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-680_3/ukb-d-680_3.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-680_3/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 17:17:07 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-680_3/ukb-d-680_3.vcf.gz ...
Read summary statistics for 13586422 SNPs.
Dropped 12710 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, 1283504 SNPs remain.
After merging with regression SNP LD, 1283504 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0362 (0.0019)
Lambda GC: 1.2455
Mean Chi^2: 1.2644
Intercept: 1.0139 (0.0073)
Ratio: 0.0526 (0.0276)
Analysis finished at Mon Nov 25 17:19:25 2019
Total time elapsed: 2.0m:17.82s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9521,
    "inflation_factor": 1.1537,
    "mean_EFFECT": 0,
    "n": 356340,
    "n_snps": 13586422,
    "n_clumped_hits": 2,
    "n_p_sig": 28,
    "n_mono": 0,
    "n_ns": 1251804,
    "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": 569270,
    "n_est": 357696.9983,
    "ratio_se_n": 1.0019,
    "mean_diff": 0.0001,
    "ratio_diff": 103.2242,
    "sd_y_est1": 0.2248,
    "sd_y_est2": 0.2252,
    "r2_sum1": 9.1974e-06,
    "r2_sum2": 0.0002,
    "r2_sum3": 0.0002,
    "r2_sum4": 0.0002,
    "ldsc_nsnp_merge_refpanel_ld": 1283504,
    "ldsc_nsnp_merge_regression_ld": 1283504,
    "ldsc_observed_scale_h2_beta": 0.0362,
    "ldsc_observed_scale_h2_se": 0.0019,
    "ldsc_intercept_beta": 1.0139,
    "ldsc_intercept_se": 0.0073,
    "ldsc_lambda_gc": 1.2455,
    "ldsc_mean_chisq": 1.2644,
    "ldsc_ratio": 0.0526
}

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 13574376 0 NA NA NA NA NA NA NA NA
character REF 0 1.0000000 1 100 0 57082 0 NA NA NA NA NA NA NA NA
character ALT 0 1.0000000 1 342 0 33338 0 NA NA NA NA NA NA NA NA
numeric CHROM 0 1.0000000 NA NA NA NA NA 9.051366e+00 6.184982e+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 7.902493e+07 5.591491e+07 3.02000e+02 3.293086e+07 7.013794e+07 1.148588e+08 2.492309e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA 2.910000e-05 3.163600e-03 -3.41769e-02 -8.898000e-04 8.000000e-06 9.070000e-04 4.367920e-02 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 2.237400e-03 2.158200e-03 4.37800e-04 6.370000e-04 1.173800e-03 3.215400e-03 1.083900e-02 ▇▂▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.769954e-01 2.950658e-01 0.00000e+00 2.157739e-01 4.687832e-01 7.327317e-01 1.000000e+00 ▇▇▆▆▆
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.769950e-01 2.950660e-01 0.00000e+00 2.157730e-01 4.687827e-01 7.327313e-01 1.000000e+00 ▇▇▆▆▆
numeric AF 0 1.0000000 NA NA NA NA NA 1.908044e-01 2.544032e-01 1.00000e-03 7.429700e-03 6.003140e-02 2.953050e-01 9.990000e-01 ▇▂▁▁▁
numeric AF_reference 569270 0.9581001 NA NA NA NA NA 1.963353e-01 2.471016e-01 0.00000e+00 5.591000e-03 8.426520e-02 3.081070e-01 1.000000e+00 ▇▂▁▁▁
numeric N 0 1.0000000 NA NA NA NA NA 3.563400e+05 0.000000e+00 3.56340e+05 3.563400e+05 3.563400e+05 3.563400e+05 3.563400e+05 ▁▁▇▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 692794 rs530212009 CA C -0.0000258 0.0009325 0.9779520 0.9779520 0.1106480 0.1894970 356340
1 693731 rs12238997 A G 0.0000760 0.0008813 0.9312689 0.9312686 0.1157970 0.1417730 356340
1 707522 rs371890604 G C 0.0003138 0.0009907 0.7514568 0.7514556 0.0972849 0.1293930 356340
1 717587 rs144155419 G A -0.0032150 0.0023639 0.1738209 0.1738207 0.0156800 0.0045926 356340
1 723329 rs189787166 A T 0.0019348 0.0069469 0.7806242 0.7806235 0.0017455 0.0003994 356340
1 730087 rs148120343 T C 0.0009013 0.0012276 0.4628231 0.4628230 0.0564590 0.0127796 356340
1 731718 rs142557973 T C 0.0003801 0.0008357 0.6492351 0.6492352 0.1217310 0.1543530 356340
1 732032 rs61770163 A C 0.0003781 0.0008915 0.6714783 0.6714781 0.1211470 0.1555510 356340
1 734349 rs141242758 T C 0.0003400 0.0008362 0.6842676 0.6842665 0.1209580 0.1525560 356340
1 740284 rs61770167 C T -0.0007403 0.0038176 0.8462440 0.8462445 0.0058056 0.0023962 356340
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
23 154923311 rs141127553 C T -0.0009710 0.0009649 0.3142722 0.3142713 0.0562156 0.0309934 356340
23 154923374 rs111332691 T A 0.0009511 0.0010610 0.3699951 0.3699942 0.0448027 0.0116556 356340
23 154925045 rs509981 C T -0.0009071 0.0005107 0.0756711 0.0756707 0.2454610 0.3634440 356340
23 154925895 rs538470 C T -0.0009809 0.0005224 0.0604102 0.0604095 0.2417790 0.3634440 356340
23 154927581 rs644138 G A -0.0009964 0.0004802 0.0379708 0.0379701 0.3020610 0.4635760 356340
23 154929412 rs557132 C T -0.0009012 0.0005108 0.0776998 0.0776982 0.2453120 0.3568210 356340
23 154929637 rs35185538 CT C -0.0007010 0.0005331 0.1885389 0.1885386 0.2295890 0.3011920 356340
23 154929952 rs4012982 CAA C -0.0009791 0.0005372 0.0683675 0.0683662 0.2392680 0.3165560 356340
23 154930230 rs781880 A G -0.0009489 0.0005107 0.0631771 0.0631760 0.2457230 0.3618540 356340
23 154930487 rs781879 T A 0.0012538 0.0017528 0.4744386 0.4744385 0.0195351 0.1263580 356340

bcf preview

1   692794  rs530212009 CA  C   .   PASS    AF=0.110648 ES:SE:LP:AF:SS:ID   -2.57705e-05:0.000932478:0.00968246:0.110648:356340:1_692794_CA_C
1   693731  rs12238997  A   G   .   PASS    AF=0.115797 ES:SE:LP:AF:SS:ID   7.60116e-05:0.000881306:0.0309249:0.115797:356340:rs12238997
1   707522  rs371890604 G   C   .   PASS    AF=0.0972849    ES:SE:LP:AF:SS:ID   0.000313777:0.000990706:0.124096:0.0972849:356340:rs371890604
1   717587  rs144155419 G   A   .   PASS    AF=0.01568  ES:SE:LP:AF:SS:ID   -0.003215:0.00236392:0.759898:0.01568:356340:rs144155419
1   723329  rs189787166 A   T   .   PASS    AF=0.00174548   ES:SE:LP:AF:SS:ID   0.00193476:0.00694691:0.107558:0.00174548:356340:rs189787166
1   730087  rs148120343 T   C   .   PASS    AF=0.056459 ES:SE:LP:AF:SS:ID   0.000901319:0.00122761:0.334585:0.056459:356340:rs148120343
1   731718  rs58276399  T   C   .   PASS    AF=0.121731 ES:SE:LP:AF:SS:ID   0.000380109:0.000835726:0.187598:0.121731:356340:rs58276399
1   732032  rs61770163  A   C   .   PASS    AF=0.121147 ES:SE:LP:AF:SS:ID   0.000378102:0.000891497:0.172968:0.121147:356340:rs61770163
1   734349  rs141242758 T   C   .   PASS    AF=0.120958 ES:SE:LP:AF:SS:ID   0.000340033:0.000836185:0.164774:0.120958:356340:rs141242758
1   740284  rs61770167  C   T   .   PASS    AF=0.0058056    ES:SE:LP:AF:SS:ID   -0.000740272:0.00381756:0.0725044:0.0058056:356340:rs61770167
1   742813  rs112573343 C   T   .   PASS    AF=0.00187615   ES:SE:LP:AF:SS:ID   0.00483631:0.0072272:0.298104:0.00187615:356340:rs112573343
1   749963  rs529266287 T   TAA .   PASS    AF=0.869751 ES:SE:LP:AF:SS:ID   -0.000482315:0.000824376:0.252974:0.869751:356340:rs529266287
1   750230  rs190826124 G   C   .   PASS    AF=0.00152269   ES:SE:LP:AF:SS:ID   -0.00821982:0.00748184:0.565546:0.00152269:356340:rs190826124
1   751343  rs28544273  T   A   .   PASS    AF=0.122921 ES:SE:LP:AF:SS:ID   0.000623519:0.000816372:0.351634:0.122921:356340:rs28544273
1   751488  rs200141114 G   GA  .   PASS    AF=0.142704 ES:SE:LP:AF:SS:ID   0.000679599:0.000806957:0.398277:0.142704:356340:rs200141114
1   751756  rs28527770  T   C   .   PASS    AF=0.123036 ES:SE:LP:AF:SS:ID   0.000626669:0.000815237:0.354504:0.123036:356340:rs28527770
1   753405  rs3115860   C   A   .   PASS    AF=0.870892 ES:SE:LP:AF:SS:ID   -0.000781125:0.000794416:0.487481:0.870892:356340:rs3115860
1   753425  rs3131970   T   C   .   PASS    AF=0.875468 ES:SE:LP:AF:SS:ID   -0.000539677:0.000807594:0.297594:0.875468:356340:rs3131970
1   753541  rs2073813   G   A   .   PASS    AF=0.128631 ES:SE:LP:AF:SS:ID   0.000755568:0.000796397:0.465014:0.128631:356340:rs2073813
1   754105  rs12184325  C   T   .   PASS    AF=0.0363599    ES:SE:LP:AF:SS:ID   0.0028941:0.00144467:1.34537:0.0363599:356340:rs12184325
1   754182  rs3131969   A   G   .   PASS    AF=0.870484 ES:SE:LP:AF:SS:ID   -0.000766919:0.000793586:0.476454:0.870484:356340:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.870586 ES:SE:LP:AF:SS:ID   -0.000762286:0.000793933:0.472388:0.870586:356340:rs3131968
1   754334  rs3131967   T   C   .   PASS    AF=0.870482 ES:SE:LP:AF:SS:ID   -0.000791399:0.000793556:0.496715:0.870482:356340:rs3131967
1   754433  rs150578204 G   A   .   PASS    AF=0.00504061   ES:SE:LP:AF:SS:ID   0.00122789:0.00407509:0.117376:0.00504061:356340:rs150578204
1   754458  rs142682604 G   T   .   PASS    AF=0.00500754   ES:SE:LP:AF:SS:ID   0.00119035:0.00408601:0.113056:0.00500754:356340:rs142682604
1   755435  rs184270342 T   G   .   PASS    AF=0.00555675   ES:SE:LP:AF:SS:ID   -0.00156097:0.00395649:0.15915:0.00555675:356340:rs184270342
1   755890  rs3115858   A   T   .   PASS    AF=0.870565 ES:SE:LP:AF:SS:ID   -0.000823967:0.000792157:0.525393:0.870565:356340:rs3115858
1   756434  rs61768170  G   C   .   PASS    AF=0.125983 ES:SE:LP:AF:SS:ID   0.000822533:0.000808314:0.51022:0.125983:356340:rs61768170
1   756604  rs3131962   A   G   .   PASS    AF=0.870131 ES:SE:LP:AF:SS:ID   -0.000817883:0.000790263:0.521877:0.870131:356340:rs3131962
1   757640  rs3115853   G   A   .   PASS    AF=0.869417 ES:SE:LP:AF:SS:ID   -0.000862008:0.000789533:0.560787:0.869417:356340:rs3115853
1   757734  rs4951929   C   T   .   PASS    AF=0.870287 ES:SE:LP:AF:SS:ID   -0.000832849:0.000790948:0.534092:0.870287:356340:rs4951929
1   757936  rs4951862   C   A   .   PASS    AF=0.870293 ES:SE:LP:AF:SS:ID   -0.000831371:0.000791005:0.532771:0.870293:356340:rs4951862
1   758144  rs3131956   A   G   .   PASS    AF=0.870301 ES:SE:LP:AF:SS:ID   -0.000834066:0.00079103:0.535067:0.870301:356340:rs3131956
1   758626  rs3131954   C   T   .   PASS    AF=0.870742 ES:SE:LP:AF:SS:ID   -0.000819617:0.000793032:0.520914:0.870742:356340:rs3131954
1   759293  rs10157329  T   A   .   PASS    AF=0.0988331    ES:SE:LP:AF:SS:ID   0.000904307:0.000921638:0.486121:0.0988331:356340:rs10157329
1   759600  rs545998451 AGT A   .   PASS    AF=0.00645051   ES:SE:LP:AF:SS:ID   -0.0038297:0.00357194:0.54722:0.00645051:356340:1_759600_AGT_A
1   759837  rs3115851   T   A   .   PASS    AF=0.87464  ES:SE:LP:AF:SS:ID   -0.000439207:0.000804883:0.23263:0.87464:356340:rs3115851
1   761732  rs2286139   C   T   .   PASS    AF=0.864041 ES:SE:LP:AF:SS:ID   -0.00091507:0.000789293:0.608513:0.864041:356340:rs2286139
1   761752  rs1057213   C   T   .   PASS    AF=0.869434 ES:SE:LP:AF:SS:ID   -0.000608601:0.000796974:0.35156:0.869434:356340:rs1057213
1   762273  rs3115849   G   A   .   PASS    AF=0.866374 ES:SE:LP:AF:SS:ID   -0.000623892:0.000797115:0.362699:0.866374:356340:rs3115849
1   762485  rs12095200  C   A   .   PASS    AF=0.098777 ES:SE:LP:AF:SS:ID   0.000441902:0.000954395:0.191551:0.098777:356340:rs12095200
1   762589  rs3115848   G   C   .   PASS    AF=0.87156  ES:SE:LP:AF:SS:ID   -0.000413045:0.000806216:0.215794:0.87156:356340:rs3115848
1   762592  rs3131950   C   G   .   PASS    AF=0.87156  ES:SE:LP:AF:SS:ID   -0.000413068:0.000806216:0.215808:0.87156:356340:rs3131950
1   762601  rs3131949   T   C   .   PASS    AF=0.87156  ES:SE:LP:AF:SS:ID   -0.000413062:0.000806232:0.215799:0.87156:356340:rs3131949
1   762632  rs3131948   T   A   .   PASS    AF=0.871936 ES:SE:LP:AF:SS:ID   -0.000385976:0.000806692:0.199064:0.871936:356340:rs3131948
1   764191  rs7515915   T   G   .   PASS    AF=0.12556  ES:SE:LP:AF:SS:ID   0.000575003:0.000807309:0.322108:0.12556:356340:rs7515915
1   766007  rs61768174  A   C   .   PASS    AF=0.10543  ES:SE:LP:AF:SS:ID   0.00118878:0.000878852:0.754078:0.10543:356340:rs61768174
1   766105  rs2519015   T   A   .   PASS    AF=0.855374 ES:SE:LP:AF:SS:ID   -0.00045394:0.000788968:0.247914:0.855374:356340:rs2519015
1   767393  rs538667473 A   C   .   PASS    AF=0.00166613   ES:SE:LP:AF:SS:ID   0.00242416:0.00696179:0.138057:0.00166613:356340:rs538667473
1   768116  rs376645387 A   AGTTTT  .   PASS    AF=0.838431 ES:SE:LP:AF:SS:ID   0.000211751:0.000777438:0.104944:0.838431:356340:rs376645387