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-30620_raw/ukb-d-30620_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-30620_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 16:34:05 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-30620_raw/ukb-d-30620_raw.vcf.gz ...
Read summary statistics for 13585999 SNPs.
Dropped 12711 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: 0.0804 (0.0066)
Lambda GC: 1.3323
Mean Chi^2: 1.5955
Intercept: 1.0457 (0.0115)
Ratio: 0.0767 (0.0193)
Analysis finished at Mon Nov 25 16:36:23 2019
Total time elapsed: 2.0m:18.12s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9521,
    "inflation_factor": 1.2023,
    "mean_EFFECT": 0.0002,
    "n": 344136,
    "n_snps": 13585999,
    "n_clumped_hits": 126,
    "n_p_sig": 14186,
    "n_mono": 0,
    "n_ns": 1251779,
    "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": 569168,
    "n_est": 345470.4829,
    "ratio_se_n": 1.0019,
    "mean_diff": -0.0002,
    "ratio_diff": 378.2076,
    "sd_y_est1": 13.5263,
    "sd_y_est2": 13.5525,
    "r2_sum1": 5.5119,
    "r2_sum2": 0.0301,
    "r2_sum3": 0.03,
    "r2_sum4": 0.03,
    "ldsc_nsnp_merge_refpanel_ld": 1283504,
    "ldsc_nsnp_merge_regression_ld": 1283504,
    "ldsc_observed_scale_h2_beta": 0.0804,
    "ldsc_observed_scale_h2_se": 0.0066,
    "ldsc_intercept_beta": 1.0457,
    "ldsc_intercept_se": 0.0115,
    "ldsc_lambda_gc": 1.3323,
    "ldsc_mean_chisq": 1.5955,
    "ldsc_ratio": 0.0767
}

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 TRUE
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 13573952 0 NA NA NA NA NA NA NA NA
character REF 0 1.0000000 1 100 0 57080 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 9.051235e+00 6.184968e+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 5.591512e+07 3.02000e+02 3.293112e+07 7.013976e+07 1.148604e+08 2.492309e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA 1.785000e-04 1.956473e-01 -9.36340e+00 -5.775600e-02 -6.560000e-04 5.601300e-02 3.768300e+00 ▁▁▁▇▁
numeric SE 0 1.0000000 NA NA NA NA NA 1.370062e-01 1.321580e-01 2.68070e-02 3.900800e-02 7.188100e-02 1.968900e-01 6.674400e-01 ▇▂▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.691044e-01 2.977086e-01 0.00000e+00 2.041498e-01 4.595598e-01 7.268303e-01 1.000000e+00 ▇▆▆▆▆
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.691039e-01 2.977089e-01 0.00000e+00 2.041524e-01 4.595635e-01 7.268312e-01 9.999999e-01 ▇▆▆▆▆
numeric AF 0 1.0000000 NA NA NA NA NA 1.908098e-01 2.544045e-01 1.00000e-03 7.431400e-03 6.004000e-02 2.953200e-01 9.990000e-01 ▇▂▁▁▁
numeric AF_reference 569168 0.9581063 NA NA NA NA NA 1.963393e-01 2.471026e-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 3.441360e+05 0.000000e+00 3.44136e+05 3.441360e+05 3.441360e+05 3.441360e+05 3.441360e+05 ▁▁▇▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 692794 rs530212009 CA C -0.0457200 0.057103 0.4233300 0.4233294 0.1105400 0.1894970 344136
1 693731 rs12238997 A G -0.0040293 0.053934 0.9404500 0.9404471 0.1158200 0.1417730 344136
1 707522 rs371890604 G C 0.0216760 0.060663 0.7208502 0.7208535 0.0972600 0.1293930 344136
1 717587 rs144155419 G A -0.2277700 0.144810 0.1157500 0.1157446 0.0156650 0.0045926 344136
1 723329 rs189787166 A T -0.7377000 0.426540 0.0837182 0.0837200 0.0017369 0.0003994 344136
1 730087 rs148120343 T C 0.0266260 0.075167 0.7231693 0.7231706 0.0564320 0.0127796 344136
1 731718 rs142557973 T C -0.0077025 0.051155 0.8803099 0.8803135 0.1217100 0.1543530 344136
1 732032 rs61770163 A C 0.0076654 0.054584 0.8883199 0.8883178 0.1211200 0.1555510 344136
1 734349 rs141242758 T C -0.0045221 0.051182 0.9296000 0.9295959 0.1209400 0.1525560 344136
1 740284 rs61770167 C T -0.0987990 0.234730 0.6738295 0.6738245 0.0057580 0.0023962 344136
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
23 154923311 rs141127553 C T -0.0003838 0.059114 0.9948200 0.9948200 0.056197 0.0309934 344136
23 154923374 rs111332691 T A 0.0489740 0.064885 0.4503799 0.4503801 0.044883 0.0116556 344136
23 154925045 rs509981 C T -0.0998450 0.031258 0.0014021 0.0014021 0.245650 0.3634440 344136
23 154925895 rs538470 C T -0.1071200 0.031975 0.0008077 0.0008078 0.241990 0.3634440 344136
23 154927581 rs644138 G A -0.0886260 0.029397 0.0025717 0.0025715 0.302240 0.4635760 344136
23 154929412 rs557132 C T -0.0995460 0.031267 0.0014537 0.0014539 0.245510 0.3568210 344136
23 154929637 rs35185538 CT C -0.1044800 0.032634 0.0013672 0.0013668 0.229760 0.3011920 344136
23 154929952 rs4012982 CAA C -0.1075800 0.032883 0.0010701 0.0010694 0.239490 0.3165560 344136
23 154930230 rs781880 A G -0.1031400 0.031262 0.0009691 0.0009696 0.245910 0.3618540 344136
23 154930487 rs781879 T A -0.1864000 0.107170 0.0819785 0.0819833 0.019560 0.1263580 344136

bcf preview

1   692794  rs530212009 CA  C   .   PASS    AF=0.11054  ES:SE:LP:AF:SS:ID   -0.04572:0.057103:0.373321:0.11054:344136:1_692794_CA_C
1   693731  rs12238997  A   G   .   PASS    AF=0.11582  ES:SE:LP:AF:SS:ID   -0.0040293:0.053934:0.0266643:0.11582:344136:rs12238997
1   707522  rs371890604 G   C   .   PASS    AF=0.09726  ES:SE:LP:AF:SS:ID   0.021676:0.060663:0.142155:0.09726:344136:rs371890604
1   717587  rs144155419 G   A   .   PASS    AF=0.015665 ES:SE:LP:AF:SS:ID   -0.22777:0.14481:0.936479:0.015665:344136:rs144155419
1   723329  rs189787166 A   T   .   PASS    AF=0.0017369    ES:SE:LP:AF:SS:ID   -0.7377:0.42654:1.07718:0.0017369:344136:rs189787166
1   730087  rs148120343 T   C   .   PASS    AF=0.056432 ES:SE:LP:AF:SS:ID   0.026626:0.075167:0.14076:0.056432:344136:rs148120343
1   731718  rs58276399  T   C   .   PASS    AF=0.12171  ES:SE:LP:AF:SS:ID   -0.0077025:0.051155:0.0553644:0.12171:344136:rs58276399
1   732032  rs61770163  A   C   .   PASS    AF=0.12112  ES:SE:LP:AF:SS:ID   0.0076654:0.054584:0.0514306:0.12112:344136:rs61770163
1   734349  rs141242758 T   C   .   PASS    AF=0.12094  ES:SE:LP:AF:SS:ID   -0.0045221:0.051182:0.0317039:0.12094:344136:rs141242758
1   740284  rs61770167  C   T   .   PASS    AF=0.005758 ES:SE:LP:AF:SS:ID   -0.098799:0.23473:0.17145:0.005758:344136:rs61770167
1   742813  rs112573343 C   T   .   PASS    AF=0.0018606    ES:SE:LP:AF:SS:ID   -0.46673:0.44519:0.530974:0.0018606:344136:rs112573343
1   749963  rs529266287 T   TAA .   PASS    AF=0.86979  ES:SE:LP:AF:SS:ID   0.0048876:0.05046:0.0348736:0.86979:344136:rs529266287
1   750230  rs190826124 G   C   .   PASS    AF=0.0015222    ES:SE:LP:AF:SS:ID   0.12781:0.45821:0.107738:0.0015222:344136:rs190826124
1   751343  rs28544273  T   A   .   PASS    AF=0.12289  ES:SE:LP:AF:SS:ID   -3.9068e-05:0.04997:0.000269346:0.12289:344136:rs28544273
1   751488  rs200141114 G   GA  .   PASS    AF=0.14271  ES:SE:LP:AF:SS:ID   -0.010147:0.049387:0.0771604:0.14271:344136:rs200141114
1   751756  rs28527770  T   C   .   PASS    AF=0.12301  ES:SE:LP:AF:SS:ID   0.00075767:0.0499:0.00529141:0.12301:344136:rs28527770
1   753405  rs3115860   C   A   .   PASS    AF=0.87095  ES:SE:LP:AF:SS:ID   0.0088216:0.048634:0.0674958:0.87095:344136:rs3115860
1   753425  rs3131970   T   C   .   PASS    AF=0.87551  ES:SE:LP:AF:SS:ID   -0.0029885:0.049434:0.0214589:0.87551:344136:rs3131970
1   753541  rs2073813   G   A   .   PASS    AF=0.12859  ES:SE:LP:AF:SS:ID   -0.0057984:0.048753:0.0431931:0.12859:344136:rs2073813
1   754105  rs12184325  C   T   .   PASS    AF=0.03631  ES:SE:LP:AF:SS:ID   0.027399:0.088529:0.120933:0.03631:344136:rs12184325
1   754182  rs3131969   A   G   .   PASS    AF=0.87054  ES:SE:LP:AF:SS:ID   0.011002:0.048583:0.0857415:0.87054:344136:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.87064  ES:SE:LP:AF:SS:ID   0.0097045:0.048605:0.0748169:0.87064:344136:rs3131968
1   754334  rs3131967   T   C   .   PASS    AF=0.87054  ES:SE:LP:AF:SS:ID   0.010648:0.048581:0.0827519:0.87054:344136:rs3131967
1   754433  rs150578204 G   A   .   PASS    AF=0.0050484    ES:SE:LP:AF:SS:ID   0.088207:0.24921:0.140634:0.0050484:344136:rs150578204
1   754458  rs142682604 G   T   .   PASS    AF=0.0050154    ES:SE:LP:AF:SS:ID   0.095377:0.24988:0.153242:0.0050154:344136:rs142682604
1   755435  rs184270342 T   G   .   PASS    AF=0.005547 ES:SE:LP:AF:SS:ID   0.0012752:0.24248:0.00182788:0.005547:344136:rs184270342
1   755890  rs3115858   A   T   .   PASS    AF=0.87063  ES:SE:LP:AF:SS:ID   0.008217:0.048497:0.062753:0.87063:344136:rs3115858
1   756434  rs61768170  G   C   .   PASS    AF=0.12593  ES:SE:LP:AF:SS:ID   -0.0041967:0.049481:0.0303931:0.12593:344136:rs61768170
1   756604  rs3131962   A   G   .   PASS    AF=0.8702   ES:SE:LP:AF:SS:ID   0.011172:0.048382:0.0875707:0.8702:344136:rs3131962
1   757640  rs3115853   G   A   .   PASS    AF=0.86947  ES:SE:LP:AF:SS:ID   0.0109:0.048338:0.0853449:0.86947:344136:rs3115853
1   757734  rs4951929   C   T   .   PASS    AF=0.87034  ES:SE:LP:AF:SS:ID   0.0099426:0.048422:0.0771137:0.87034:344136:rs4951929
1   757936  rs4951862   C   A   .   PASS    AF=0.87035  ES:SE:LP:AF:SS:ID   0.0098351:0.048426:0.076207:0.87035:344136:rs4951862
1   758144  rs3131956   A   G   .   PASS    AF=0.87036  ES:SE:LP:AF:SS:ID   0.010026:0.048427:0.0777989:0.87036:344136:rs3131956
1   758626  rs3131954   C   T   .   PASS    AF=0.8708   ES:SE:LP:AF:SS:ID   0.0086522:0.04855:0.0662294:0.8708:344136:rs3131954
1   759293  rs10157329  T   A   .   PASS    AF=0.098801 ES:SE:LP:AF:SS:ID   0.027617:0.056425:0.204447:0.098801:344136:rs10157329
1   759600  rs545998451 AGT A   .   PASS    AF=0.0064331    ES:SE:LP:AF:SS:ID   -0.058707:0.21907:0.103083:0.0064331:344136:1_759600_AGT_A
1   759837  rs3115851   T   A   .   PASS    AF=0.87469  ES:SE:LP:AF:SS:ID   0.0048804:0.04927:0.0356979:0.87469:344136:rs3115851
1   761732  rs2286139   C   T   .   PASS    AF=0.8641   ES:SE:LP:AF:SS:ID   0.013272:0.048326:0.105906:0.8641:344136:rs2286139
1   761752  rs1057213   C   T   .   PASS    AF=0.86948  ES:SE:LP:AF:SS:ID   0.0042629:0.048787:0.0313443:0.86948:344136:rs1057213
1   762273  rs3115849   G   A   .   PASS    AF=0.86642  ES:SE:LP:AF:SS:ID   0.020007:0.048796:0.166343:0.86642:344136:rs3115849
1   762485  rs12095200  C   A   .   PASS    AF=0.098755 ES:SE:LP:AF:SS:ID   0.014222:0.058414:0.0927822:0.098755:344136:rs12095200
1   762589  rs3115848   G   C   .   PASS    AF=0.8716   ES:SE:LP:AF:SS:ID   0.012681:0.049354:0.0984218:0.8716:344136:rs3115848
1   762592  rs3131950   C   G   .   PASS    AF=0.8716   ES:SE:LP:AF:SS:ID   0.012681:0.049354:0.0984164:0.8716:344136:rs3131950
1   762601  rs3131949   T   C   .   PASS    AF=0.8716   ES:SE:LP:AF:SS:ID   0.012628:0.049355:0.0979645:0.8716:344136:rs3131949
1   762632  rs3131948   T   A   .   PASS    AF=0.87197  ES:SE:LP:AF:SS:ID   0.0097079:0.049383:0.0735804:0.87197:344136:rs3131948
1   764191  rs7515915   T   G   .   PASS    AF=0.12553  ES:SE:LP:AF:SS:ID   0.0010756:0.049417:0.00760998:0.12553:344136:rs7515915
1   766007  rs61768174  A   C   .   PASS    AF=0.1054   ES:SE:LP:AF:SS:ID   0.026004:0.05381:0.201412:0.1054:344136:rs61768174
1   766105  rs2519015   T   A   .   PASS    AF=0.85544  ES:SE:LP:AF:SS:ID   0.021026:0.048306:0.178244:0.85544:344136:rs2519015
1   767393  rs538667473 A   C   .   PASS    AF=0.0016557    ES:SE:LP:AF:SS:ID   -0.74125:0.42761:1.08086:0.0016557:344136:rs538667473
1   768116  rs376645387 A   AGTTTT  .   PASS    AF=0.83825  ES:SE:LP:AF:SS:ID   0.01326:0.047567:0.107666:0.83825:344136:rs376645387