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_23116.vcf.gz --id UKB-b:7212 --data /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/raw-output/data.batch_23116.txt.gz --cohort_controls 454823 --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-7212/UKB-b-7212_data.vcf.gz \
--ref-ld-chr ../reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-7212/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-7212/UKB-b-7212_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: 0.2173 (0.0064)
Lambda GC: 2.378
Mean Chi^2: 3.1593
Intercept: 1.1821 (0.0163)
Ratio: 0.0843 (0.0075)
Analysis finished at Thu Oct 17 14:41:56 2019
Total time elapsed: 1.0m:38.65s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9499,
    "inflation_factor": 1.8418,
    "mean_EFFECT": 0,
    "n": "-Inf",
    "n_snps": 9851866,
    "n_clumped_hits": 424,
    "n_p_sig": 59364,
    "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": 0.2173,
    "ldsc_observed_scale_h2_se": 0.0064,
    "ldsc_intercept_beta": 1.1821,
    "ldsc_intercept_se": 0.0163,
    "ldsc_lambda_gc": 2.378,
    "ldsc_mean_chisq": 3.1593,
    "ldsc_ratio": 0.0843
}
 

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 1.000000 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+07 828.000000 3.259061e+07 6.948835e+07 1.145912e+08 2.492385e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA NA NA 4.010000e-05 8.585100e-03 -0.189693 -3.272000e-03 1.180000e-05 3.298200e-03 1.539040e-01 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA NA NA 5.457500e-03 5.165400e-03 0.001525 1.869700e-03 3.135200e-03 7.233500e-03 8.021240e-02 ▇▁▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA NA NA 3.999698e-01 3.111531e-01 0.000000 1.100001e-01 3.599996e-01 6.700003e-01 1.000000e+00 ▇▅▃▃▃
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA NA NA 3.999716e-01 3.111318e-01 0.000000 1.057677e-01 3.566341e-01 6.666888e-01 9.999996e-01 ▇▅▃▃▃
numeric AF 0 1.0000000 NA NA NA NA NA NA NA 2.035077e-01 2.568614e-01 0.000985 1.316900e-02 7.791400e-02 3.164560e-01 9.990060e-01 ▇▂▁▁▁
numeric AF_reference 184849 0.9812372 NA NA NA NA NA NA NA 2.068392e-01 2.482924e-01 0.000000 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 -0.0010979 0.0028030 0.6999999 0.6953049 0.623735 0.7821490 NA
1 54676 rs2462492 C T 0.0034801 0.0027776 0.2099999 0.2102332 0.400351 NA NA
1 86028 rs114608975 T C 0.0072692 0.0044400 0.1000000 0.1015810 0.103561 0.0277556 NA
1 91536 rs6702460 G T 0.0017224 0.0027342 0.5300002 0.5287160 0.456844 0.4207270 NA
1 234313 rs8179466 C T -0.0078928 0.0053936 0.1400000 0.1433678 0.074495 NA NA
1 534192 rs6680723 C T -0.0008421 0.0031237 0.7899998 0.7874822 0.240934 NA NA
1 546697 rs12025928 A G 0.0020188 0.0038967 0.5999997 0.6044011 0.913462 NA NA
1 693731 rs12238997 A G -0.0005444 0.0026190 0.8400000 0.8353448 0.116213 0.1417730 NA
1 705882 rs72631875 G A -0.0011177 0.0038349 0.7700005 0.7706979 0.067323 0.0315495 NA
1 706368 rs55727773 A G -0.0010007 0.0019394 0.6100002 0.6058525 0.515785 0.2751600 NA
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51219704 rs147475742 G A 0.0012550 0.0040912 0.7600007 0.7590290 0.041965 0.0473243 NA
22 51219766 rs182321900 C T -0.0127517 0.0190414 0.5000000 0.5030600 0.001942 NA NA
22 51220146 rs868950473 C T -0.0144751 0.0188601 0.4400003 0.4427851 0.001991 NA NA
22 51221190 rs369304721 G A 0.0038368 0.0040839 0.3500000 0.3474720 0.049759 NA NA
22 51221731 rs115055839 T C 0.0041534 0.0030548 0.1700000 0.1739535 0.073276 0.0625000 NA
22 51222100 rs114553188 G T -0.0010545 0.0035966 0.7700005 0.7693778 0.054488 0.0880591 NA
22 51223637 rs375798137 G A -0.0008646 0.0036140 0.8100000 0.8109123 0.054117 0.0788738 NA
22 51229805 rs9616985 T C 0.0040979 0.0030659 0.1800002 0.1813531 0.073109 0.0730831 NA
22 51232488 rs376461333 A G 0.0031163 0.0072212 0.6700003 0.6660642 0.020056 NA NA
22 51237063 rs3896457 T C 0.0021770 0.0018761 0.2500000 0.2458885 0.297895 0.2050720 NA

bcf preview

1   49298   rs10399793  T   C   .   PASS    AF=0.623735 ES:SE:LP:AF:ID  -0.00109786:0.00280305:0.154902:0.623735:rs10399793
1   54676   rs2462492   C   T   .   PASS    AF=0.400351 ES:SE:LP:AF:ID  0.00348006:0.00277755:0.677781:0.400351:rs2462492
1   86028   rs114608975 T   C   .   PASS    AF=0.103561 ES:SE:LP:AF:ID  0.00726925:0.00443995:1:0.103561:rs114608975
1   91536   rs6702460   G   T   .   PASS    AF=0.456844 ES:SE:LP:AF:ID  0.00172245:0.00273419:0.275724:0.456844:rs6702460
1   234313  rs8179466   C   T   .   PASS    AF=0.074495 ES:SE:LP:AF:ID  -0.0078928:0.0053936:0.853872:0.074495:rs8179466
1   534192  rs6680723   C   T   .   PASS    AF=0.240934 ES:SE:LP:AF:ID  -0.000842081:0.00312366:0.102373:0.240934:rs6680723
1   546697  rs12025928  A   G   .   PASS    AF=0.913462 ES:SE:LP:AF:ID  0.00201882:0.00389672:0.221849:0.913462:rs12025928
1   693731  rs12238997  A   G   .   PASS    AF=0.116213 ES:SE:LP:AF:ID  -0.000544374:0.00261905:0.0757207:0.116213:rs12238997
1   705882  rs72631875  G   A   .   PASS    AF=0.067323 ES:SE:LP:AF:ID  -0.00111774:0.00383494:0.113509:0.067323:rs72631875
1   706368  rs12029736  A   G   .   PASS    AF=0.515785 ES:SE:LP:AF:ID  -0.00100071:0.00193935:0.21467:0.515785:rs12029736
1   714596  rs149887893 T   C   .   PASS    AF=0.032986 ES:SE:LP:AF:ID  -0.000938351:0.00488962:0.0705811:0.032986:rs149887893
1   715265  rs12184267  C   T   .   PASS    AF=0.036598 ES:SE:LP:AF:ID  -0.00179225:0.00444181:0.161151:0.036598:rs12184267
1   715367  rs12184277  A   G   .   PASS    AF=0.036717 ES:SE:LP:AF:ID  -0.00145643:0.00442468:0.130768:0.036717:rs12184277
1   717485  rs12184279  C   A   .   PASS    AF=0.036414 ES:SE:LP:AF:ID  -0.00268456:0.00445684:0.259637:0.036414:rs12184279
1   717587  rs144155419 G   A   .   PASS    AF=0.016391 ES:SE:LP:AF:ID  -0.00285699:0.00686395:0.167491:0.016391:rs144155419
1   720381  rs116801199 G   T   .   PASS    AF=0.036953 ES:SE:LP:AF:ID  -0.00220934:0.00440743:0.207608:0.036953:rs116801199
1   721290  rs12565286  G   C   .   PASS    AF=0.037051 ES:SE:LP:AF:ID  -0.00229039:0.00439221:0.221849:0.037051:rs12565286
1   722670  rs116030099 T   C   .   PASS    AF=0.10124  ES:SE:LP:AF:ID  0.00277617:0.003199:0.408935:0.10124:rs116030099
1   723891  rs2977670   G   C   .   PASS    AF=0.959098 ES:SE:LP:AF:ID  0.00376472:0.00423515:0.431798:0.959098:rs2977670
1   724849  rs12126395  C   A   .   PASS    AF=0.031461 ES:SE:LP:AF:ID  0.00726998:0.00768347:0.468521:0.031461:rs12126395
1   725060  rs865924913 A   T   .   PASS    AF=0.053255 ES:SE:LP:AF:ID  -0.00101628:0.0061119:0.0604807:0.053255:rs865924913
1   726794  rs28454925  C   G   .   PASS    AF=0.036573 ES:SE:LP:AF:ID  -0.00291776:0.00442042:0.29243:0.036573:rs28454925
1   729632  rs116720794 C   T   .   PASS    AF=0.03689  ES:SE:LP:AF:ID  -0.00377409:0.00438017:0.408935:0.03689:rs116720794
1   729679  rs4951859   C   G   .   PASS    AF=0.843325 ES:SE:LP:AF:ID  0.00196029:0.00226921:0.408935:0.843325:rs4951859
1   730087  rs148120343 T   C   .   PASS    AF=0.055854 ES:SE:LP:AF:ID  -0.0044109:0.00367501:0.638272:0.055854:rs148120343
1   731718  rs58276399  T   C   .   PASS    AF=0.122188 ES:SE:LP:AF:ID  -0.00101064:0.00248442:0.167491:0.122188:rs58276399
1   732989  rs369030935 C   T   .   PASS    AF=0.025732 ES:SE:LP:AF:ID  -0.00435694:0.00610457:0.318759:0.025732:rs369030935
1   734349  rs141242758 T   C   .   PASS    AF=0.121428 ES:SE:LP:AF:ID  -0.000770612:0.00248547:0.119186:0.121428:rs141242758
1   736289  rs79010578  T   A   .   PASS    AF=0.132214 ES:SE:LP:AF:ID  -0.00159705:0.0024493:0.29243:0.132214:rs79010578
1   736689  rs181876450 T   C   .   PASS    AF=0.011122 ES:SE:LP:AF:ID  0.00671861:0.00891093:0.346787:0.011122:rs181876450
1   740284  rs61770167  C   T   .   PASS    AF=0.005693 ES:SE:LP:AF:ID  0.0220332:0.0114951:1.25964:0.005693:rs61770167
1   742813  rs112573343 C   T   .   PASS    AF=0.002287 ES:SE:LP:AF:ID  0.00102363:0.0192448:0.0177288:0.002287:rs112573343
1   746189  rs139221807 A   G   .   PASS    AF=0.001037 ES:SE:LP:AF:ID  0.00934609:0.0314803:0.113509:0.001037:rs139221807
1   752478  rs146277091 G   A   .   PASS    AF=0.036804 ES:SE:LP:AF:ID  -0.00270051:0.00433592:0.275724:0.036804:rs146277091
1   752566  rs3094315   G   A   .   PASS    AF=0.839055 ES:SE:LP:AF:ID  0.00170206:0.00219744:0.356547:0.839055:rs3094315
1   752721  rs3131972   A   G   .   PASS    AF=0.838682 ES:SE:LP:AF:ID  0.002099:0.00219503:0.468521:0.838682:rs3131972
1   753405  rs3115860   C   A   .   PASS    AF=0.869876 ES:SE:LP:AF:ID  0.00108257:0.00235567:0.187087:0.869876:rs3115860
1   753541  rs2073813   G   A   .   PASS    AF=0.129763 ES:SE:LP:AF:ID  -0.00174904:0.00236059:0.337242:0.129763:rs2073813
1   754063  rs12184312  G   T   .   PASS    AF=0.037317 ES:SE:LP:AF:ID  -0.00361099:0.00426243:0.39794:0.037317:rs12184312
1   754105  rs12184325  C   T   .   PASS    AF=0.037561 ES:SE:LP:AF:ID  -0.00339907:0.00423544:0.376751:0.037561:rs12184325
1   754182  rs3131969   A   G   .   PASS    AF=0.869221 ES:SE:LP:AF:ID  0.00145395:0.00235104:0.267606:0.869221:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.869318 ES:SE:LP:AF:ID  0.00143219:0.00235197:0.267606:0.869318:rs3131968
1   754211  rs12184313  G   A   .   PASS    AF=0.037514 ES:SE:LP:AF:ID  -0.00363647:0.00425402:0.408935:0.037514:rs12184313
1   754334  rs3131967   T   C   .   PASS    AF=0.869224 ES:SE:LP:AF:ID  0.00148316:0.00235099:0.275724:0.869224:rs3131967
1   754433  rs150578204 G   A   .   PASS    AF=0.005132 ES:SE:LP:AF:ID  -0.00915489:0.012052:0.346787:0.005132:rs150578204
1   754458  rs142682604 G   T   .   PASS    AF=0.005098 ES:SE:LP:AF:ID  -0.00930885:0.0120832:0.356547:0.005098:rs142682604
1   754503  rs3115859   G   A   .   PASS    AF=0.838139 ES:SE:LP:AF:ID  0.00215368:0.00218899:0.481486:0.838139:rs3115859
1   754629  rs10454459  A   G   .   PASS    AF=0.037527 ES:SE:LP:AF:ID  -0.00399525:0.00426003:0.455932:0.037527:rs10454459
1   754964  rs3131966   C   T   .   PASS    AF=0.838771 ES:SE:LP:AF:ID  0.00213378:0.00219516:0.481486:0.838771:rs3131966
1   755240  rs181660517 T   G   .   PASS    AF=0.013776 ES:SE:LP:AF:ID  0.0113432:0.00765909:0.853872:0.013776:rs181660517