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-30850_raw/ukb-d-30850_raw.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-30850_raw/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 14:54:05 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-30850_raw/ukb-d-30850_raw.vcf.gz ...
Read summary statistics for 13585068 SNPs.
Dropped 12707 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, 1283501 SNPs remain.
After merging with regression SNP LD, 1283501 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0901 (0.0157)
Lambda GC: 1.2989
Mean Chi^2: 1.5951
Intercept: 1.0455 (0.0113)
Ratio: 0.0764 (0.0189)
Analysis finished at Mon Nov 25 14:56:23 2019
Total time elapsed: 2.0m:18.17s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9521,
    "inflation_factor": 1.2038,
    "mean_EFFECT": 0,
    "n": 312102,
    "n_snps": 13585068,
    "n_clumped_hits": 122,
    "n_p_sig": 27448,
    "n_mono": 0,
    "n_ns": 1251749,
    "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": 568966,
    "n_est": 313515.2601,
    "ratio_se_n": 1.0023,
    "mean_diff": -0,
    "ratio_diff": 6.1685,
    "sd_y_est1": 2.6795,
    "sd_y_est2": 2.6855,
    "r2_sum1": 0.2827,
    "r2_sum2": 0.0394,
    "r2_sum3": 0.0392,
    "r2_sum4": 0.0386,
    "ldsc_nsnp_merge_refpanel_ld": 1283501,
    "ldsc_nsnp_merge_regression_ld": 1283501,
    "ldsc_observed_scale_h2_beta": 0.0901,
    "ldsc_observed_scale_h2_se": 0.0157,
    "ldsc_intercept_beta": 1.0455,
    "ldsc_intercept_se": 0.0113,
    "ldsc_lambda_gc": 1.2989,
    "ldsc_mean_chisq": 1.5951,
    "ldsc_ratio": 0.0765
}

Flags

name value
af_correlation FALSE
inflation_factor TRUE
n FALSE
is_snpid_non_unique TRUE
mean_EFFECT_nonfinite FALSE
mean_EFFECT_05 FALSE
mean_EFFECT_01 FALSE
mean_chisq TRUE
n_p_sig TRUE
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 13573025 0 NA NA NA NA NA NA NA NA
character REF 0 1.0000000 1 100 0 57081 0 NA NA NA NA NA NA NA NA
character ALT 0 1.0000000 1 342 0 33337 0 NA NA NA NA NA NA NA NA
numeric CHROM 0 1.0000000 NA NA NA NA NA 9.051273e+00 6.184938e+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 7.902581e+07 5.591529e+07 3.02000e+02 3.293089e+07 7.013920e+07 1.148611e+08 2.492309e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA 2.420000e-05 4.103510e-02 -1.34170e+00 -1.192400e-02 -6.930000e-05 1.176000e-02 8.726600e-01 ▁▁▂▇▁
numeric SE 0 1.0000000 NA NA NA NA NA 2.849150e-02 2.748560e-02 5.49860e-03 8.114200e-03 1.495000e-02 4.093500e-02 1.394600e-01 ▇▂▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.687425e-01 2.985226e-01 0.00000e+00 2.020999e-01 4.592805e-01 7.276206e-01 1.000000e+00 ▇▆▆▆▆
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.687420e-01 2.985229e-01 0.00000e+00 2.021013e-01 4.592775e-01 7.276205e-01 9.999998e-01 ▇▆▆▆▆
numeric AF 0 1.0000000 NA NA NA NA NA 1.908226e-01 2.544084e-01 1.00000e-03 7.433500e-03 6.005700e-02 2.953400e-01 9.990000e-01 ▇▂▁▁▁
numeric AF_reference 568966 0.9581183 NA NA NA NA NA 1.963496e-01 2.471053e-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 3.121020e+05 0.000000e+00 3.12102e+05 3.121020e+05 3.121020e+05 3.121020e+05 3.121020e+05 ▁▁▇▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 692794 rs530212009 CA C -0.0036113 0.011882 0.7611706 0.7611810 0.1105700 0.1894970 312102
1 693731 rs12238997 A G -0.0127630 0.011226 0.2555701 0.2555741 0.1157900 0.1417730 312102
1 707522 rs371890604 G C -0.0070844 0.012625 0.5747103 0.5747017 0.0972050 0.1293930 312102
1 717587 rs144155419 G A -0.0304890 0.030149 0.3118897 0.3118837 0.0156560 0.0045926 312102
1 723329 rs189787166 A T 0.1346800 0.089494 0.1323299 0.1323484 0.0017138 0.0003994 312102
1 730087 rs148120343 T C 0.0052498 0.015635 0.7370399 0.7370426 0.0565080 0.0127796 312102
1 731718 rs142557973 T C -0.0077224 0.010644 0.4681403 0.4681351 0.1217200 0.1543530 312102
1 732032 rs61770163 A C -0.0093536 0.011358 0.4102003 0.4102094 0.1211100 0.1555510 312102
1 734349 rs141242758 T C -0.0079594 0.010649 0.4548205 0.4548030 0.1209500 0.1525560 312102
1 740284 rs61770167 C T -0.0570180 0.048896 0.2435701 0.2435709 0.0057506 0.0023962 312102
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
23 154923311 rs141127553 C T 0.018299 0.0121290 0.1313799 0.1313759 0.056136 0.0309934 312102
23 154923374 rs111332691 T A -0.010506 0.0133370 0.4308697 0.4308527 0.044702 0.0116556 312102
23 154925045 rs509981 C T 0.024029 0.0064087 0.0001773 0.0001772 0.245850 0.3634440 312102
23 154925895 rs538470 C T 0.026137 0.0065557 0.0000669 0.0000669 0.242170 0.3634440 312102
23 154927581 rs644138 G A 0.025774 0.0060271 0.0000190 0.0000190 0.302350 0.4635760 312102
23 154929412 rs557132 C T 0.023906 0.0064105 0.0001922 0.0001921 0.245700 0.3568210 312102
23 154929637 rs35185538 CT C 0.022467 0.0066889 0.0007830 0.0007827 0.230090 0.3011920 312102
23 154929952 rs4012982 CAA C 0.027533 0.0067411 0.0000442 0.0000442 0.239690 0.3165560 312102
23 154930230 rs781880 A G 0.024476 0.0064095 0.0001342 0.0001342 0.246100 0.3618540 312102
23 154930487 rs781879 T A 0.011998 0.0219670 0.5849503 0.5849402 0.019591 0.1263580 312102

bcf preview

1   692794  rs530212009 CA  C   .   PASS    AF=0.11057  ES:SE:LP:AF:SS:ID   -0.0036113:0.011882:0.118518:0.11057:312102:1_692794_CA_C
1   693731  rs12238997  A   G   .   PASS    AF=0.11579  ES:SE:LP:AF:SS:ID   -0.012763:0.011226:0.59249:0.11579:312102:rs12238997
1   707522  rs371890604 G   C   .   PASS    AF=0.097205 ES:SE:LP:AF:SS:ID   -0.0070844:0.012625:0.240551:0.097205:312102:rs371890604
1   717587  rs144155419 G   A   .   PASS    AF=0.015656 ES:SE:LP:AF:SS:ID   -0.030489:0.030149:0.505999:0.015656:312102:rs144155419
1   723329  rs189787166 A   T   .   PASS    AF=0.0017138    ES:SE:LP:AF:SS:ID   0.13468:0.089494:0.878342:0.0017138:312102:rs189787166
1   730087  rs148120343 T   C   .   PASS    AF=0.056508 ES:SE:LP:AF:SS:ID   0.0052498:0.015635:0.132509:0.056508:312102:rs148120343
1   731718  rs58276399  T   C   .   PASS    AF=0.12172  ES:SE:LP:AF:SS:ID   -0.0077224:0.010644:0.329624:0.12172:312102:rs58276399
1   732032  rs61770163  A   C   .   PASS    AF=0.12111  ES:SE:LP:AF:SS:ID   -0.0093536:0.011358:0.387004:0.12111:312102:rs61770163
1   734349  rs141242758 T   C   .   PASS    AF=0.12095  ES:SE:LP:AF:SS:ID   -0.0079594:0.010649:0.34216:0.12095:312102:rs141242758
1   740284  rs61770167  C   T   .   PASS    AF=0.0057506    ES:SE:LP:AF:SS:ID   -0.057018:0.048896:0.613376:0.0057506:312102:rs61770167
1   742813  rs112573343 C   T   .   PASS    AF=0.0018642    ES:SE:LP:AF:SS:ID   -0.10125:0.092581:0.562075:0.0018642:312102:rs112573343
1   749963  rs529266287 T   TAA .   PASS    AF=0.86987  ES:SE:LP:AF:SS:ID   0.0079179:0.010501:0.345958:0.86987:312102:rs529266287
1   750230  rs190826124 G   C   .   PASS    AF=0.0015184    ES:SE:LP:AF:SS:ID   -0.054962:0.095381:0.248375:0.0015184:312102:rs190826124
1   751343  rs28544273  T   A   .   PASS    AF=0.12283  ES:SE:LP:AF:SS:ID   -0.0055999:0.010399:0.228979:0.12283:312102:rs28544273
1   751488  rs200141114 G   GA  .   PASS    AF=0.14265  ES:SE:LP:AF:SS:ID   -0.0070459:0.010279:0.307127:0.14265:312102:rs200141114
1   751756  rs28527770  T   C   .   PASS    AF=0.12294  ES:SE:LP:AF:SS:ID   -0.0054855:0.010385:0.223778:0.12294:312102:rs28527770
1   753405  rs3115860   C   A   .   PASS    AF=0.87099  ES:SE:LP:AF:SS:ID   0.0075344:0.01012:0.340502:0.87099:312102:rs3115860
1   753425  rs3131970   T   C   .   PASS    AF=0.87559  ES:SE:LP:AF:SS:ID   0.0056413:0.010289:0.233974:0.87559:312102:rs3131970
1   753541  rs2073813   G   A   .   PASS    AF=0.12856  ES:SE:LP:AF:SS:ID   -0.0072569:0.010144:0.323874:0.12856:312102:rs2073813
1   754105  rs12184325  C   T   .   PASS    AF=0.036378 ES:SE:LP:AF:SS:ID   -0.0046434:0.018404:0.0964705:0.036378:312102:rs12184325
1   754182  rs3131969   A   G   .   PASS    AF=0.87058  ES:SE:LP:AF:SS:ID   0.0081205:0.010109:0.374893:0.87058:312102:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.87069  ES:SE:LP:AF:SS:ID   0.0075334:0.010114:0.340692:0.87069:312102:rs3131968
1   754334  rs3131967   T   C   .   PASS    AF=0.87058  ES:SE:LP:AF:SS:ID   0.0084074:0.010109:0.391923:0.87058:312102:rs3131967
1   754433  rs150578204 G   A   .   PASS    AF=0.0050665    ES:SE:LP:AF:SS:ID   -0.026385:0.051769:0.214471:0.0050665:312102:rs150578204
1   754458  rs142682604 G   T   .   PASS    AF=0.0050345    ES:SE:LP:AF:SS:ID   -0.024093:0.051903:0.19212:0.0050345:312102:rs142682604
1   755435  rs184270342 T   G   .   PASS    AF=0.0055257    ES:SE:LP:AF:SS:ID   0.07592:0.050551:0.875724:0.0055257:312102:rs184270342
1   755890  rs3115858   A   T   .   PASS    AF=0.87067  ES:SE:LP:AF:SS:ID   0.0082668:0.010091:0.384397:0.87067:312102:rs3115858
1   756434  rs61768170  G   C   .   PASS    AF=0.12589  ES:SE:LP:AF:SS:ID   -0.0068969:0.010296:0.298467:0.12589:312102:rs61768170
1   756604  rs3131962   A   G   .   PASS    AF=0.87024  ES:SE:LP:AF:SS:ID   0.0076565:0.010067:0.349761:0.87024:312102:rs3131962
1   757640  rs3115853   G   A   .   PASS    AF=0.86952  ES:SE:LP:AF:SS:ID   0.0088531:0.010058:0.421659:0.86952:312102:rs3115853
1   757734  rs4951929   C   T   .   PASS    AF=0.87039  ES:SE:LP:AF:SS:ID   0.0075715:0.010076:0.344506:0.87039:312102:rs4951929
1   757936  rs4951862   C   A   .   PASS    AF=0.8704   ES:SE:LP:AF:SS:ID   0.0075685:0.010076:0.344305:0.8704:312102:rs4951862
1   758144  rs3131956   A   G   .   PASS    AF=0.87041  ES:SE:LP:AF:SS:ID   0.0075538:0.010077:0.343442:0.87041:312102:rs3131956
1   758626  rs3131954   C   T   .   PASS    AF=0.87085  ES:SE:LP:AF:SS:ID   0.0085537:0.010102:0.401024:0.87085:312102:rs3131954
1   759293  rs10157329  T   A   .   PASS    AF=0.098704 ES:SE:LP:AF:SS:ID   -0.0047479:0.011745:0.163651:0.098704:312102:rs10157329
1   759600  rs545998451 AGT A   .   PASS    AF=0.0064042    ES:SE:LP:AF:SS:ID   0.065485:0.04569:0.818785:0.0064042:312102:1_759600_AGT_A
1   759837  rs3115851   T   A   .   PASS    AF=0.87478  ES:SE:LP:AF:SS:ID   0.0063167:0.010255:0.26929:0.87478:312102:rs3115851
1   761732  rs2286139   C   T   .   PASS    AF=0.86413  ES:SE:LP:AF:SS:ID   0.0086629:0.010056:0.410084:0.86413:312102:rs2286139
1   761752  rs1057213   C   T   .   PASS    AF=0.86954  ES:SE:LP:AF:SS:ID   0.0078305:0.010152:0.356025:0.86954:312102:rs1057213
1   762273  rs3115849   G   A   .   PASS    AF=0.86646  ES:SE:LP:AF:SS:ID   0.0092754:0.010154:0.442493:0.86646:312102:rs3115849
1   762485  rs12095200  C   A   .   PASS    AF=0.098633 ES:SE:LP:AF:SS:ID   -0.0029922:0.01216:0.0938698:0.098633:312102:rs12095200
1   762589  rs3115848   G   C   .   PASS    AF=0.87167  ES:SE:LP:AF:SS:ID   0.0072261:0.010271:0.317196:0.87167:312102:rs3115848
1   762592  rs3131950   C   G   .   PASS    AF=0.87167  ES:SE:LP:AF:SS:ID   0.0072261:0.010271:0.317196:0.87167:312102:rs3131950
1   762601  rs3131949   T   C   .   PASS    AF=0.87167  ES:SE:LP:AF:SS:ID   0.0071246:0.010272:0.311651:0.87167:312102:rs3131949
1   762632  rs3131948   T   A   .   PASS    AF=0.87205  ES:SE:LP:AF:SS:ID   0.0069172:0.010277:0.300232:0.87205:312102:rs3131948
1   764191  rs7515915   T   G   .   PASS    AF=0.12545  ES:SE:LP:AF:SS:ID   -0.0062547:0.010285:0.265136:0.12545:312102:rs7515915
1   766007  rs61768174  A   C   .   PASS    AF=0.10535  ES:SE:LP:AF:SS:ID   -0.0047526:0.011199:0.17309:0.10535:312102:rs61768174
1   766105  rs2519015   T   A   .   PASS    AF=0.85548  ES:SE:LP:AF:SS:ID   0.0082372:0.010052:0.384544:0.85548:312102:rs2519015
1   767393  rs538667473 A   C   .   PASS    AF=0.0016292    ES:SE:LP:AF:SS:ID   0.13244:0.089784:0.853283:0.0016292:312102:rs538667473
1   768116  rs376645387 A   AGTTTT  .   PASS    AF=0.83851  ES:SE:LP:AF:SS:ID   0.0020912:0.0099019:0.0794906:0.83851:312102:rs376645387