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-20079_5/ukb-d-20079_5.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-20079_5/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 16:36:30 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-20079_5/ukb-d-20079_5.vcf.gz ...
Read summary statistics for 13055098 SNPs.
Dropped 11961 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, 1283403 SNPs remain.
After merging with regression SNP LD, 1283403 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: -0.0014 (0.0088)
Lambda GC: 0.9937
Mean Chi^2: 0.9913
Intercept: 0.9927 (0.0063)
Ratio: NA (mean chi^2 < 1)
Analysis finished at Mon Nov 25 16:38:44 2019
Total time elapsed: 2.0m:13.99s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9513,
    "inflation_factor": 0.9979,
    "mean_EFFECT": -0,
    "n": 51427,
    "n_snps": 13055098,
    "n_clumped_hits": 0,
    "n_p_sig": 1,
    "n_mono": 0,
    "n_ns": 1231540,
    "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": 441001,
    "n_est": 51640.4288,
    "ratio_se_n": 1.0021,
    "mean_diff": -0,
    "ratio_diff": 67.0131,
    "sd_y_est1": 0.3789,
    "sd_y_est2": 0.3796,
    "r2_sum1": 0,
    "r2_sum2": 0,
    "r2_sum3": 0,
    "r2_sum4": 0,
    "ldsc_nsnp_merge_refpanel_ld": 1283403,
    "ldsc_nsnp_merge_regression_ld": 1283403,
    "ldsc_observed_scale_h2_beta": "NA",
    "ldsc_observed_scale_h2_se": "NA",
    "ldsc_intercept_beta": 0.9927,
    "ldsc_intercept_se": 0.0063,
    "ldsc_lambda_gc": 0.9937,
    "ldsc_mean_chisq": 0.9913,
    "ldsc_ratio": 0.8391
}

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 TRUE
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 1.00000 3 94 0 13043791 0 NA NA NA NA NA NA NA NA
character REF 0 1.00000 1 100 0 55966 0 NA NA NA NA NA NA NA NA
character ALT 0 1.00000 1 342 0 33002 0 NA NA NA NA NA NA NA NA
numeric CHROM 0 1.00000 NA NA NA NA NA 9.057666e+00 6.185619e+00 1.00000e+00 4.000000e+00 8.000000e+00 1.300000e+01 2.300000e+01 ▇▅▅▂▂
numeric POS 0 1.00000 NA NA NA NA NA 7.898199e+07 5.593691e+07 3.02000e+02 3.284702e+07 7.005748e+07 1.148242e+08 2.492309e+08 ▇▆▅▂▁
numeric EFFECT 0 1.00000 NA NA NA NA NA -2.220000e-05 1.208570e-02 -1.36982e-01 -3.489800e-03 -3.000000e-05 3.404300e-03 1.603010e-01 ▁▁▇▁▁
numeric SE 0 1.00000 NA NA NA NA NA 8.875100e-03 8.178600e-03 1.94490e-03 2.788000e-03 4.876000e-03 1.260540e-02 4.387950e-02 ▇▂▁▁▁
numeric PVAL 0 1.00000 NA NA NA NA NA 5.005302e-01 2.887443e-01 0.00000e+00 2.506502e-01 5.004550e-01 7.506906e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.00000 NA NA NA NA NA 5.005271e-01 2.887462e-01 0.00000e+00 2.506449e-01 5.004521e-01 7.506886e-01 1.000000e+00 ▇▇▇▇▇
numeric AF 0 1.00000 NA NA NA NA NA 1.981692e-01 2.561519e-01 1.41400e-03 9.463600e-03 6.955300e-02 3.098960e-01 9.985860e-01 ▇▂▁▁▁
numeric AF_reference 441001 0.96622 NA NA NA NA NA 2.019722e-01 2.483257e-01 0.00000e+00 6.988800e-03 9.205270e-02 3.186900e-01 1.000000e+00 ▇▂▁▁▁
numeric N 0 1.00000 NA NA NA NA NA 5.142700e+04 0.000000e+00 5.14270e+04 5.142700e+04 5.142700e+04 5.142700e+04 5.142700e+04 ▁▁▇▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 692794 rs530212009 CA C 0.0018976 0.0041128 0.6445224 0.6445205 0.1121000 0.1894970 51427
1 693731 rs12238997 A G -0.0011190 0.0039084 0.7746384 0.7746367 0.1168090 0.1417730 51427
1 707522 rs371890604 G C 0.0052518 0.0043834 0.2308788 0.2308741 0.0982930 0.1293930 51427
1 717587 rs144155419 G A -0.0187795 0.0105968 0.0763695 0.0763637 0.0154808 0.0045926 51427
1 723329 rs189787166 A T 0.0433932 0.0301179 0.1496529 0.1496475 0.0017973 0.0003994 51427
1 730087 rs148120343 T C 0.0045171 0.0054427 0.4065828 0.4065787 0.0570822 0.0127796 51427
1 731718 rs142557973 T C -0.0009811 0.0037140 0.7916496 0.7916495 0.1225210 0.1543530 51427
1 732032 rs61770163 A C 0.0022494 0.0039592 0.5699385 0.5699350 0.1216510 0.1555510 51427
1 734349 rs141242758 T C -0.0011319 0.0037160 0.7606712 0.7606700 0.1217650 0.1525560 51427
1 740284 rs61770167 C T -0.0012245 0.0162401 0.9398949 0.9398952 0.0062329 0.0023962 51427
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
23 154923311 rs141127553 C T -0.0014271 0.0043695 0.7439676 0.7439662 0.0542488 0.0309934 51427
23 154923374 rs111332691 T A -0.0083393 0.0047331 0.0780890 0.0780828 0.0445389 0.0116556 51427
23 154925045 rs509981 C T -0.0010473 0.0022754 0.6453094 0.6453078 0.2434190 0.3634440 51427
23 154925895 rs538470 C T -0.0001725 0.0023244 0.9408359 0.9408351 0.2401390 0.3634440 51427
23 154927581 rs644138 G A -0.0012626 0.0021403 0.5552518 0.5552499 0.2981050 0.4635760 51427
23 154929412 rs557132 C T -0.0010561 0.0022762 0.6426537 0.6426530 0.2432580 0.3568210 51427
23 154929637 rs35185538 CT C -0.0001425 0.0023717 0.9520990 0.9520992 0.2278210 0.3011920 51427
23 154929952 rs4012982 CAA C -0.0007116 0.0023949 0.7663762 0.7663764 0.2374290 0.3165560 51427
23 154930230 rs781880 A G -0.0007651 0.0022752 0.7366734 0.7366721 0.2438260 0.3618540 51427
23 154930487 rs781879 T A -0.0148076 0.0079113 0.0612534 0.0612488 0.0189843 0.1263580 51427

bcf preview

1   692794  rs530212009 CA  C   .   PASS    AF=0.1121   ES:SE:LP:AF:SS:ID   0.0018976:0.00411281:0.190762:0.1121:51427:1_692794_CA_C
1   693731  rs12238997  A   G   .   PASS    AF=0.116809 ES:SE:LP:AF:SS:ID   -0.00111902:0.00390835:0.110901:0.116809:51427:rs12238997
1   707522  rs371890604 G   C   .   PASS    AF=0.098293 ES:SE:LP:AF:SS:ID   0.00525182:0.00438342:0.636616:0.098293:51427:rs371890604
1   717587  rs144155419 G   A   .   PASS    AF=0.0154808    ES:SE:LP:AF:SS:ID   -0.0187795:0.0105968:1.11708:0.0154808:51427:rs144155419
1   723329  rs189787166 A   T   .   PASS    AF=0.00179726   ES:SE:LP:AF:SS:ID   0.0433932:0.0301179:0.824915:0.00179726:51427:rs189787166
1   730087  rs148120343 T   C   .   PASS    AF=0.0570822    ES:SE:LP:AF:SS:ID   0.00451709:0.00544274:0.390851:0.0570822:51427:rs148120343
1   731718  rs58276399  T   C   .   PASS    AF=0.122521 ES:SE:LP:AF:SS:ID   -0.000981135:0.00371404:0.101467:0.122521:51427:rs58276399
1   732032  rs61770163  A   C   .   PASS    AF=0.121651 ES:SE:LP:AF:SS:ID   0.00224938:0.00395915:0.244172:0.121651:51427:rs61770163
1   734349  rs141242758 T   C   .   PASS    AF=0.121765 ES:SE:LP:AF:SS:ID   -0.00113191:0.00371604:0.118803:0.121765:51427:rs141242758
1   740284  rs61770167  C   T   .   PASS    AF=0.0062329    ES:SE:LP:AF:SS:ID   -0.00122453:0.0162401:0.0269207:0.0062329:51427:rs61770167
1   742813  rs112573343 C   T   .   PASS    AF=0.00176649   ES:SE:LP:AF:SS:ID   0.0154998:0.0337468:0.189752:0.00176649:51427:rs112573343
1   749963  rs529266287 T   TAA .   PASS    AF=0.868613 ES:SE:LP:AF:SS:ID   -0.000465645:0.00365812:0.0463799:0.868613:51427:rs529266287
1   750230  rs190826124 G   C   .   PASS    AF=0.00158492   ES:SE:LP:AF:SS:ID   -0.0034392:0.0328233:0.0378434:0.00158492:51427:rs190826124
1   751343  rs28544273  T   A   .   PASS    AF=0.123957 ES:SE:LP:AF:SS:ID   0.000310572:0.00362388:0.030722:0.123957:51427:rs28544273
1   751488  rs200141114 G   GA  .   PASS    AF=0.143385 ES:SE:LP:AF:SS:ID   0.000172208:0.00359544:0.0169157:0.143385:51427:rs200141114
1   751756  rs28527770  T   C   .   PASS    AF=0.124126 ES:SE:LP:AF:SS:ID   0.000170135:0.00361786:0.0166029:0.124126:51427:rs28527770
1   753405  rs3115860   C   A   .   PASS    AF=0.869933 ES:SE:LP:AF:SS:ID   0.000885984:0.00352595:0.0960412:0.869933:51427:rs3115860
1   753425  rs3131970   T   C   .   PASS    AF=0.874426 ES:SE:LP:AF:SS:ID   0.00040188:0.003582:0.040639:0.874426:51427:rs3131970
1   753541  rs2073813   G   A   .   PASS    AF=0.129659 ES:SE:LP:AF:SS:ID   -0.000858776:0.00353463:0.0925688:0.129659:51427:rs2073813
1   754105  rs12184325  C   T   .   PASS    AF=0.0369164    ES:SE:LP:AF:SS:ID   0.00211966:0.00636634:0.131253:0.0369164:51427:rs12184325
1   754182  rs3131969   A   G   .   PASS    AF=0.869554 ES:SE:LP:AF:SS:ID   0.00084741:0.00352265:0.0915702:0.869554:51427:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.869648 ES:SE:LP:AF:SS:ID   0.000955501:0.00352449:0.104405:0.869648:51427:rs3131968
1   754334  rs3131967   T   C   .   PASS    AF=0.86957  ES:SE:LP:AF:SS:ID   0.000834121:0.00352265:0.0900045:0.86957:51427:rs3131967
1   754433  rs150578204 G   A   .   PASS    AF=0.00531261   ES:SE:LP:AF:SS:ID   -0.0160726:0.0176555:0.440517:0.00531261:51427:rs150578204
1   754458  rs142682604 G   T   .   PASS    AF=0.00527727   ES:SE:LP:AF:SS:ID   -0.0161943:0.0177019:0.443356:0.00527727:51427:rs142682604
1   755435  rs184270342 T   G   .   PASS    AF=0.0057746    ES:SE:LP:AF:SS:ID   0.0449129:0.017264:2.0323:0.0057746:51427:rs184270342
1   755890  rs3115858   A   T   .   PASS    AF=0.869706 ES:SE:LP:AF:SS:ID   0.00103833:0.00351734:0.11473:0.869706:51427:rs3115858
1   756434  rs61768170  G   C   .   PASS    AF=0.12702  ES:SE:LP:AF:SS:ID   -0.000702684:0.0035873:0.0732955:0.12702:51427:rs61768170
1   756604  rs3131962   A   G   .   PASS    AF=0.869213 ES:SE:LP:AF:SS:ID   0.000965334:0.00350809:0.106136:0.869213:51427:rs3131962
1   757640  rs3115853   G   A   .   PASS    AF=0.868449 ES:SE:LP:AF:SS:ID   0.00061735:0.00350469:0.0654122:0.868449:51427:rs3115853
1   757734  rs4951929   C   T   .   PASS    AF=0.869419 ES:SE:LP:AF:SS:ID   0.00100406:0.00351196:0.110722:0.869419:51427:rs4951929
1   757936  rs4951862   C   A   .   PASS    AF=0.869426 ES:SE:LP:AF:SS:ID   0.00100158:0.00351218:0.11041:0.869426:51427:rs4951862
1   758144  rs3131956   A   G   .   PASS    AF=0.869437 ES:SE:LP:AF:SS:ID   0.000991294:0.00351235:0.10915:0.869437:51427:rs3131956
1   758626  rs3131954   C   T   .   PASS    AF=0.869848 ES:SE:LP:AF:SS:ID   0.00114204:0.00352055:0.127469:0.869848:51427:rs3131954
1   759293  rs10157329  T   A   .   PASS    AF=0.0999077    ES:SE:LP:AF:SS:ID   0.0018371:0.00408263:0.185268:0.0999077:51427:rs10157329
1   759600  rs545998451 AGT A   .   PASS    AF=0.00659027   ES:SE:LP:AF:SS:ID   0.0458123:0.0156803:2.45799:0.00659027:51427:1_759600_AGT_A
1   759837  rs3115851   T   A   .   PASS    AF=0.87358  ES:SE:LP:AF:SS:ID   0.000990253:0.00357141:0.107031:0.87358:51427:rs3115851
1   761732  rs2286139   C   T   .   PASS    AF=0.86295  ES:SE:LP:AF:SS:ID   0.000644219:0.00350374:0.0684816:0.86295:51427:rs2286139
1   761752  rs1057213   C   T   .   PASS    AF=0.868667 ES:SE:LP:AF:SS:ID   0.00108624:0.00353811:0.119852:0.868667:51427:rs1057213
1   762273  rs3115849   G   A   .   PASS    AF=0.8652   ES:SE:LP:AF:SS:ID   0.00164547:0.00353654:0.192644:0.8652:51427:rs3115849
1   762485  rs12095200  C   A   .   PASS    AF=0.0992889    ES:SE:LP:AF:SS:ID   -0.000190929:0.00424445:0.0158685:0.0992889:51427:rs12095200
1   762589  rs3115848   G   C   .   PASS    AF=0.870459 ES:SE:LP:AF:SS:ID   0.00106657:0.00357629:0.116039:0.870459:51427:rs3115848
1   762592  rs3131950   C   G   .   PASS    AF=0.870459 ES:SE:LP:AF:SS:ID   0.00106591:0.00357629:0.11596:0.870459:51427:rs3131950
1   762601  rs3131949   T   C   .   PASS    AF=0.870456 ES:SE:LP:AF:SS:ID   0.00106497:0.00357631:0.115845:0.870456:51427:rs3131949
1   762632  rs3131948   T   A   .   PASS    AF=0.870829 ES:SE:LP:AF:SS:ID   0.00121219:0.00357835:0.133834:0.870829:51427:rs3131948
1   764191  rs7515915   T   G   .   PASS    AF=0.126636 ES:SE:LP:AF:SS:ID   -0.00103236:0.00358234:0.111703:0.126636:51427:rs7515915
1   766007  rs61768174  A   C   .   PASS    AF=0.106247 ES:SE:LP:AF:SS:ID   0.00215027:0.00390122:0.23544:0.106247:51427:rs61768174
1   766105  rs2519015   T   A   .   PASS    AF=0.854084 ES:SE:LP:AF:SS:ID   0.000885357:0.00350338:0.0966446:0.854084:51427:rs2519015
1   767393  rs538667473 A   C   .   PASS    AF=0.00168817   ES:SE:LP:AF:SS:ID   0.0447916:0.0303835:0.852534:0.00168817:51427:rs538667473
1   768116  rs376645387 A   AGTTTT  .   PASS    AF=0.836377 ES:SE:LP:AF:SS:ID   0.00342217:0.00343096:0.496813:0.836377:51427:rs376645387