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-6072_1/ukb-d-6072_1.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-6072_1/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 17:05:42 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-6072_1/ukb-d-6072_1.vcf.gz ...
Read summary statistics for 13547121 SNPs.
Dropped 12656 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, 1283497 SNPs remain.
After merging with regression SNP LD, 1283497 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0067 (0.0079)
Lambda GC: 1.0162
Mean Chi^2: 1.0139
Intercept: 1.0067 (0.0055)
Ratio: 0.485 (0.3979)
Analysis finished at Mon Nov 25 17:08:00 2019
Total time elapsed: 2.0m:17.55s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9521,
    "inflation_factor": 1.0155,
    "mean_EFFECT": -8.261e-06,
    "n": 54601,
    "n_snps": 13547121,
    "n_clumped_hits": 0,
    "n_p_sig": 3,
    "n_mono": 0,
    "n_ns": 1250492,
    "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": 557715,
    "n_est": 54843.6545,
    "ratio_se_n": 1.0022,
    "mean_diff": -0,
    "ratio_diff": 60.6517,
    "sd_y_est1": 0.352,
    "sd_y_est2": 0.3528,
    "r2_sum1": 0,
    "r2_sum2": 0,
    "r2_sum3": 0,
    "r2_sum4": 0,
    "ldsc_nsnp_merge_refpanel_ld": 1283497,
    "ldsc_nsnp_merge_regression_ld": 1283497,
    "ldsc_observed_scale_h2_beta": 0.0067,
    "ldsc_observed_scale_h2_se": 0.0079,
    "ldsc_intercept_beta": 1.0067,
    "ldsc_intercept_se": 0.0055,
    "ldsc_lambda_gc": 1.0162,
    "ldsc_mean_chisq": 1.0139,
    "ldsc_ratio": 0.482
}

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 13535128 0 NA NA NA NA NA NA NA NA
character REF 0 1.0000000 1 100 0 57010 0 NA NA NA NA NA NA NA NA
character ALT 0 1.0000000 1 342 0 33322 0 NA NA NA NA NA NA NA NA
numeric CHROM 0 1.0000000 NA NA NA NA NA 9.051400e+00 6.184649e+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 7.902292e+07 5.591773e+07 3.02000e+02 3.292300e+07 7.013570e+07 1.148571e+08 2.492309e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA -8.300000e-06 1.237100e-02 -1.73484e-01 -3.239900e-03 2.550000e-05 3.317500e-03 1.290000e-01 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 8.877000e-03 8.544800e-03 1.74670e-03 2.545300e-03 4.671800e-03 1.274010e-02 4.407140e-02 ▇▂▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.976623e-01 2.885858e-01 0.00000e+00 2.476088e-01 4.966895e-01 7.470884e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.976593e-01 2.885875e-01 0.00000e+00 2.476040e-01 4.966872e-01 7.470874e-01 9.999999e-01 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA 1.913359e-01 2.545268e-01 1.00000e-03 7.582800e-03 6.064980e-02 2.963110e-01 9.990000e-01 ▇▂▁▁▁
numeric AF_reference 557715 0.9588315 NA NA NA NA NA 1.967170e-01 2.471856e-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 5.460100e+04 0.000000e+00 5.46010e+04 5.460100e+04 5.460100e+04 5.460100e+04 5.460100e+04 ▁▁▇▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 692794 rs530212009 CA C -0.0025828 0.0037069 0.4859639 0.4859612 0.1121670 0.1894970 54601
1 693731 rs12238997 A G -0.0021262 0.0035120 0.5449015 0.5449001 0.1172240 0.1417730 54601
1 707522 rs371890604 G C -0.0067841 0.0039401 0.0851079 0.0851024 0.0985402 0.1293930 54601
1 717587 rs144155419 G A 0.0070428 0.0095659 0.4615885 0.4615856 0.0154660 0.0045926 54601
1 723329 rs189787166 A T 0.0103216 0.0271100 0.7034059 0.7034033 0.0017770 0.0003994 54601
1 730087 rs148120343 T C -0.0015115 0.0048923 0.7573576 0.7573557 0.0572311 0.0127796 54601
1 731718 rs142557973 T C -0.0029889 0.0033333 0.3698818 0.3698781 0.1230760 0.1543530 54601
1 732032 rs61770163 A C -0.0039586 0.0035473 0.2644527 0.2644487 0.1228430 0.1555510 54601
1 734349 rs141242758 T C -0.0028549 0.0033362 0.3921399 0.3921354 0.1222480 0.1525560 54601
1 740284 rs61770167 C T 0.0077818 0.0143109 0.5866067 0.5866021 0.0065623 0.0023962 54601
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
23 154923311 rs141127553 C T 0.0000322 0.0039174 0.9934390 0.9934393 0.0542740 0.0309934 54601
23 154923374 rs111332691 T A -0.0086066 0.0042581 0.0432594 0.0432545 0.0443124 0.0116556 54601
23 154925045 rs509981 C T 0.0034078 0.0020458 0.0957679 0.0957614 0.2427170 0.3634440 54601
23 154925895 rs538470 C T 0.0037609 0.0020918 0.0721938 0.0721884 0.2391000 0.3634440 54601
23 154927581 rs644138 G A 0.0030851 0.0019243 0.1088970 0.1088923 0.2974210 0.4635760 54601
23 154929412 rs557132 C T 0.0034769 0.0020466 0.0893429 0.0893375 0.2425560 0.3568210 54601
23 154929637 rs35185538 CT C 0.0032266 0.0021368 0.1310509 0.1310450 0.2268210 0.3011920 54601
23 154929952 rs4012982 CAA C 0.0034914 0.0021504 0.1044619 0.1044553 0.2368600 0.3165560 54601
23 154930230 rs781880 A G 0.0033906 0.0020462 0.0975102 0.0975027 0.2429450 0.3618540 54601
23 154930487 rs781879 T A 0.0115298 0.0071660 0.1076299 0.1076233 0.0186678 0.1263580 54601

bcf preview

1   692794  rs530212009 CA  C   .   PASS    AF=0.112167 ES:SE:LP:AF:SS:ID   -0.00258275:0.00370687:0.313396:0.112167:54601:1_692794_CA_C
1   693731  rs12238997  A   G   .   PASS    AF=0.117224 ES:SE:LP:AF:SS:ID   -0.00212621:0.00351196:0.263682:0.117224:54601:rs12238997
1   707522  rs371890604 G   C   .   PASS    AF=0.0985402    ES:SE:LP:AF:SS:ID   -0.00678412:0.00394009:1.07003:0.0985402:54601:rs371890604
1   717587  rs144155419 G   A   .   PASS    AF=0.015466 ES:SE:LP:AF:SS:ID   0.00704279:0.00956591:0.335745:0.015466:54601:rs144155419
1   723329  rs189787166 A   T   .   PASS    AF=0.00177696   ES:SE:LP:AF:SS:ID   0.0103216:0.02711:0.152794:0.00177696:54601:rs189787166
1   730087  rs148120343 T   C   .   PASS    AF=0.0572311    ES:SE:LP:AF:SS:ID   -0.00151151:0.00489233:0.120699:0.0572311:54601:rs148120343
1   731718  rs58276399  T   C   .   PASS    AF=0.123076 ES:SE:LP:AF:SS:ID   -0.00298894:0.00333326:0.431937:0.123076:54601:rs58276399
1   732032  rs61770163  A   C   .   PASS    AF=0.122843 ES:SE:LP:AF:SS:ID   -0.0039586:0.00354733:0.577652:0.122843:54601:rs61770163
1   734349  rs141242758 T   C   .   PASS    AF=0.122248 ES:SE:LP:AF:SS:ID   -0.00285494:0.00333618:0.406559:0.122248:54601:rs141242758
1   740284  rs61770167  C   T   .   PASS    AF=0.00656229   ES:SE:LP:AF:SS:ID   0.00778179:0.0143109:0.231653:0.00656229:54601:rs61770167
1   742813  rs112573343 C   T   .   PASS    AF=0.00185668   ES:SE:LP:AF:SS:ID   0.0275911:0.0294826:0.456729:0.00185668:54601:rs112573343
1   749963  rs529266287 T   TAA .   PASS    AF=0.868271 ES:SE:LP:AF:SS:ID   0.00309575:0.00328664:0.460625:0.868271:54601:rs529266287
1   750230  rs190826124 G   C   .   PASS    AF=0.00155377   ES:SE:LP:AF:SS:ID   -0.00575086:0.0297053:0.0723771:0.00155377:54601:rs190826124
1   751343  rs28544273  T   A   .   PASS    AF=0.124309 ES:SE:LP:AF:SS:ID   -0.00441132:0.00325593:0.755802:0.124309:54601:rs28544273
1   751488  rs200141114 G   GA  .   PASS    AF=0.143544 ES:SE:LP:AF:SS:ID   -0.00379675:0.00323129:0.619785:0.143544:54601:rs200141114
1   751756  rs28527770  T   C   .   PASS    AF=0.12444  ES:SE:LP:AF:SS:ID   -0.00436225:0.00325068:0.74565:0.12444:54601:rs28527770
1   753405  rs3115860   C   A   .   PASS    AF=0.869364 ES:SE:LP:AF:SS:ID   0.00291682:0.00316664:0.447335:0.869364:54601:rs3115860
1   753425  rs3131970   T   C   .   PASS    AF=0.874135 ES:SE:LP:AF:SS:ID   0.00404413:0.00321921:0.679789:0.874135:54601:rs3131970
1   753541  rs2073813   G   A   .   PASS    AF=0.130177 ES:SE:LP:AF:SS:ID   -0.00321591:0.00317396:0.507295:0.130177:54601:rs2073813
1   754105  rs12184325  C   T   .   PASS    AF=0.0366477    ES:SE:LP:AF:SS:ID   0.00538285:0.00575788:0.456104:0.0366477:54601:rs12184325
1   754182  rs3131969   A   G   .   PASS    AF=0.868994 ES:SE:LP:AF:SS:ID   0.00277314:0.00316397:0.419329:0.868994:54601:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.869113 ES:SE:LP:AF:SS:ID   0.00291451:0.00316594:0.447001:0.869113:54601:rs3131968
1   754334  rs3131967   T   C   .   PASS    AF=0.869005 ES:SE:LP:AF:SS:ID   0.00287031:0.00316386:0.438547:0.869005:54601:rs3131967
1   754433  rs150578204 G   A   .   PASS    AF=0.00525718   ES:SE:LP:AF:SS:ID   -0.00755108:0.0159878:0.196056:0.00525718:54601:rs150578204
1   754458  rs142682604 G   T   .   PASS    AF=0.00522769   ES:SE:LP:AF:SS:ID   -0.00761455:0.0160295:0.197388:0.00522769:54601:rs142682604
1   755435  rs184270342 T   G   .   PASS    AF=0.00558307   ES:SE:LP:AF:SS:ID   0.00075095:0.0158039:0.0167789:0.00558307:54601:rs184270342
1   755890  rs3115858   A   T   .   PASS    AF=0.869113 ES:SE:LP:AF:SS:ID   0.00306415:0.00315877:0.478827:0.869113:54601:rs3115858
1   756434  rs61768170  G   C   .   PASS    AF=0.127452 ES:SE:LP:AF:SS:ID   -0.00390415:0.00322235:0.646513:0.127452:54601:rs61768170
1   756604  rs3131962   A   G   .   PASS    AF=0.868711 ES:SE:LP:AF:SS:ID   0.00317732:0.00315167:0.503911:0.868711:54601:rs3131962
1   757640  rs3115853   G   A   .   PASS    AF=0.867803 ES:SE:LP:AF:SS:ID   0.00329011:0.00314674:0.529049:0.867803:54601:rs3115853
1   757734  rs4951929   C   T   .   PASS    AF=0.868861 ES:SE:LP:AF:SS:ID   0.00300735:0.00315409:0.468072:0.868861:54601:rs4951929
1   757936  rs4951862   C   A   .   PASS    AF=0.868867 ES:SE:LP:AF:SS:ID   0.00300528:0.0031543:0.467605:0.868867:54601:rs4951862
1   758144  rs3131956   A   G   .   PASS    AF=0.868877 ES:SE:LP:AF:SS:ID   0.00301485:0.00315441:0.469544:0.868877:54601:rs3131956
1   758626  rs3131954   C   T   .   PASS    AF=0.869274 ES:SE:LP:AF:SS:ID   0.00309893:0.00316221:0.485325:0.869274:54601:rs3131954
1   759293  rs10157329  T   A   .   PASS    AF=0.100036 ES:SE:LP:AF:SS:ID   -0.00562633:0.00367245:0.901291:0.100036:54601:rs10157329
1   759600  rs545998451 AGT A   .   PASS    AF=0.0063348    ES:SE:LP:AF:SS:ID   -0.00749554:0.0143814:0.220237:0.0063348:54601:1_759600_AGT_A
1   759837  rs3115851   T   A   .   PASS    AF=0.873359 ES:SE:LP:AF:SS:ID   0.00388249:0.00321029:0.644895:0.873359:54601:rs3115851
1   761732  rs2286139   C   T   .   PASS    AF=0.862434 ES:SE:LP:AF:SS:ID   0.00302011:0.00314701:0.472084:0.862434:54601:rs2286139
1   761752  rs1057213   C   T   .   PASS    AF=0.868143 ES:SE:LP:AF:SS:ID   0.00340129:0.00318058:0.545311:0.868143:54601:rs1057213
1   762273  rs3115849   G   A   .   PASS    AF=0.86478  ES:SE:LP:AF:SS:ID   0.00342745:0.00317756:0.551677:0.86478:54601:rs3115849
1   762485  rs12095200  C   A   .   PASS    AF=0.099864 ES:SE:LP:AF:SS:ID   -0.00233368:0.00380436:0.267929:0.099864:54601:rs12095200
1   762589  rs3115848   G   C   .   PASS    AF=0.870135 ES:SE:LP:AF:SS:ID   0.00419657:0.00321413:0.717439:0.870135:54601:rs3115848
1   762592  rs3131950   C   G   .   PASS    AF=0.870135 ES:SE:LP:AF:SS:ID   0.00419709:0.00321413:0.717564:0.870135:54601:rs3131950
1   762601  rs3131949   T   C   .   PASS    AF=0.870132 ES:SE:LP:AF:SS:ID   0.0041965:0.00321414:0.717419:0.870132:54601:rs3131949
1   762632  rs3131948   T   A   .   PASS    AF=0.870557 ES:SE:LP:AF:SS:ID   0.0041076:0.00321639:0.695557:0.870557:54601:rs3131948
1   764191  rs7515915   T   G   .   PASS    AF=0.12686  ES:SE:LP:AF:SS:ID   -0.00390596:0.00321926:0.647787:0.12686:54601:rs7515915
1   766007  rs61768174  A   C   .   PASS    AF=0.106633 ES:SE:LP:AF:SS:ID   -0.0039962:0.00350393:0.595018:0.106633:54601:rs61768174
1   766105  rs2519015   T   A   .   PASS    AF=0.853891 ES:SE:LP:AF:SS:ID   0.00333566:0.00315008:0.538137:0.853891:54601:rs2519015
1   767393  rs538667473 A   C   .   PASS    AF=0.00168043   ES:SE:LP:AF:SS:ID   0.00648342:0.0273019:0.0902878:0.00168043:54601:rs538667473
1   768116  rs376645387 A   AGTTTT  .   PASS    AF=0.8364   ES:SE:LP:AF:SS:ID   0.00352472:0.00309155:0.594751:0.8364:54601:rs376645387