -0.0609786:0.0479831:0.690804:0.00172477:35558:rs538667473
1   768116  rs376645387 A   AGTTTT  .   PASS    AF=0.837784 ES:SE:LP:AF:SS:ID   -0.000838109:0.00542313:0.0569103:0.837784:35558:rs376645387