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_1498.vcf.gz --id UKB-b:5237 --data /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/raw-output/data.batch_1498.txt.gz --cohort_controls 428860 --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-5237/UKB-b-5237_data.vcf.gz \
--ref-ld-chr ../reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-5237/ldsc.txt \
--w-ld-chr ../reference/eur_w_ld_chr/ 

Beginning analysis at Thu Oct 17 14:45:05 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-5237/UKB-b-5237_data.vcf.gz ...
Read summary statistics for 9851866 SNPs.
Dropped 14738 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, 1289166 SNPs remain.
After merging with regression SNP LD, 1289166 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0478 (0.0029)
Lambda GC: 1.3517
Mean Chi^2: 1.4614
Intercept: 1.054 (0.0083)
Ratio: 0.117 (0.0179)
Analysis finished at Thu Oct 17 14:46:40 2019
Total time elapsed: 1.0m:35.28s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9499,
    "inflation_factor": 1.2544,
    "mean_EFFECT": -0.0001,
    "n": "-Inf",
    "n_snps": 9851866,
    "n_clumped_hits": 40,
    "n_p_sig": 3265,
    "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": 184849,
    "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": 1289166,
    "ldsc_nsnp_merge_regression_ld": 1289166,
    "ldsc_observed_scale_h2_beta": 0.0478,
    "ldsc_observed_scale_h2_se": 0.0029,
    "ldsc_intercept_beta": 1.054,
    "ldsc_intercept_se": 0.0083,
    "ldsc_lambda_gc": 1.3517,
    "ldsc_mean_chisq": 1.4614,
    "ldsc_ratio": 0.117
}
 

Flags

name value
af_correlation FALSE
inflation_factor TRUE
n TRUE
is_snpid_non_unique FALSE
mean_EFFECT_nonfinite FALSE
mean_EFFECT_05 FALSE
mean_EFFECT_01 FALSE
mean_chisq TRUE
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 9837196 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 9851866 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 8.622825e+00 5.748290e+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 7.886027e+07 5.628334e+07 828.0000000 3.259061e+07 6.948835e+07 1.145912e+08 2.492385e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA NA NA -5.990000e-05 7.954500e-03 -0.1894140 -2.621700e-03 -3.210000e-05 2.565900e-03 1.116580e-01 ▁▁▁▇▁
numeric SE 0 1.0000000 NA NA NA NA NA NA NA 5.563000e-03 5.265600e-03 0.0015566 1.905600e-03 3.195300e-03 7.373300e-03 8.183400e-02 ▇▁▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA NA NA 4.647283e-01 2.982690e-01 0.0000000 2.000000e-01 4.500005e-01 7.199992e-01 1.000000e+00 ▇▆▆▆▆
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA NA NA 4.647308e-01 2.982448e-01 0.0000000 1.979665e-01 4.522216e-01 7.233075e-01 9.999999e-01 ▇▆▆▆▆
numeric AF 0 1.0000000 NA NA NA NA NA NA NA 2.035078e-01 2.568626e-01 0.0009700 1.316800e-02 7.791500e-02 3.164540e-01 9.990230e-01 ▇▂▁▁▁
numeric AF_reference 184849 0.9812372 NA NA NA NA NA NA NA 2.068392e-01 2.482924e-01 0.0000000 1.198080e-02 9.984030e-02 3.202880e-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 -0.0018541 0.0028630 0.5199996 0.5172382 0.623631 0.7821490 NA
1 54676 rs2462492 C T 0.0056297 0.0028374 0.0470002 0.0472488 0.400513 NA NA
1 86028 rs114608975 T C 0.0029739 0.0045351 0.5099998 0.5119782 0.103535 0.0277556 NA
1 91536 rs6702460 G T 0.0021120 0.0027941 0.4500005 0.4497113 0.456852 0.4207270 NA
1 234313 rs8179466 C T 0.0029510 0.0055117 0.5900000 0.5923643 0.074498 NA NA
1 534192 rs6680723 C T 0.0014128 0.0031918 0.6600001 0.6580290 0.240829 NA NA
1 546697 rs12025928 A G 0.0027905 0.0039786 0.4799997 0.4830624 0.913410 NA NA
1 693731 rs12238997 A G 0.0018155 0.0026762 0.5000000 0.4975151 0.116184 0.1417730 NA
1 705882 rs72631875 G A -0.0019152 0.0039203 0.6300007 0.6251652 0.067197 0.0315495 NA
1 706368 rs55727773 A G -0.0006354 0.0019806 0.7499995 0.7483374 0.515729 0.2751600 NA
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51219704 rs147475742 G A -0.0102834 0.0041607 0.0129999 0.0134525 0.041908 0.0473243 NA
22 51219766 rs182321900 C T -0.0096809 0.0193395 0.6200004 0.6166681 0.001942 NA NA
22 51220146 rs868950473 C T -0.0118049 0.0191791 0.5400003 0.5382189 0.001987 NA NA
22 51221190 rs369304721 G A -0.0101237 0.0041568 0.0150000 0.0148728 0.049629 NA NA
22 51221731 rs115055839 T C -0.0078590 0.0031080 0.0109999 0.0114510 0.073083 0.0625000 NA
22 51222100 rs114553188 G T -0.0017790 0.0036603 0.6300007 0.6269519 0.054335 0.0880591 NA
22 51223637 rs375798137 G A -0.0019610 0.0036777 0.5900000 0.5938892 0.053969 0.0788738 NA
22 51229805 rs9616985 T C -0.0074592 0.0031190 0.0170000 0.0167797 0.072931 0.0730831 NA
22 51232488 rs376461333 A G -0.0041716 0.0073502 0.5700002 0.5703360 0.019998 NA NA
22 51237063 rs3896457 T C -0.0001326 0.0019060 0.9400001 0.9445566 0.298090 0.2050720 NA

bcf preview

1   49298   rs10399793  T   C   .   PASS    AF=0.623631 ES:SE:LP:AF:ID  -0.00185409:0.00286298:0.283997:0.623631:rs10399793
1   54676   rs2462492   C   T   .   PASS    AF=0.400513 ES:SE:LP:AF:ID  0.00562968:0.00283745:1.3279:0.400513:rs2462492
1   86028   rs114608975 T   C   .   PASS    AF=0.103535 ES:SE:LP:AF:ID  0.00297392:0.00453507:0.29243:0.103535:rs114608975
1   91536   rs6702460   G   T   .   PASS    AF=0.456852 ES:SE:LP:AF:ID  0.00211202:0.00279406:0.346787:0.456852:rs6702460
1   234313  rs8179466   C   T   .   PASS    AF=0.074498 ES:SE:LP:AF:ID  0.00295102:0.00551167:0.229148:0.074498:rs8179466
1   534192  rs6680723   C   T   .   PASS    AF=0.240829 ES:SE:LP:AF:ID  0.00141281:0.00319181:0.180456:0.240829:rs6680723
1   546697  rs12025928  A   G   .   PASS    AF=0.91341  ES:SE:LP:AF:ID  0.00279054:0.00397861:0.318759:0.91341:rs12025928
1   693731  rs12238997  A   G   .   PASS    AF=0.116184 ES:SE:LP:AF:ID  0.00181554:0.00267619:0.30103:0.116184:rs12238997
1   705882  rs72631875  G   A   .   PASS    AF=0.067197 ES:SE:LP:AF:ID  -0.00191525:0.00392033:0.200659:0.067197:rs72631875
1   706368  rs12029736  A   G   .   PASS    AF=0.515729 ES:SE:LP:AF:ID  -0.000635444:0.00198061:0.124939:0.515729:rs12029736
1   714596  rs149887893 T   C   .   PASS    AF=0.032884 ES:SE:LP:AF:ID  -0.0094794:0.00500347:1.23657:0.032884:rs149887893
1   715265  rs12184267  C   T   .   PASS    AF=0.036485 ES:SE:LP:AF:ID  -0.00916126:0.00454498:1.35655:0.036485:rs12184267
1   715367  rs12184277  A   G   .   PASS    AF=0.036604 ES:SE:LP:AF:ID  -0.00962584:0.00452757:1.48149:0.036604:rs12184277
1   717485  rs12184279  C   A   .   PASS    AF=0.036305 ES:SE:LP:AF:ID  -0.00983745:0.00456003:1.50864:0.036305:rs12184279
1   717587  rs144155419 G   A   .   PASS    AF=0.01638  ES:SE:LP:AF:ID  0.00294176:0.0070118:0.173925:0.01638:rs144155419
1   720381  rs116801199 G   T   .   PASS    AF=0.03685  ES:SE:LP:AF:ID  -0.00885778:0.00450925:1.3098:0.03685:rs116801199
1   721290  rs12565286  G   C   .   PASS    AF=0.036944 ES:SE:LP:AF:ID  -0.00892039:0.00449399:1.3279:0.036944:rs12565286
1   722670  rs116030099 T   C   .   PASS    AF=0.10118  ES:SE:LP:AF:ID  -0.000564941:0.00327094:0.0655015:0.10118:rs116030099
1   723891  rs2977670   G   C   .   PASS    AF=0.959242 ES:SE:LP:AF:ID  0.00844573:0.00433401:1.29243:0.959242:rs2977670
1   724849  rs12126395  C   A   .   PASS    AF=0.031458 ES:SE:LP:AF:ID  0.00328017:0.00785468:0.167491:0.031458:rs12126395
1   725060  rs865924913 A   T   .   PASS    AF=0.053253 ES:SE:LP:AF:ID  0.00160246:0.00624756:0.09691:0.053253:rs865924913
1   726794  rs28454925  C   G   .   PASS    AF=0.036461 ES:SE:LP:AF:ID  -0.00994594:0.00452264:1.55284:0.036461:rs28454925
1   729632  rs116720794 C   T   .   PASS    AF=0.036771 ES:SE:LP:AF:ID  -0.00928722:0.00448155:1.42022:0.036771:rs116720794
1   729679  rs4951859   C   G   .   PASS    AF=0.843483 ES:SE:LP:AF:ID  0.000928072:0.00231961:0.161151:0.843483:rs4951859
1   730087  rs148120343 T   C   .   PASS    AF=0.05584  ES:SE:LP:AF:ID  0.00206579:0.00375517:0.236572:0.05584:rs148120343
1   731718  rs58276399  T   C   .   PASS    AF=0.122174 ES:SE:LP:AF:ID  0.00165956:0.00253868:0.29243:0.122174:rs58276399
1   732989  rs369030935 C   T   .   PASS    AF=0.025719 ES:SE:LP:AF:ID  0.00271514:0.00623986:0.180456:0.025719:rs369030935
1   734349  rs141242758 T   C   .   PASS    AF=0.121415 ES:SE:LP:AF:ID  0.00168681:0.00253978:0.29243:0.121415:rs141242758
1   736289  rs79010578  T   A   .   PASS    AF=0.132141 ES:SE:LP:AF:ID  -0.00200746:0.00250324:0.376751:0.132141:rs79010578
1   736689  rs181876450 T   C   .   PASS    AF=0.011179 ES:SE:LP:AF:ID  0.00568074:0.00907139:0.275724:0.011179:rs181876450
1   740284  rs61770167  C   T   .   PASS    AF=0.005701 ES:SE:LP:AF:ID  -0.0137792:0.0117429:0.619789:0.005701:rs61770167
1   742813  rs112573343 C   T   .   PASS    AF=0.002282 ES:SE:LP:AF:ID  0.00836312:0.0196739:0.173925:0.002282:rs112573343
1   746189  rs139221807 A   G   .   PASS    AF=0.001025 ES:SE:LP:AF:ID  0.00795713:0.0324261:0.091515:0.001025:rs139221807
1   752478  rs146277091 G   A   .   PASS    AF=0.036687 ES:SE:LP:AF:ID  -0.00837586:0.00443618:1.22915:0.036687:rs146277091
1   752566  rs3094315   G   A   .   PASS    AF=0.839295 ES:SE:LP:AF:ID  0.00121373:0.00224668:0.229148:0.839295:rs3094315
1   752721  rs3131972   A   G   .   PASS    AF=0.838932 ES:SE:LP:AF:ID  0.00117522:0.00224424:0.221849:0.838932:rs3131972
1   753405  rs3115860   C   A   .   PASS    AF=0.869978 ES:SE:LP:AF:ID  -0.00136328:0.00240787:0.244125:0.869978:rs3115860
1   753541  rs2073813   G   A   .   PASS    AF=0.129666 ES:SE:LP:AF:ID  0.00153727:0.00241277:0.283997:0.129666:rs2073813
1   754063  rs12184312  G   T   .   PASS    AF=0.037201 ES:SE:LP:AF:ID  -0.00805062:0.00436042:1.18709:0.037201:rs12184312
1   754105  rs12184325  C   T   .   PASS    AF=0.037444 ES:SE:LP:AF:ID  -0.00773614:0.00433286:1.13077:0.037444:rs12184325
1   754182  rs3131969   A   G   .   PASS    AF=0.869328 ES:SE:LP:AF:ID  -0.00135974:0.00240313:0.244125:0.869328:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.869429 ES:SE:LP:AF:ID  -0.00131098:0.00240411:0.229148:0.869429:rs3131968
1   754211  rs12184313  G   A   .   PASS    AF=0.037404 ES:SE:LP:AF:ID  -0.00825564:0.00435149:1.23657:0.037404:rs12184313
1   754334  rs3131967   T   C   .   PASS    AF=0.869331 ES:SE:LP:AF:ID  -0.0012472:0.00240309:0.221849:0.869331:rs3131967
1   754433  rs150578204 G   A   .   PASS    AF=0.005078 ES:SE:LP:AF:ID  0.013867:0.0123858:0.585027:0.005078:rs150578204
1   754458  rs142682604 G   T   .   PASS    AF=0.005044 ES:SE:LP:AF:ID  0.0137012:0.0124184:0.568636:0.005044:rs142682604
1   754503  rs3115859   G   A   .   PASS    AF=0.838381 ES:SE:LP:AF:ID  0.00130619:0.00223785:0.251812:0.838381:rs3115859
1   754629  rs10454459  A   G   .   PASS    AF=0.037419 ES:SE:LP:AF:ID  -0.00835018:0.00435747:1.25964:0.037419:rs10454459
1   754964  rs3131966   C   T   .   PASS    AF=0.839009 ES:SE:LP:AF:ID  0.00129601:0.00224413:0.251812:0.839009:rs3131966
1   755240  rs181660517 T   G   .   PASS    AF=0.01382  ES:SE:LP:AF:ID  0.00516268:0.00781079:0.29243:0.01382:rs181660517