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_6/ukb-d-680_6.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_6/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 17:18:26 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-680_6/ukb-d-680_6.vcf.gz ...
Read summary statistics for 10768473 SNPs.
Dropped 8740 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, 1281459 SNPs remain.
After merging with regression SNP LD, 1281459 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.002 (0.0013)
Lambda GC: 1.0066
Mean Chi^2: 1.006
Intercept: 0.9921 (0.007)
Ratio < 0 (usually indicates GC correction).
Analysis finished at Mon Nov 25 17:20:19 2019
Total time elapsed: 1.0m:53.02s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9451,
    "inflation_factor": 1.0057,
    "mean_EFFECT": -8.7529e-08,
    "n": 356340,
    "n_snps": 10768473,
    "n_clumped_hits": 0,
    "n_p_sig": 0,
    "n_mono": 0,
    "n_ns": 1126209,
    "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": 213072,
    "n_est": 356822.5666,
    "ratio_se_n": 1.0007,
    "mean_diff": -1.0246e-06,
    "ratio_diff": 21.5154,
    "sd_y_est1": 0.0822,
    "sd_y_est2": 0.0822,
    "r2_sum1": 0,
    "r2_sum2": 0,
    "r2_sum3": 0,
    "r2_sum4": 0,
    "ldsc_nsnp_merge_refpanel_ld": 1281459,
    "ldsc_nsnp_merge_regression_ld": 1281459,
    "ldsc_observed_scale_h2_beta": 0.002,
    "ldsc_observed_scale_h2_se": 0.0013,
    "ldsc_intercept_beta": 0.9921,
    "ldsc_intercept_se": 0.007,
    "ldsc_lambda_gc": 1.0066,
    "ldsc_mean_chisq": 1.006,
    "ldsc_ratio": -1.3167
}

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 10760310 0 NA NA NA NA NA NA NA NA
character REF 0 1.0000000 1 100 0 50469 0 NA NA NA NA NA NA NA NA
character ALT 0 1.0000000 1 342 0 31065 0 NA NA NA NA NA NA NA NA
numeric CHROM 0 1.0000000 NA NA NA NA NA 9.075031e+00 6.179537e+00 1.0000e+00 4.000000e+00 8.000000e+00 1.300000e+01 2.300000e+01 ▇▅▅▂▂
numeric POS 0 1.0000000 NA NA NA NA NA 7.880559e+07 5.603964e+07 3.0200e+02 3.257831e+07 6.976655e+07 1.147371e+08 2.492309e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA -1.000000e-07 5.626000e-04 -5.1829e-03 -2.334000e-04 -2.500000e-06 2.290000e-04 6.987000e-03 ▁▂▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 4.624000e-04 3.225000e-04 1.6020e-04 2.178000e-04 3.128000e-04 6.139000e-04 1.772000e-03 ▇▂▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.992473e-01 2.889710e-01 1.0000e-07 2.486841e-01 4.987880e-01 7.498838e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.992468e-01 2.889713e-01 1.0000e-07 2.486828e-01 4.987880e-01 7.498825e-01 1.000000e+00 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA 2.377699e-01 2.622265e-01 5.1889e-03 2.715960e-02 1.253870e-01 3.806800e-01 9.948110e-01 ▇▂▂▁▁
numeric AF_reference 213072 0.9802134 NA NA NA NA NA 2.378100e-01 2.532504e-01 0.0000e+00 2.695690e-02 1.423720e-01 3.781950e-01 1.000000e+00 ▇▂▂▁▁
numeric N 0 1.0000000 NA NA NA NA NA 3.563400e+05 0.000000e+00 3.5634e+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 -0.0001228 0.0003413 0.7190234 0.7190240 0.1106480 0.1894970 356340
1 693731 rs12238997 A G 0.0000580 0.0003225 0.8572480 0.8572480 0.1157970 0.1417730 356340
1 707522 rs371890604 G C -0.0000720 0.0003626 0.8426340 0.8426339 0.0972849 0.1293930 356340
1 717587 rs144155419 G A 0.0000905 0.0008651 0.9167031 0.9167033 0.0156800 0.0045926 356340
1 730087 rs148120343 T C 0.0000612 0.0004493 0.8915590 0.8915593 0.0564590 0.0127796 356340
1 731718 rs142557973 T C -0.0000319 0.0003058 0.9169579 0.9169578 0.1217310 0.1543530 356340
1 732032 rs61770163 A C 0.0000172 0.0003263 0.9580481 0.9580478 0.1211470 0.1555510 356340
1 734349 rs141242758 T C -0.0000403 0.0003060 0.8952980 0.8952975 0.1209580 0.1525560 356340
1 740284 rs61770167 C T -0.0006461 0.0013971 0.6437259 0.6437261 0.0058056 0.0023962 356340
1 749963 rs529266287 T TAA 0.0001506 0.0003017 0.6176821 0.6176820 0.8697510 0.7641770 356340
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
23 154923311 rs141127553 C T -0.0001582 0.0003531 0.6541013 0.6541012 0.0562156 0.0309934 356340
23 154923374 rs111332691 T A 0.0000957 0.0003883 0.8053300 0.8053302 0.0448027 0.0116556 356340
23 154925045 rs509981 C T 0.0002486 0.0001869 0.1834180 0.1834162 0.2454610 0.3634440 356340
23 154925895 rs538470 C T 0.0002407 0.0001912 0.2079462 0.2079454 0.2417790 0.3634440 356340
23 154927581 rs644138 G A 0.0001764 0.0001757 0.3153639 0.3153619 0.3020610 0.4635760 356340
23 154929412 rs557132 C T 0.0002445 0.0001869 0.1908288 0.1908279 0.2453120 0.3568210 356340
23 154929637 rs35185538 CT C 0.0003340 0.0001951 0.0868560 0.0868551 0.2295890 0.3011920 356340
23 154929952 rs4012982 CAA C 0.0002488 0.0001966 0.2057302 0.2057279 0.2392680 0.3165560 356340
23 154930230 rs781880 A G 0.0002585 0.0001869 0.1665962 0.1665947 0.2457230 0.3618540 356340
23 154930487 rs781879 T A 0.0004435 0.0006415 0.4893719 0.4893716 0.0195351 0.1263580 356340

bcf preview

1   692794  rs530212009 CA  C   .   PASS    AF=0.110648 ES:SE:LP:AF:SS:ID   -0.00012277:0.000341252:0.143257:0.110648:356340:1_692794_CA_C
1   693731  rs12238997  A   G   .   PASS    AF=0.115797 ES:SE:LP:AF:SS:ID   5.80151e-05:0.000322524:0.0668935:0.115797:356340:rs12238997
1   707522  rs371890604 G   C   .   PASS    AF=0.0972849    ES:SE:LP:AF:SS:ID   -7.19776e-05:0.000362561:0.074361:0.0972849:356340:rs371890604
1   717587  rs144155419 G   A   .   PASS    AF=0.01568  ES:SE:LP:AF:SS:ID   9.04792e-05:0.000865107:0.0377713:0.01568:356340:rs144155419
1   730087  rs148120343 T   C   .   PASS    AF=0.056459 ES:SE:LP:AF:SS:ID   6.1248e-05:0.000449258:0.0498499:0.056459:356340:rs148120343
1   731718  rs58276399  T   C   .   PASS    AF=0.121731 ES:SE:LP:AF:SS:ID   -3.18893e-05:0.000305844:0.0376506:0.121731:356340:rs58276399
1   732032  rs61770163  A   C   .   PASS    AF=0.121147 ES:SE:LP:AF:SS:ID   1.71621e-05:0.000326254:0.0186127:0.121147:356340:rs61770163
1   734349  rs141242758 T   C   .   PASS    AF=0.120958 ES:SE:LP:AF:SS:ID   -4.02724e-05:0.000306012:0.0480324:0.120958:356340:rs141242758
1   740284  rs61770167  C   T   .   PASS    AF=0.0058056    ES:SE:LP:AF:SS:ID   -0.000646143:0.00139708:0.191299:0.0058056:356340:rs61770167
1   749963  rs529266287 T   TAA .   PASS    AF=0.869751 ES:SE:LP:AF:SS:ID   0.000150585:0.00030169:0.209235:0.869751:356340:rs529266287
1   751343  rs28544273  T   A   .   PASS    AF=0.122921 ES:SE:LP:AF:SS:ID   -7.54444e-05:0.000298761:0.0965649:0.122921:356340:rs28544273
1   751488  rs200141114 G   GA  .   PASS    AF=0.142704 ES:SE:LP:AF:SS:ID   -0.000188513:0.000295316:0.281291:0.142704:356340:rs200141114
1   751756  rs28527770  T   C   .   PASS    AF=0.123036 ES:SE:LP:AF:SS:ID   -7.50407e-05:0.000298346:0.0961447:0.123036:356340:rs28527770
1   753405  rs3115860   C   A   .   PASS    AF=0.870892 ES:SE:LP:AF:SS:ID   3.24497e-05:0.000290727:0.0404206:0.870892:356340:rs3115860
1   753425  rs3131970   T   C   .   PASS    AF=0.875468 ES:SE:LP:AF:SS:ID   0.00011908:0.000295549:0.163034:0.875468:356340:rs3131970
1   753541  rs2073813   G   A   .   PASS    AF=0.128631 ES:SE:LP:AF:SS:ID   -2.61508e-05:0.000291451:0.0322158:0.128631:356340:rs2073813
1   754105  rs12184325  C   T   .   PASS    AF=0.0363599    ES:SE:LP:AF:SS:ID   0.00101213:0.000528696:1.25516:0.0363599:356340:rs12184325
1   754182  rs3131969   A   G   .   PASS    AF=0.870484 ES:SE:LP:AF:SS:ID   4.82394e-05:0.000290423:0.0614413:0.870484:356340:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.870586 ES:SE:LP:AF:SS:ID   6.64559e-05:0.00029055:0.0866721:0.870586:356340:rs3131968
1   754334  rs3131967   T   C   .   PASS    AF=0.870482 ES:SE:LP:AF:SS:ID   4.23203e-05:0.000290412:0.0534799:0.870482:356340:rs3131967
1   755435  rs184270342 T   G   .   PASS    AF=0.00555675   ES:SE:LP:AF:SS:ID   0.00229468:0.00144792:0.946879:0.00555675:356340:rs184270342
1   755890  rs3115858   A   T   .   PASS    AF=0.870565 ES:SE:LP:AF:SS:ID   2.11995e-05:0.0002899:0.0260851:0.870565:356340:rs3115858
1   756434  rs61768170  G   C   .   PASS    AF=0.125983 ES:SE:LP:AF:SS:ID   -2.48203e-05:0.000295812:0.0300569:0.125983:356340:rs61768170
1   756604  rs3131962   A   G   .   PASS    AF=0.870131 ES:SE:LP:AF:SS:ID   6.21357e-06:0.000289207:0.00750878:0.870131:356340:rs3131962
1   757640  rs3115853   G   A   .   PASS    AF=0.869417 ES:SE:LP:AF:SS:ID   3.6712e-05:0.00028894:0.046291:0.869417:356340:rs3115853
1   757734  rs4951929   C   T   .   PASS    AF=0.870287 ES:SE:LP:AF:SS:ID   1.94366e-05:0.000289457:0.0238959:0.870287:356340:rs4951929
1   757936  rs4951862   C   A   .   PASS    AF=0.870293 ES:SE:LP:AF:SS:ID   1.96726e-05:0.000289478:0.024192:0.870293:356340:rs4951862
1   758144  rs3131956   A   G   .   PASS    AF=0.870301 ES:SE:LP:AF:SS:ID   1.93102e-05:0.000289487:0.023734:0.870301:356340:rs3131956
1   758626  rs3131954   C   T   .   PASS    AF=0.870742 ES:SE:LP:AF:SS:ID   3.64362e-05:0.00029022:0.0457136:0.870742:356340:rs3131954
1   759293  rs10157329  T   A   .   PASS    AF=0.0988331    ES:SE:LP:AF:SS:ID   -9.83224e-05:0.000337285:0.113137:0.0988331:356340:rs10157329
1   759600  rs545998451 AGT A   .   PASS    AF=0.00645051   ES:SE:LP:AF:SS:ID   0.00222034:0.00130719:1.04865:0.00645051:356340:1_759600_AGT_A
1   759837  rs3115851   T   A   .   PASS    AF=0.87464  ES:SE:LP:AF:SS:ID   0.00011981:0.000294557:0.16482:0.87464:356340:rs3115851
1   761732  rs2286139   C   T   .   PASS    AF=0.864041 ES:SE:LP:AF:SS:ID   5.52458e-05:0.000288852:0.0714393:0.864041:356340:rs2286139
1   761752  rs1057213   C   T   .   PASS    AF=0.869434 ES:SE:LP:AF:SS:ID   6.50185e-05:0.000291662:0.0842863:0.869434:356340:rs1057213
1   762273  rs3115849   G   A   .   PASS    AF=0.866374 ES:SE:LP:AF:SS:ID   8.52842e-05:0.000291714:0.113501:0.866374:356340:rs3115849
1   762485  rs12095200  C   A   .   PASS    AF=0.098777 ES:SE:LP:AF:SS:ID   -9.7702e-06:0.000349272:0.00980149:0.098777:356340:rs12095200
1   762589  rs3115848   G   C   .   PASS    AF=0.87156  ES:SE:LP:AF:SS:ID   0.000130862:0.000295045:0.182183:0.87156:356340:rs3115848
1   762592  rs3131950   C   G   .   PASS    AF=0.87156  ES:SE:LP:AF:SS:ID   0.000130865:0.000295045:0.182188:0.87156:356340:rs3131950
1   762601  rs3131949   T   C   .   PASS    AF=0.87156  ES:SE:LP:AF:SS:ID   0.000130478:0.00029505:0.181557:0.87156:356340:rs3131949
1   762632  rs3131948   T   A   .   PASS    AF=0.871936 ES:SE:LP:AF:SS:ID   0.000139479:0.000295218:0.196134:0.871936:356340:rs3131948
1   764191  rs7515915   T   G   .   PASS    AF=0.12556  ES:SE:LP:AF:SS:ID   -7.47787e-05:0.000295445:0.0968085:0.12556:356340:rs7515915
1   766007  rs61768174  A   C   .   PASS    AF=0.10543  ES:SE:LP:AF:SS:ID   -4.54412e-05:0.000321627:0.0517607:0.10543:356340:rs61768174
1   766105  rs2519015   T   A   .   PASS    AF=0.855374 ES:SE:LP:AF:SS:ID   0.000140114:0.000288732:0.202397:0.855374:356340:rs2519015
1   768116  rs376645387 A   AGTTTT  .   PASS    AF=0.838431 ES:SE:LP:AF:SS:ID   -0.000301069:0.000284512:0.53765:0.838431:356340:rs376645387
1   768253  rs2977608   A   C   .   PASS    AF=0.763424 ES:SE:LP:AF:SS:ID   -0.000159878:0.000228969:0.314239:0.763424:356340:rs2977608
1   768448  rs12562034  G   A   .   PASS    AF=0.105855 ES:SE:LP:AF:SS:ID   0.000358295:0.000315498:0.591584:0.105855:356340:rs12562034
1   768819  rs12562811  C   T   .   PASS    AF=0.00766712   ES:SE:LP:AF:SS:ID   0.00331634:0.00117346:2.3268:0.00766712:356340:rs12562811
1   769138  rs59306077  CAT C   .   PASS    AF=0.12893  ES:SE:LP:AF:SS:ID   -1.71855e-05:0.00029131:0.0209267:0.12893:356340:rs762168062
1   769223  rs60320384  C   G   .   PASS    AF=0.1286   ES:SE:LP:AF:SS:ID   8.02846e-06:0.00029104:0.00966425:0.1286:356340:rs60320384
1   769963  rs7518545   G   A   .   PASS    AF=0.105148 ES:SE:LP:AF:SS:ID   0.0003769:0.000317879:0.627545:0.105148:356340:rs7518545