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-22640_9/ukb-d-22640_9.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-22640_9/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 16:36:39 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-22640_9/ukb-d-22640_9.vcf.gz ...
Read summary statistics for 13031556 SNPs.
Dropped 11928 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, 1283393 SNPs remain.
After merging with regression SNP LD, 1283393 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0269 (0.0163)
Lambda GC: 1.021
Mean Chi^2: 1.0117
Intercept: 0.9982 (0.0057)
Ratio < 0 (usually indicates GC correction).
Analysis finished at Mon Nov 25 16:38:42 2019
Total time elapsed: 2.0m:2.46s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9512,
    "inflation_factor": 1.0097,
    "mean_EFFECT": -0.0001,
    "n": 25697,
    "n_snps": 13031556,
    "n_clumped_hits": 0,
    "n_p_sig": 0,
    "n_mono": 0,
    "n_ns": 1230339,
    "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": 439303,
    "n_est": 25864.4282,
    "ratio_se_n": 1.0033,
    "mean_diff": -0.0001,
    "ratio_diff": 9.7633,
    "sd_y_est1": 0.4668,
    "sd_y_est2": 0.4683,
    "r2_sum1": 0,
    "r2_sum2": 0,
    "r2_sum3": 0,
    "r2_sum4": 0,
    "ldsc_nsnp_merge_refpanel_ld": 1283393,
    "ldsc_nsnp_merge_regression_ld": 1283393,
    "ldsc_observed_scale_h2_beta": 0.0269,
    "ldsc_observed_scale_h2_se": 0.0163,
    "ldsc_intercept_beta": 0.9982,
    "ldsc_intercept_se": 0.0057,
    "ldsc_lambda_gc": 1.021,
    "ldsc_mean_chisq": 1.0117,
    "ldsc_ratio": -0.1538
}

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 13020281 0 NA NA NA NA NA NA NA NA
character REF 0 1.0000000 1 100 0 55893 0 NA NA NA NA NA NA NA NA
character ALT 0 1.0000000 1 342 0 32963 0 NA NA NA NA NA NA NA NA
numeric CHROM 0 1.0000000 NA NA NA NA NA 9.057601e+00 6.185730e+00 1.0000e+00 4.000000e+00 8.000000e+00 1.300000e+01 2.300000e+01 ▇▅▅▂▂
numeric POS 0 1.0000000 NA NA NA NA NA 7.898377e+07 5.593597e+07 3.0200e+02 3.284665e+07 7.006543e+07 1.148221e+08 2.492309e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA -5.910000e-05 2.093650e-02 -2.4289e-01 -6.073900e-03 -2.810000e-05 5.978200e-03 2.786800e-01 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 1.539810e-02 1.416980e-02 3.2979e-03 4.857000e-03 8.473300e-03 2.184990e-02 8.280490e-02 ▇▂▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.984457e-01 2.888107e-01 4.0000e-07 2.481070e-01 4.979331e-01 7.482694e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.984395e-01 2.888145e-01 4.0000e-07 2.480963e-01 4.979273e-01 7.482673e-01 9.999999e-01 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA 1.984921e-01 2.562260e-01 1.4264e-03 9.561400e-03 6.995700e-02 3.105640e-01 9.985740e-01 ▇▂▁▁▁
numeric AF_reference 439303 0.9662893 NA NA NA NA NA 2.022579e-01 2.483906e-01 0.0000e+00 6.988800e-03 9.245210e-02 3.192890e-01 1.000000e+00 ▇▂▁▁▁
numeric N 0 1.0000000 NA NA NA NA NA 2.569700e+04 0.000000e+00 2.5697e+04 2.569700e+04 2.569700e+04 2.569700e+04 2.569700e+04 ▁▁▇▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 692794 rs530212009 CA C 0.0013557 0.0071646 0.8499230 0.8499219 0.1121430 0.1894970 25697
1 693731 rs12238997 A G 0.0024142 0.0068420 0.7241991 0.7241965 0.1165660 0.1417730 25697
1 707522 rs371890604 G C 0.0051210 0.0077024 0.5061439 0.5061382 0.0975760 0.1293930 25697
1 717587 rs144155419 G A 0.0017053 0.0181530 0.9251569 0.9251561 0.0160183 0.0045926 25697
1 723329 rs189787166 A T 0.0316814 0.0503016 0.5288116 0.5288066 0.0019672 0.0003994 25697
1 730087 rs148120343 T C -0.0068075 0.0093972 0.4688166 0.4688106 0.0579332 0.0127796 25697
1 731718 rs142557973 T C 0.0005367 0.0064842 0.9340401 0.9340397 0.1229090 0.1543530 25697
1 732032 rs61770163 A C -0.0008338 0.0069082 0.9039310 0.9039305 0.1227700 0.1555510 25697
1 734349 rs141242758 T C 0.0005430 0.0064880 0.9333031 0.9333027 0.1221900 0.1525560 25697
1 740284 rs61770167 C T 0.0273058 0.0307453 0.3744786 0.3744712 0.0054168 0.0023962 25697
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
23 154923311 rs141127553 C T -0.0028587 0.0072357 0.6927826 0.6927794 0.0569276 0.0309934 25697
23 154923374 rs111332691 T A 0.0006220 0.0080146 0.9381420 0.9381417 0.0445188 0.0116556 25697
23 154925045 rs509981 C T 0.0027511 0.0038845 0.4788098 0.4788037 0.2412010 0.3634440 25697
23 154925895 rs538470 C T 0.0031929 0.0039697 0.4212249 0.4212173 0.2377450 0.3634440 25697
23 154927581 rs644138 G A 0.0015144 0.0036396 0.6773513 0.6773481 0.2986200 0.4635760 25697
23 154929412 rs557132 C T 0.0027595 0.0038863 0.4776777 0.4776716 0.2409870 0.3568210 25697
23 154929637 rs35185538 CT C 0.0008763 0.0040494 0.8286810 0.8286790 0.2268160 0.3011920 25697
23 154929952 rs4012982 CAA C 0.0037091 0.0040909 0.3645818 0.3645735 0.2348550 0.3165560 25697
23 154930230 rs781880 A G 0.0028230 0.0038837 0.4673099 0.4673039 0.2415200 0.3618540 25697
23 154930487 rs781879 T A -0.0002578 0.0134771 0.9847410 0.9847411 0.0189835 0.1263580 25697

bcf preview

1   692794  rs530212009 CA  C   .   PASS    AF=0.112143 ES:SE:LP:AF:SS:ID   0.00135567:0.00716459:0.0706204:0.112143:25697:1_692794_CA_C
1   693731  rs12238997  A   G   .   PASS    AF=0.116566 ES:SE:LP:AF:SS:ID   0.00241424:0.006842:0.140142:0.116566:25697:rs12238997
1   707522  rs371890604 G   C   .   PASS    AF=0.097576 ES:SE:LP:AF:SS:ID   0.00512104:0.0077024:0.295726:0.097576:25697:rs371890604
1   717587  rs144155419 G   A   .   PASS    AF=0.0160183    ES:SE:LP:AF:SS:ID   0.00170531:0.018153:0.0337846:0.0160183:25697:rs144155419
1   723329  rs189787166 A   T   .   PASS    AF=0.00196719   ES:SE:LP:AF:SS:ID   0.0316814:0.0503016:0.276699:0.00196719:25697:rs189787166
1   730087  rs148120343 T   C   .   PASS    AF=0.0579332    ES:SE:LP:AF:SS:ID   -0.0068075:0.00939723:0.328997:0.0579332:25697:rs148120343
1   731718  rs58276399  T   C   .   PASS    AF=0.122909 ES:SE:LP:AF:SS:ID   0.000536657:0.00648423:0.0296345:0.122909:25697:rs58276399
1   732032  rs61770163  A   C   .   PASS    AF=0.12277  ES:SE:LP:AF:SS:ID   -0.000833806:0.00690822:0.0438647:0.12277:25697:rs61770163
1   734349  rs141242758 T   C   .   PASS    AF=0.12219  ES:SE:LP:AF:SS:ID   0.000542984:0.00648802:0.0299773:0.12219:25697:rs141242758
1   740284  rs61770167  C   T   .   PASS    AF=0.00541682   ES:SE:LP:AF:SS:ID   0.0273058:0.0307453:0.426573:0.00541682:25697:rs61770167
1   742813  rs112573343 C   T   .   PASS    AF=0.00179627   ES:SE:LP:AF:SS:ID   0.0339769:0.0574109:0.256509:0.00179627:25697:rs112573343
1   749963  rs529266287 T   TAA .   PASS    AF=0.867932 ES:SE:LP:AF:SS:ID   -0.00331704:0.00636883:0.220047:0.867932:25697:rs529266287
1   750230  rs190826124 G   C   .   PASS    AF=0.0017537    ES:SE:LP:AF:SS:ID   -0.0354217:0.0532779:0.295717:0.0017537:25697:rs190826124
1   751343  rs28544273  T   A   .   PASS    AF=0.12446  ES:SE:LP:AF:SS:ID   0.00162655:0.00631759:0.0986381:0.12446:25697:rs28544273
1   751488  rs200141114 G   GA  .   PASS    AF=0.143673 ES:SE:LP:AF:SS:ID   0.00169197:0.00626315:0.103998:0.143673:25697:rs200141114
1   751756  rs28527770  T   C   .   PASS    AF=0.124586 ES:SE:LP:AF:SS:ID   0.00141357:0.00630964:0.0847411:0.124586:25697:rs28527770
1   753405  rs3115860   C   A   .   PASS    AF=0.869298 ES:SE:LP:AF:SS:ID   -0.00167939:0.00615559:0.105135:0.869298:25697:rs3115860
1   753425  rs3131970   T   C   .   PASS    AF=0.873888 ES:SE:LP:AF:SS:ID   -0.00286724:0.00625093:0.189458:0.873888:25697:rs3131970
1   753541  rs2073813   G   A   .   PASS    AF=0.130223 ES:SE:LP:AF:SS:ID   0.00204838:0.00617452:0.13072:0.130223:25697:rs2073813
1   754105  rs12184325  C   T   .   PASS    AF=0.0356073    ES:SE:LP:AF:SS:ID   -0.00345515:0.0112904:0.119422:0.0356073:25697:rs12184325
1   754182  rs3131969   A   G   .   PASS    AF=0.86893  ES:SE:LP:AF:SS:ID   -0.00204606:0.00615112:0.131112:0.86893:25697:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.869072 ES:SE:LP:AF:SS:ID   -0.0019568:0.00615463:0.12463:0.869072:25697:rs3131968
1   754334  rs3131967   T   C   .   PASS    AF=0.868931 ES:SE:LP:AF:SS:ID   -0.00205746:0.00615091:0.131939:0.868931:25697:rs3131967
1   754433  rs150578204 G   A   .   PASS    AF=0.0049226    ES:SE:LP:AF:SS:ID   0.0260315:0.0322237:0.377586:0.0049226:25697:rs150578204
1   754458  rs142682604 G   T   .   PASS    AF=0.00489216   ES:SE:LP:AF:SS:ID   0.025884:0.0322997:0.373737:0.00489216:25697:rs142682604
1   755435  rs184270342 T   G   .   PASS    AF=0.00561735   ES:SE:LP:AF:SS:ID   -0.034814:0.030172:0.60455:0.00561735:25697:rs184270342
1   755890  rs3115858   A   T   .   PASS    AF=0.868988 ES:SE:LP:AF:SS:ID   -0.0019568:0.00613884:0.124989:0.868988:25697:rs3115858
1   756434  rs61768170  G   C   .   PASS    AF=0.127576 ES:SE:LP:AF:SS:ID   0.00196554:0.0062606:0.122883:0.127576:25697:rs61768170
1   756604  rs3131962   A   G   .   PASS    AF=0.868487 ES:SE:LP:AF:SS:ID   -0.00172434:0.00612289:0.108889:0.868487:25697:rs3131962
1   757640  rs3115853   G   A   .   PASS    AF=0.867984 ES:SE:LP:AF:SS:ID   -0.00205282:0.00612249:0.132292:0.867984:25697:rs3115853
1   757734  rs4951929   C   T   .   PASS    AF=0.868672 ES:SE:LP:AF:SS:ID   -0.00175135:0.00612769:0.110683:0.868672:25697:rs4951929
1   757936  rs4951862   C   A   .   PASS    AF=0.868677 ES:SE:LP:AF:SS:ID   -0.00174924:0.00612805:0.110529:0.868677:25697:rs4951862
1   758144  rs3131956   A   G   .   PASS    AF=0.868677 ES:SE:LP:AF:SS:ID   -0.00174055:0.00612806:0.10992:0.868677:25697:rs3131956
1   758626  rs3131954   C   T   .   PASS    AF=0.86918  ES:SE:LP:AF:SS:ID   -0.00161076:0.00614628:0.10058:0.86918:25697:rs3131954
1   759293  rs10157329  T   A   .   PASS    AF=0.09951  ES:SE:LP:AF:SS:ID   0.00382778:0.00716191:0.226926:0.09951:25697:rs10157329
1   759600  rs545998451 AGT A   .   PASS    AF=0.00646211   ES:SE:LP:AF:SS:ID   -0.0408445:0.0274428:0.864327:0.00646211:25697:1_759600_AGT_A
1   759837  rs3115851   T   A   .   PASS    AF=0.873078 ES:SE:LP:AF:SS:ID   -0.00241031:0.00623236:0.155553:0.873078:25697:rs3115851
1   761732  rs2286139   C   T   .   PASS    AF=0.862503 ES:SE:LP:AF:SS:ID   -0.00275466:0.00611505:0.185503:0.862503:25697:rs2286139
1   761752  rs1057213   C   T   .   PASS    AF=0.867879 ES:SE:LP:AF:SS:ID   -0.00147116:0.00617437:0.0906178:0.867879:25697:rs1057213
1   762273  rs3115849   G   A   .   PASS    AF=0.86493  ES:SE:LP:AF:SS:ID   -0.00101504:0.00618119:0.0606984:0.86493:25697:rs3115849
1   762485  rs12095200  C   A   .   PASS    AF=0.0994497    ES:SE:LP:AF:SS:ID   0.00572934:0.00740531:0.35741:0.0994497:25697:rs12095200
1   762589  rs3115848   G   C   .   PASS    AF=0.870274 ES:SE:LP:AF:SS:ID   -0.00135607:0.00625166:0.0818239:0.870274:25697:rs3115848
1   762592  rs3131950   C   G   .   PASS    AF=0.870274 ES:SE:LP:AF:SS:ID   -0.00135536:0.00625166:0.0817777:0.870274:25697:rs3131950
1   762601  rs3131949   T   C   .   PASS    AF=0.870271 ES:SE:LP:AF:SS:ID   -0.00135442:0.00625168:0.0817159:0.870271:25697:rs3131949
1   762632  rs3131948   T   A   .   PASS    AF=0.870593 ES:SE:LP:AF:SS:ID   -0.00110562:0.00625297:0.0656758:0.870593:25697:rs3131948
1   764191  rs7515915   T   G   .   PASS    AF=0.12718  ES:SE:LP:AF:SS:ID   0.00216232:0.0062543:0.136947:0.12718:25697:rs7515915
1   766007  rs61768174  A   C   .   PASS    AF=0.106621 ES:SE:LP:AF:SS:ID   0.00145357:0.00679891:0.0805511:0.106621:25697:rs61768174
1   766105  rs2519015   T   A   .   PASS    AF=0.853855 ES:SE:LP:AF:SS:ID   -0.00231431:0.00609624:0.15229:0.853855:25697:rs2519015
1   767393  rs538667473 A   C   .   PASS    AF=0.00184915   ES:SE:LP:AF:SS:ID   0.0369537:0.050612:0.332255:0.00184915:25697:rs538667473
1   768116  rs376645387 A   AGTTTT  .   PASS    AF=0.838998 ES:SE:LP:AF:SS:ID   0.00245284:0.006042:0.164454:0.838998:25697:rs376645387