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-5328_0/ukb-d-5328_0.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-5328_0/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 17:07:16 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-5328_0/ukb-d-5328_0.vcf.gz ...
Read summary statistics for 12258528 SNPs.
Dropped 10830 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, 1283133 SNPs remain.
After merging with regression SNP LD, 1283133 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0902 (0.0744)
Lambda GC: 1.0044
Mean Chi^2: 0.9962
Intercept: 0.9859 (0.0063)
Ratio: NA (mean chi^2 < 1)
Analysis finished at Mon Nov 25 17:09:39 2019
Total time elapsed: 2.0m:22.62s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9496,
    "inflation_factor": 1.047,
    "mean_EFFECT": 0,
    "n": 5786,
    "n_snps": 12258528,
    "n_clumped_hits": 12,
    "n_p_sig": 206,
    "n_mono": 0,
    "n_ns": 1195956,
    "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": 316798,
    "n_est": 5831.7465,
    "ratio_se_n": 1.0039,
    "mean_diff": 0.0002,
    "ratio_diff": 175.3873,
    "sd_y_est1": 0.1558,
    "sd_y_est2": 0.1564,
    "r2_sum1": 0.0021,
    "r2_sum2": 0.0847,
    "r2_sum3": 0.0841,
    "r2_sum4": 0.0751,
    "ldsc_nsnp_merge_refpanel_ld": 1283133,
    "ldsc_nsnp_merge_regression_ld": 1283133,
    "ldsc_observed_scale_h2_beta": 0.0902,
    "ldsc_observed_scale_h2_se": 0.0744,
    "ldsc_intercept_beta": 0.9859,
    "ldsc_intercept_se": 0.0063,
    "ldsc_lambda_gc": 1.0044,
    "ldsc_mean_chisq": 0.9962,
    "ldsc_ratio": 3.7105
}

Flags

name value
af_correlation FALSE
inflation_factor FALSE
n TRUE
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 1.0000000 3 94 0 12248328 0 NA NA NA NA NA NA NA NA
character REF 0 1.0000000 1 100 0 54008 0 NA NA NA NA NA NA NA NA
character ALT 0 1.0000000 1 342 0 32350 0 NA NA NA NA NA NA NA NA
numeric CHROM 0 1.0000000 NA NA NA NA NA 9.065585e+00 6.185050e+00 1.0000000 4.000000e+00 8.000000e+00 1.300000e+01 2.300000e+01 ▇▅▅▂▂
numeric POS 0 1.0000000 NA NA NA NA NA 7.892537e+07 5.597980e+07 302.0000000 3.273278e+07 6.996358e+07 1.147895e+08 2.492309e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA 2.800000e-05 1.212020e-02 -0.2275140 -3.623300e-03 2.428000e-04 4.273300e-03 1.420050e-01 ▁▁▂▇▁
numeric SE 0 1.0000000 NA NA NA NA NA 9.231400e-03 7.857900e-03 0.0023501 3.351700e-03 5.441900e-03 1.283240e-02 4.743180e-02 ▇▂▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.989803e-01 2.862923e-01 0.0000000 2.571550e-01 4.900992e-01 7.479852e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.989526e-01 2.863088e-01 0.0000000 2.571073e-01 4.900705e-01 7.479734e-01 9.999998e-01 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA 2.103956e-01 2.586484e-01 0.0022150 1.364080e-02 8.636300e-02 3.332870e-01 9.977850e-01 ▇▂▁▁▁
numeric AF_reference 316798 0.9741569 NA NA NA NA NA 2.123056e-01 2.502735e-01 0.0000000 1.038340e-02 1.067550e-01 3.370610e-01 1.000000e+00 ▇▂▁▁▁
numeric N 0 1.0000000 NA NA NA NA NA 5.786000e+03 0.000000e+00 5786.0000000 5.786000e+03 5.786000e+03 5.786000e+03 5.786000e+03 ▁▁▇▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 692794 rs530212009 CA C 0.0048762 0.0050141 0.3308491 0.3308089 0.1134050 0.1894970 5786
1 693731 rs12238997 A G 0.0037068 0.0048227 0.4421473 0.4421156 0.1156780 0.1417730 5786
1 707522 rs371890604 G C 0.0079852 0.0053736 0.1373359 0.1372813 0.0987746 0.1293930 5786
1 717587 rs144155419 G A -0.0248327 0.0139311 0.0747137 0.0746617 0.0136764 0.0045926 5786
1 730087 rs148120343 T C 0.0123525 0.0065729 0.0602518 0.0602025 0.0584680 0.0127796 5786
1 731718 rs142557973 T C 0.0024987 0.0045647 0.5841266 0.5841068 0.1219240 0.1543530 5786
1 732032 rs61770163 A C 0.0039221 0.0048799 0.4215897 0.4215569 0.1215660 0.1555510 5786
1 734349 rs141242758 T C 0.0026165 0.0045680 0.5668133 0.5667904 0.1211870 0.1525560 5786
1 740284 rs61770167 C T -0.0079140 0.0178017 0.6566531 0.6566367 0.0074846 0.0023962 5786
1 749963 rs529266287 T TAA -0.0043230 0.0045313 0.3401019 0.3400624 0.8713470 0.7641770 5786
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
23 154923311 rs141127553 C T 0.0021483 0.0051356 0.6757359 0.6757198 0.0566537 0.0309934 5786
23 154923374 rs111332691 T A -0.0017379 0.0054767 0.7510053 0.7509938 0.0478742 0.0116556 5786
23 154925045 rs509981 C T -0.0004950 0.0027929 0.8593281 0.8593224 0.2411450 0.3634440 5786
23 154925895 rs538470 C T -0.0007673 0.0028614 0.7885768 0.7885675 0.2376660 0.3634440 5786
23 154927581 rs644138 G A 0.0001478 0.0026156 0.9549260 0.9549236 0.2980750 0.4635760 5786
23 154929412 rs557132 C T -0.0005044 0.0027950 0.8567930 0.8567862 0.2410090 0.3568210 5786
23 154929637 rs35185538 CT C 0.0000805 0.0029224 0.9780150 0.9780139 0.2262540 0.3011920 5786
23 154929952 rs4012982 CAA C -0.0009041 0.0029538 0.7595598 0.7595476 0.2337370 0.3165560 5786
23 154930230 rs781880 A G -0.0004236 0.0027937 0.8794951 0.8794901 0.2417050 0.3618540 5786
23 154930487 rs781879 T A -0.0037139 0.0091740 0.6856145 0.6856001 0.0199491 0.1263580 5786

bcf preview

1   692794  rs530212009 CA  C   .   PASS    AF=0.113405 ES:SE:LP:AF:SS:ID   0.00487618:0.00501414:0.48037:0.113405:5786:1_692794_CA_C
1   693731  rs12238997  A   G   .   PASS    AF=0.115678 ES:SE:LP:AF:SS:ID   0.00370682:0.00482266:0.354433:0.115678:5786:rs12238997
1   707522  rs371890604 G   C   .   PASS    AF=0.0987746    ES:SE:LP:AF:SS:ID   0.00798517:0.00537363:0.862216:0.0987746:5786:rs371890604
1   717587  rs144155419 G   A   .   PASS    AF=0.0136764    ES:SE:LP:AF:SS:ID   -0.0248327:0.0139311:1.1266:0.0136764:5786:rs144155419
1   730087  rs148120343 T   C   .   PASS    AF=0.058468 ES:SE:LP:AF:SS:ID   0.0123525:0.0065729:1.22003:0.058468:5786:rs148120343
1   731718  rs58276399  T   C   .   PASS    AF=0.121924 ES:SE:LP:AF:SS:ID   0.00249872:0.00456474:0.233493:0.121924:5786:rs58276399
1   732032  rs61770163  A   C   .   PASS    AF=0.121566 ES:SE:LP:AF:SS:ID   0.00392208:0.00487989:0.37511:0.121566:5786:rs61770163
1   734349  rs141242758 T   C   .   PASS    AF=0.121187 ES:SE:LP:AF:SS:ID   0.00261651:0.00456805:0.24656:0.121187:5786:rs141242758
1   740284  rs61770167  C   T   .   PASS    AF=0.0074846    ES:SE:LP:AF:SS:ID   -0.00791395:0.0178017:0.182664:0.0074846:5786:rs61770167
1   749963  rs529266287 T   TAA .   PASS    AF=0.871347 ES:SE:LP:AF:SS:ID   -0.00432305:0.0045313:0.468391:0.871347:5786:rs529266287
1   751343  rs28544273  T   A   .   PASS    AF=0.121263 ES:SE:LP:AF:SS:ID   0.00282517:0.0044831:0.276873:0.121263:5786:rs28544273
1   751488  rs200141114 G   GA  .   PASS    AF=0.140959 ES:SE:LP:AF:SS:ID   0.0013891:0.00446299:0.121695:0.140959:5786:rs200141114
1   751756  rs28527770  T   C   .   PASS    AF=0.121381 ES:SE:LP:AF:SS:ID   0.00270373:0.00447542:0.262981:0.121381:5786:rs28527770
1   753405  rs3115860   C   A   .   PASS    AF=0.872185 ES:SE:LP:AF:SS:ID   -0.00252289:0.0043674:0.249095:0.872185:5786:rs3115860
1   753425  rs3131970   T   C   .   PASS    AF=0.878042 ES:SE:LP:AF:SS:ID   -0.00191687:0.00444622:0.176269:0.878042:5786:rs3131970
1   753541  rs2073813   G   A   .   PASS    AF=0.128    ES:SE:LP:AF:SS:ID   0.0026977:0.00436554:0.270324:0.128:5786:rs2073813
1   754105  rs12184325  C   T   .   PASS    AF=0.0366402    ES:SE:LP:AF:SS:ID   0.0161338:0.00782427:1.40616:0.0366402:5786:rs12184325
1   754182  rs3131969   A   G   .   PASS    AF=0.871813 ES:SE:LP:AF:SS:ID   -0.00256725:0.00436137:0.254824:0.871813:5786:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.871984 ES:SE:LP:AF:SS:ID   -0.0025273:0.00436358:0.249884:0.871984:5786:rs3131968
1   754334  rs3131967   T   C   .   PASS    AF=0.871817 ES:SE:LP:AF:SS:ID   -0.00257254:0.00436128:0.255466:0.871817:5786:rs3131967
1   754433  rs150578204 G   A   .   PASS    AF=0.00449903   ES:SE:LP:AF:SS:ID   0.00732036:0.023514:0.121726:0.00449903:5786:rs150578204
1   754458  rs142682604 G   T   .   PASS    AF=0.00447531   ES:SE:LP:AF:SS:ID   0.00720231:0.0235658:0.119243:0.00447531:5786:rs142682604
1   755435  rs184270342 T   G   .   PASS    AF=0.00555804   ES:SE:LP:AF:SS:ID   -0.0513793:0.0216986:1.74656:0.00555804:5786:rs184270342
1   755890  rs3115858   A   T   .   PASS    AF=0.872024 ES:SE:LP:AF:SS:ID   -0.00252288:0.00435554:0.249914:0.872024:5786:rs3115858
1   756434  rs61768170  G   C   .   PASS    AF=0.124644 ES:SE:LP:AF:SS:ID   0.00239547:0.00444385:0.229243:0.124644:5786:rs61768170
1   756604  rs3131962   A   G   .   PASS    AF=0.8715   ES:SE:LP:AF:SS:ID   -0.00262727:0.00434457:0.263296:0.8715:5786:rs3131962
1   757640  rs3115853   G   A   .   PASS    AF=0.87103  ES:SE:LP:AF:SS:ID   -0.0027097:0.00433797:0.273903:0.87103:5786:rs3115853
1   757734  rs4951929   C   T   .   PASS    AF=0.871881 ES:SE:LP:AF:SS:ID   -0.00255189:0.00435042:0.25375:0.871881:5786:rs4951929
1   757936  rs4951862   C   A   .   PASS    AF=0.871885 ES:SE:LP:AF:SS:ID   -0.00255113:0.0043507:0.25364:0.871885:5786:rs4951862
1   758144  rs3131956   A   G   .   PASS    AF=0.871888 ES:SE:LP:AF:SS:ID   -0.00255355:0.00435065:0.253934:0.871888:5786:rs3131956
1   758626  rs3131954   C   T   .   PASS    AF=0.872279 ES:SE:LP:AF:SS:ID   -0.00248113:0.0043621:0.244492:0.872279:5786:rs3131954
1   759293  rs10157329  T   A   .   PASS    AF=0.0990037    ES:SE:LP:AF:SS:ID   0.00452126:0.00504958:0.431066:0.0990037:5786:rs10157329
1   759600  rs545998451 AGT A   .   PASS    AF=0.006736 ES:SE:LP:AF:SS:ID   -0.0479188:0.0187489:1.9739:0.006736:5786:1_759600_AGT_A
1   759837  rs3115851   T   A   .   PASS    AF=0.877243 ES:SE:LP:AF:SS:ID   -0.00273963:0.00443733:0.270032:0.877243:5786:rs3115851
1   761732  rs2286139   C   T   .   PASS    AF=0.865639 ES:SE:LP:AF:SS:ID   -0.00376108:0.00433523:0.413783:0.865639:5786:rs2286139
1   761752  rs1057213   C   T   .   PASS    AF=0.870796 ES:SE:LP:AF:SS:ID   -0.00355208:0.0043886:0.378486:0.870796:5786:rs1057213
1   762273  rs3115849   G   A   .   PASS    AF=0.86726  ES:SE:LP:AF:SS:ID   -0.0028973:0.00437956:0.293892:0.86726:5786:rs3115849
1   762485  rs12095200  C   A   .   PASS    AF=0.0964539    ES:SE:LP:AF:SS:ID   0.00370514:0.00526966:0.316939:0.0964539:5786:rs12095200
1   762589  rs3115848   G   C   .   PASS    AF=0.873004 ES:SE:LP:AF:SS:ID   -0.00179924:0.00442939:0.164559:0.873004:5786:rs3115848
1   762592  rs3131950   C   G   .   PASS    AF=0.873004 ES:SE:LP:AF:SS:ID   -0.00179924:0.00442939:0.164559:0.873004:5786:rs3131950
1   762601  rs3131949   T   C   .   PASS    AF=0.873001 ES:SE:LP:AF:SS:ID   -0.00179994:0.0044294:0.164632:0.873001:5786:rs3131949
1   762632  rs3131948   T   A   .   PASS    AF=0.873618 ES:SE:LP:AF:SS:ID   -0.00166558:0.00443894:0.150267:0.873618:5786:rs3131948
1   764191  rs7515915   T   G   .   PASS    AF=0.124076 ES:SE:LP:AF:SS:ID   0.00296497:0.00443839:0.297446:0.124076:5786:rs7515915
1   766007  rs61768174  A   C   .   PASS    AF=0.106952 ES:SE:LP:AF:SS:ID   0.00631342:0.00476452:0.732373:0.106952:5786:rs61768174
1   766105  rs2519015   T   A   .   PASS    AF=0.858256 ES:SE:LP:AF:SS:ID   -0.00471921:0.00435045:0.555841:0.858256:5786:rs2519015
1   768116  rs376645387 A   AGTTTT  .   PASS    AF=0.838099 ES:SE:LP:AF:SS:ID   0.00410952:0.00421686:0.481714:0.838099:5786:rs376645387
1   768253  rs2977608   A   C   .   PASS    AF=0.762581 ES:SE:LP:AF:SS:ID   -0.0002828:0.00341005:0.0296954:0.762581:5786:rs2977608
1   768448  rs12562034  G   A   .   PASS    AF=0.107847 ES:SE:LP:AF:SS:ID   -0.00287766:0.00463288:0.272025:0.107847:5786:rs12562034
1   768819  rs12562811  C   T   .   PASS    AF=0.0069722    ES:SE:LP:AF:SS:ID   -0.0057743:0.018509:0.122012:0.0069722:5786:rs12562811
1   769138  rs59306077  CAT C   .   PASS    AF=0.127893 ES:SE:LP:AF:SS:ID   0.00318616:0.00436782:0.331849:0.127893:5786:rs762168062