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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    "gwas_harmonisation_command": "--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/vcf_09_19b/bgzip_vcf/data.batch_3085.vcf.gz --id UKB-b:17952 --data /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/raw-output/data.batch_3085.txt.gz --cohort_controls 40613 --ref /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/human_g1k_v37.fasta --json /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/ukb_gwas.json; 1.1.1",
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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/public/UKB-b-17952/UKB-b-17952_data.vcf.gz \
--ref-ld-chr ../reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-17952/ldsc.txt \
--w-ld-chr ../reference/eur_w_ld_chr/ 

Beginning analysis at Thu Oct 17 14:40:18 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-17952/UKB-b-17952_data.vcf.gz ...
Read summary statistics for 7939558 SNPs.
Dropped 6016 SNPs with duplicated rs numbers.
Reading reference panel LD Score from ../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 ../reference/eur_w_ld_chr/[1-22] ...
Read regression weight LD Scores for 1290028 SNPs.
After merging with reference panel LD, 1281557 SNPs remain.
After merging with regression SNP LD, 1281557 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.2533 (0.0305)
Lambda GC: 1.1492
Mean Chi^2: 1.2246
Intercept: 1.0149 (0.01)
Ratio: 0.0663 (0.0446)
Analysis finished at Thu Oct 17 14:41:49 2019
Total time elapsed: 1.0m:31.12s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9425,
    "inflation_factor": 1.0966,
    "mean_EFFECT": -5.6766e-06,
    "n": "-Inf",
    "n_snps": 9851866,
    "n_clumped_hits": 41,
    "n_p_sig": 2740,
    "n_mono": 0,
    "n_ns": 0,
    "n_mac": 0,
    "is_snpid_unique": true,
    "n_miss_EFFECT": 0,
    "n_miss_SE": 0,
    "n_miss_PVAL": 0,
    "n_miss_AF": 0,
    "n_miss_AF_reference": 74070,
    "n_est": "NA",
    "ratio_se_n": "NA",
    "mean_diff": "NaN",
    "ratio_diff": "NaN",
    "sd_y_est1": "NaN",
    "sd_y_est2": "NA",
    "r2_sum1": 0,
    "r2_sum2": 0,
    "r2_sum3": 0,
    "r2_sum4": 0,
    "ldsc_nsnp_merge_refpanel_ld": 1281557,
    "ldsc_nsnp_merge_regression_ld": 1281557,
    "ldsc_observed_scale_h2_beta": 0.2533,
    "ldsc_observed_scale_h2_se": 0.0305,
    "ldsc_intercept_beta": 1.0149,
    "ldsc_intercept_se": 0.01,
    "ldsc_lambda_gc": 1.1492,
    "ldsc_mean_chisq": 1.2246,
    "ldsc_ratio": 0.0663
}
 

Flags

name value
af_correlation FALSE
inflation_factor FALSE
n TRUE
is_snpid_non_unique FALSE
mean_EFFECT_nonfinite FALSE
mean_EFFECT_05 FALSE
mean_EFFECT_01 FALSE
mean_chisq FALSE
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 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 logical.mean logical.count numeric.mean numeric.sd numeric.p0 numeric.p25 numeric.p50 numeric.p75 numeric.p100 numeric.hist
character ID 0 1.0000000 3 58 0 7933569 0 NA NA NA NA NA NA NA NA NA NA
character REF 0 1.0000000 1 1 0 4 0 NA NA NA NA NA NA NA NA NA NA
character ALT 0 1.0000000 1 1 0 4 0 NA NA NA NA NA NA NA NA NA NA
logical N 7939558 0.0000000 NA NA NA NA NA NaN : NA NA NA NA NA NA NA NA
numeric CHROM 0 1.0000000 NA NA NA NA NA NA NA 8.660405e+00 5.763588e+00 1.0000000 4.000000e+00 8.000000e+00 1.300000e+01 2.200000e+01 ▇▅▅▂▂
numeric POS 0 1.0000000 NA NA NA NA NA NA NA 7.870876e+07 5.642285e+07 828.0000000 3.225644e+07 6.918309e+07 1.145575e+08 2.492385e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA NA NA -5.700000e-06 1.685000e-02 -0.2028520 -8.004700e-03 -1.150000e-05 7.985900e-03 1.879900e-01 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA NA NA 1.392580e-02 8.272900e-03 0.0063973 7.412600e-03 1.027170e-02 1.827560e-02 7.746890e-02 ▇▂▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA NA NA 4.815280e-01 2.944327e-01 0.0000000 2.200002e-01 4.799997e-01 7.400005e-01 1.000000e+00 ▇▇▇▆▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA NA NA 4.815287e-01 2.944071e-01 0.0000000 2.217557e-01 4.753724e-01 7.369978e-01 9.999997e-01 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA NA NA 2.471889e-01 2.607850e-01 0.0086180 3.650920e-02 1.388410e-01 3.914740e-01 9.913820e-01 ▇▂▂▁▁
numeric AF_reference 74070 0.9906708 NA NA NA NA NA NA NA 2.463905e-01 2.526037e-01 0.0000000 3.873800e-02 1.541530e-01 3.865810e-01 1.000000e+00 ▇▃▂▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 49298 rs200943160 T C 0.0011228 0.0117580 0.9199999 0.9239237 0.623882 0.7821490 NA
1 54676 rs2462492 C T -0.0256436 0.0116790 0.0280001 0.0281133 0.401861 NA NA
1 86028 rs114608975 T C 0.0080182 0.0184892 0.6600001 0.6645278 0.103927 0.0277556 NA
1 91536 rs6702460 G T -0.0234813 0.0114048 0.0400000 0.0395042 0.458825 0.4207270 NA
1 234313 rs8179466 C T -0.0274260 0.0228004 0.2300001 0.2290252 0.073683 NA NA
1 534192 rs6680723 C T -0.0105416 0.0130188 0.4199997 0.4181004 0.242155 NA NA
1 546697 rs12025928 A G 0.0244151 0.0166133 0.1400000 0.1416670 0.915728 NA NA
1 693731 rs12238997 A G 0.0109102 0.0111703 0.3300000 0.3287102 0.112708 0.1417730 NA
1 705882 rs72631875 G A 0.0035976 0.0164690 0.8300000 0.8270834 0.064258 0.0315495 NA
1 706368 rs55727773 A G -0.0042307 0.0081686 0.5999997 0.6045108 0.513756 0.2751600 NA
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51219006 rs28729663 G A 0.0103683 0.0098115 0.2900000 0.2906239 0.139274 0.2052720 NA
22 51219387 rs9616832 T C -0.0025858 0.0126315 0.8400000 0.8377959 0.076170 0.0654952 NA
22 51219704 rs147475742 G A -0.0014906 0.0171069 0.9299999 0.9305665 0.042286 0.0473243 NA
22 51221190 rs369304721 G A 0.0052313 0.0170028 0.7600007 0.7583313 0.051070 NA NA
22 51221731 rs115055839 T C -0.0009805 0.0126319 0.9400001 0.9381307 0.075698 0.0625000 NA
22 51222100 rs114553188 G T 0.0252776 0.0151691 0.0959997 0.0956362 0.053592 0.0880591 NA
22 51223637 rs375798137 G A 0.0255403 0.0152400 0.0940005 0.0937631 0.053223 0.0788738 NA
22 51229805 rs9616985 T C 0.0000985 0.0126783 0.9900000 0.9938023 0.075449 0.0730831 NA
22 51232488 rs376461333 A G 0.0621624 0.0302138 0.0400000 0.0396461 0.019783 NA NA
22 51237063 rs3896457 T C -0.0121359 0.0078167 0.1199999 0.1205291 0.300040 0.2050720 NA

bcf preview

1   49298   rs10399793  T   C   .   PASS    AF=0.623882 ES:SE:LP:AF:ID  0.0011228:0.011758:0.0362122:0.623882:rs10399793
1   54676   rs2462492   C   T   .   PASS    AF=0.401861 ES:SE:LP:AF:ID  -0.0256436:0.011679:1.55284:0.401861:rs2462492
1   86028   rs114608975 T   C   .   PASS    AF=0.103927 ES:SE:LP:AF:ID  0.00801822:0.0184892:0.180456:0.103927:rs114608975
1   91536   rs6702460   G   T   .   PASS    AF=0.458825 ES:SE:LP:AF:ID  -0.0234813:0.0114048:1.39794:0.458825:rs6702460
1   234313  rs8179466   C   T   .   PASS    AF=0.073683 ES:SE:LP:AF:ID  -0.027426:0.0228004:0.638272:0.073683:rs8179466
1   534192  rs6680723   C   T   .   PASS    AF=0.242155 ES:SE:LP:AF:ID  -0.0105416:0.0130188:0.376751:0.242155:rs6680723
1   546697  rs12025928  A   G   .   PASS    AF=0.915728 ES:SE:LP:AF:ID  0.0244151:0.0166133:0.853872:0.915728:rs12025928
1   693731  rs12238997  A   G   .   PASS    AF=0.112708 ES:SE:LP:AF:ID  0.0109102:0.0111703:0.481486:0.112708:rs12238997
1   705882  rs72631875  G   A   .   PASS    AF=0.064258 ES:SE:LP:AF:ID  0.00359755:0.016469:0.0809219:0.064258:rs72631875
1   706368  rs12029736  A   G   .   PASS    AF=0.513756 ES:SE:LP:AF:ID  -0.00423072:0.0081686:0.221849:0.513756:rs12029736
1   714596  rs149887893 T   C   .   PASS    AF=0.031782 ES:SE:LP:AF:ID  -0.0179011:0.0209311:0.408935:0.031782:rs149887893
1   715265  rs12184267  C   T   .   PASS    AF=0.035201 ES:SE:LP:AF:ID  -0.0178881:0.0190286:0.455932:0.035201:rs12184267
1   715367  rs12184277  A   G   .   PASS    AF=0.035252 ES:SE:LP:AF:ID  -0.0181028:0.0189701:0.468521:0.035252:rs12184277
1   717485  rs12184279  C   A   .   PASS    AF=0.035033 ES:SE:LP:AF:ID  -0.0166183:0.0190879:0.420216:0.035033:rs12184279
1   717587  rs144155419 G   A   .   PASS    AF=0.016372 ES:SE:LP:AF:ID  -0.0262693:0.0289318:0.443698:0.016372:rs144155419
1   720381  rs116801199 G   T   .   PASS    AF=0.035597 ES:SE:LP:AF:ID  -0.0160701:0.0188682:0.408935:0.035597:rs116801199
1   721290  rs12565286  G   C   .   PASS    AF=0.035636 ES:SE:LP:AF:ID  -0.0146742:0.0188175:0.356547:0.035636:rs12565286
1   722670  rs116030099 T   C   .   PASS    AF=0.1009   ES:SE:LP:AF:ID  -0.00228176:0.0134668:0.0604807:0.1009:rs116030099
1   723891  rs2977670   G   C   .   PASS    AF=0.96074  ES:SE:LP:AF:ID  0.0105305:0.0181566:0.251812:0.96074:rs2977670
1   724849  rs12126395  C   A   .   PASS    AF=0.031119 ES:SE:LP:AF:ID  -0.0647409:0.0323392:1.34679:0.031119:rs12126395
1   725060  rs865924913 A   T   .   PASS    AF=0.05433  ES:SE:LP:AF:ID  0.02786:0.0254837:0.568636:0.05433:rs865924913
1   726794  rs28454925  C   G   .   PASS    AF=0.035163 ES:SE:LP:AF:ID  -0.0159918:0.0189442:0.39794:0.035163:rs28454925
1   729632  rs116720794 C   T   .   PASS    AF=0.035499 ES:SE:LP:AF:ID  -0.0175433:0.0187552:0.455932:0.035499:rs116720794
1   729679  rs4951859   C   G   .   PASS    AF=0.848068 ES:SE:LP:AF:ID  -0.00644706:0.0096614:0.30103:0.848068:rs4951859
1   730087  rs148120343 T   C   .   PASS    AF=0.054239 ES:SE:LP:AF:ID  0.0156263:0.0156568:0.49485:0.054239:rs148120343
1   731718  rs58276399  T   C   .   PASS    AF=0.118715 ES:SE:LP:AF:ID  0.0133123:0.0105771:0.677781:0.118715:rs58276399
1   732989  rs369030935 C   T   .   PASS    AF=0.026176 ES:SE:LP:AF:ID  -0.0284014:0.0253928:0.585027:0.026176:rs369030935
1   734349  rs141242758 T   C   .   PASS    AF=0.117985 ES:SE:LP:AF:ID  0.0131423:0.0105864:0.677781:0.117985:rs141242758
1   736289  rs79010578  T   A   .   PASS    AF=0.127457 ES:SE:LP:AF:ID  0.0119379:0.0104584:0.60206:0.127457:rs79010578
1   736689  rs181876450 T   C   .   PASS    AF=0.011719 ES:SE:LP:AF:ID  -0.0242567:0.0360218:0.30103:0.011719:rs181876450
1   752478  rs146277091 G   A   .   PASS    AF=0.035231 ES:SE:LP:AF:ID  -0.0161213:0.0186128:0.408935:0.035231:rs146277091
1   752566  rs3094315   G   A   .   PASS    AF=0.844081 ES:SE:LP:AF:ID  -0.00597072:0.00936569:0.283997:0.844081:rs3094315
1   752721  rs3131972   A   G   .   PASS    AF=0.843762 ES:SE:LP:AF:ID  -0.00637345:0.00935585:0.30103:0.843762:rs3131972
1   753405  rs3115860   C   A   .   PASS    AF=0.873824 ES:SE:LP:AF:ID  -0.0116489:0.0100421:0.60206:0.873824:rs3115860
1   753541  rs2073813   G   A   .   PASS    AF=0.125756 ES:SE:LP:AF:ID  0.0132714:0.0100701:0.721246:0.125756:rs2073813
1   754063  rs12184312  G   T   .   PASS    AF=0.035873 ES:SE:LP:AF:ID  -0.015524:0.018257:0.39794:0.035873:rs12184312
1   754105  rs12184325  C   T   .   PASS    AF=0.036099 ES:SE:LP:AF:ID  -0.0159502:0.0181436:0.420216:0.036099:rs12184325
1   754182  rs3131969   A   G   .   PASS    AF=0.873233 ES:SE:LP:AF:ID  -0.012155:0.0100238:0.638272:0.873233:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.873396 ES:SE:LP:AF:ID  -0.0116786:0.01003:0.619789:0.873396:rs3131968
1   754211  rs12184313  G   A   .   PASS    AF=0.036056 ES:SE:LP:AF:ID  -0.014631:0.0182274:0.376751:0.036056:rs12184313
1   754334  rs3131967   T   C   .   PASS    AF=0.87325  ES:SE:LP:AF:ID  -0.0122593:0.0100233:0.657577:0.87325:rs3131967
1   754503  rs3115859   G   A   .   PASS    AF=0.843261 ES:SE:LP:AF:ID  -0.00641544:0.00933367:0.309804:0.843261:rs3115859
1   754629  rs10454459  A   G   .   PASS    AF=0.036051 ES:SE:LP:AF:ID  -0.0142726:0.0182569:0.366532:0.036051:rs10454459
1   754964  rs3131966   C   T   .   PASS    AF=0.843845 ES:SE:LP:AF:ID  -0.00634589:0.00935988:0.30103:0.843845:rs3131966
1   755240  rs181660517 T   G   .   PASS    AF=0.014003 ES:SE:LP:AF:ID  -0.0107536:0.032074:0.130768:0.014003:rs181660517
1   755775  rs3131965   A   G   .   PASS    AF=0.844672 ES:SE:LP:AF:ID  -0.00828352:0.00948514:0.420216:0.844672:rs3131965
1   755890  rs3115858   A   T   .   PASS    AF=0.873462 ES:SE:LP:AF:ID  -0.0116061:0.0100109:0.60206:0.873462:rs3115858
1   756604  rs3131962   A   G   .   PASS    AF=0.872965 ES:SE:LP:AF:ID  -0.0120711:0.00998491:0.638272:0.872965:rs3131962
1   757640  rs3115853   G   A   .   PASS    AF=0.872051 ES:SE:LP:AF:ID  -0.0111073:0.00996779:0.568636:0.872051:rs3115853
1   757734  rs4951929   C   T   .   PASS    AF=0.873174 ES:SE:LP:AF:ID  -0.0114022:0.0099951:0.60206:0.873174:rs4951929