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/public/UKB-b-11002/UKB-b-11002_data.vcf.gz \
--ref-ld-chr ../reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-11002/ldsc.txt \
--w-ld-chr ../reference/eur_w_ld_chr/ 

Beginning analysis at Thu Oct 17 14:40:19 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-11002/UKB-b-11002_data.vcf.gz ...
Read summary statistics for 3665349 SNPs.
Dropped 616 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, 888301 SNPs remain.
After merging with regression SNP LD, 888301 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0014 (0.0013)
Lambda GC: 1.1658
Mean Chi^2: 1.1551
Intercept: 1.1404 (0.0091)
Ratio: 0.9055 (0.0589)
Analysis finished at Thu Oct 17 14:41:05 2019
Total time elapsed: 46.08s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.8604,
    "inflation_factor": 1.1474,
    "mean_EFFECT": -5.564e-07,
    "n": "-Inf",
    "n_snps": 9851866,
    "n_clumped_hits": 0,
    "n_p_sig": 0,
    "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": 29558,
    "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": 888301,
    "ldsc_nsnp_merge_regression_ld": 888301,
    "ldsc_observed_scale_h2_beta": 0.0014,
    "ldsc_observed_scale_h2_se": 0.0013,
    "ldsc_intercept_beta": 1.1404,
    "ldsc_intercept_se": 0.0091,
    "ldsc_lambda_gc": 1.1658,
    "ldsc_mean_chisq": 1.1551,
    "ldsc_ratio": 0.9052
}

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 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 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 3664736 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 3665349 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 8.661462e+00 5.772053e+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 7.855171e+07 5.677222e+07 828.0000000 3.157377e+07 6.888161e+07 1.147274e+08 2.492385e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA NA NA -6.000000e-07 1.876000e-04 -0.0010903 -1.255000e-04 -6.000000e-07 1.249000e-04 1.234800e-03 ▁▂▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA NA NA 1.733000e-04 1.980000e-05 0.0001467 1.561000e-04 1.670000e-04 1.872000e-04 5.366000e-04 ▇▁▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA NA NA 4.758561e-01 2.947558e-01 0.0000002 2.099999e-01 4.700002e-01 7.300002e-01 1.000000e+00 ▇▇▆▆▆
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA NA NA 4.758565e-01 2.947307e-01 0.0000002 2.146733e-01 4.653677e-01 7.309399e-01 9.999992e-01 ▇▇▆▆▆
numeric AF 0 1.0000000 NA NA NA NA NA NA NA 4.082805e-01 2.015751e-01 0.1397770 2.317390e-01 3.664530e-01 5.604360e-01 8.602220e-01 ▇▅▃▃▂
numeric AF_reference 29558 0.9919358 NA NA NA NA NA NA NA 3.954904e-01 2.092266e-01 0.0000000 2.240420e-01 3.610220e-01 5.479230e-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 -0.0006448 0.0002699 0.0170000 0.0168913 0.623765 0.782149 NA
1 54676 rs2462492 C T 0.0006426 0.0002674 0.0160000 0.0162601 0.400401 NA NA
1 91536 rs6702460 G T -0.0000192 0.0002633 0.9400001 0.9419253 0.456846 0.420727 NA
1 534192 rs6680723 C T -0.0001406 0.0003007 0.6400000 0.6401928 0.240959 NA NA
1 706368 rs55727773 A G 0.0001754 0.0001867 0.3500000 0.3475920 0.515645 0.275160 NA
1 729679 rs4951859 C G 0.0000262 0.0002184 0.9000000 0.9045851 0.843204 0.639976 NA
1 752566 rs3094315 G A 0.0000215 0.0002115 0.9199999 0.9188957 0.838945 0.718251 NA
1 752721 rs3131972 A G 0.0000302 0.0002113 0.8900000 0.8863200 0.838573 0.653355 NA
1 754503 rs3115859 G A 0.0000228 0.0002107 0.9100000 0.9137216 0.838026 0.663938 NA
1 754964 rs3131966 C T 0.0000256 0.0002113 0.9000000 0.9037243 0.838657 0.663339 NA
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51182485 rs6009961 A G 0.0002316 0.0001764 0.1900002 0.1890342 0.715502 0.6383790 NA
22 51186143 rs2879914 T C 0.0001418 0.0001635 0.3900004 0.3860136 0.381825 0.2733630 NA
22 51186228 rs3865766 C T 0.0000731 0.0001594 0.6499995 0.6466829 0.451061 0.4532750 NA
22 51192586 rs5771006 G A -0.0000017 0.0002147 0.9900000 0.9936994 0.167627 0.0848642 NA
22 51193227 rs34608236 T G 0.0000448 0.0002195 0.8400000 0.8384075 0.168490 0.0692891 NA
22 51197266 rs61290853 A G 0.0000064 0.0001646 0.9699999 0.9689316 0.386333 0.4229230 NA
22 51198027 rs34939255 A G 0.0000509 0.0001863 0.7800007 0.7846459 0.254562 0.0984425 NA
22 51211106 rs9628250 T C 0.0002272 0.0001847 0.2200002 0.2185724 0.271547 0.1671330 NA
22 51212875 rs2238837 A C -0.0000308 0.0001755 0.8600001 0.8607741 0.331457 0.3724040 NA
22 51237063 rs3896457 T C 0.0000733 0.0001796 0.6800001 0.6831473 0.297974 0.2050720 NA

bcf preview

1   49298   rs10399793  T   C   .   PASS    AF=0.623765 ES:SE:LP:AF:ID  -0.00064484:0.000269913:1.76955:0.623765:rs10399793
1   54676   rs2462492   C   T   .   PASS    AF=0.400401 ES:SE:LP:AF:ID  0.000642571:0.000267401:1.79588:0.400401:rs2462492
1   91536   rs6702460   G   T   .   PASS    AF=0.456846 ES:SE:LP:AF:ID  -1.91806e-05:0.000263288:0.0268721:0.456846:rs6702460
1   534192  rs6680723   C   T   .   PASS    AF=0.240959 ES:SE:LP:AF:ID  -0.000140577:0.000300745:0.19382:0.240959:rs6680723
1   706368  rs12029736  A   G   .   PASS    AF=0.515645 ES:SE:LP:AF:ID  0.000175358:0.000186696:0.455932:0.515645:rs12029736
1   729679  rs4951859   C   G   .   PASS    AF=0.843204 ES:SE:LP:AF:ID  2.61823e-05:0.00021842:0.0457575:0.843204:rs4951859
1   752566  rs3094315   G   A   .   PASS    AF=0.838945 ES:SE:LP:AF:ID  2.15385e-05:0.000211525:0.0362122:0.838945:rs3094315
1   752721  rs3131972   A   G   .   PASS    AF=0.838573 ES:SE:LP:AF:ID  3.02075e-05:0.000211297:0.05061:0.838573:rs3131972
1   754503  rs3115859   G   A   .   PASS    AF=0.838026 ES:SE:LP:AF:ID  2.28296e-05:0.000210711:0.0409586:0.838026:rs3115859
1   754964  rs3131966   C   T   .   PASS    AF=0.838657 ES:SE:LP:AF:ID  2.55588e-05:0.000211303:0.0457575:0.838657:rs3131966
1   755775  rs3131965   A   G   .   PASS    AF=0.83977  ES:SE:LP:AF:ID  4.93517e-05:0.00021416:0.0861861:0.83977:rs3131965
1   760912  rs1048488   C   T   .   PASS    AF=0.838306 ES:SE:LP:AF:ID  9.23671e-08:0.000210311:-0:0.838306:rs1048488
1   761147  rs3115850   T   C   .   PASS    AF=0.838427 ES:SE:LP:AF:ID  -1.34181e-06:0.000210459:0.00436481:0.838427:rs3115850
1   763394  rs3115847   G   A   .   PASS    AF=0.706753 ES:SE:LP:AF:ID  0.000223101:0.000218884:0.508638:0.706753:rs3115847
1   768253  rs2977608   A   C   .   PASS    AF=0.761297 ES:SE:LP:AF:ID  3.37755e-05:0.000178647:0.0705811:0.761297:rs2977608
1   776546  rs12124819  A   G   .   PASS    AF=0.265385 ES:SE:LP:AF:ID  -0.000158764:0.000199556:0.366532:0.265385:rs12124819
1   795988  rs59380221  C   T   .   PASS    AF=0.143053 ES:SE:LP:AF:ID  -0.000473531:0.000234038:1.36653:0.143053:rs59380221
1   798400  rs10900604  A   G   .   PASS    AF=0.206591 ES:SE:LP:AF:ID  -9.68188e-05:0.00019058:0.21467:0.206591:rs10900604
1   798959  rs11240777  G   A   .   PASS    AF=0.20642  ES:SE:LP:AF:ID  -9.23056e-05:0.000190662:0.200659:0.20642:rs11240777
1   808631  rs11240779  G   A   .   PASS    AF=0.772619 ES:SE:LP:AF:ID  -4.01415e-05:0.000181373:0.0861861:0.772619:rs11240779
1   808928  rs11240780  C   T   .   PASS    AF=0.772847 ES:SE:LP:AF:ID  -3.71533e-05:0.000181678:0.0757207:0.772847:rs11240780
1   814495  rs74461805  C   A   .   PASS    AF=0.340396 ES:SE:LP:AF:ID  0.000205573:0.000255993:0.376751:0.340396:rs74461805
1   830181  rs28444699  A   G   .   PASS    AF=0.697255 ES:SE:LP:AF:ID  0.000316165:0.000171273:1.18709:0.697255:rs28444699
1   831489  rs4970385   C   T   .   PASS    AF=0.705397 ES:SE:LP:AF:ID  0.000106416:0.000168173:0.275724:0.705397:rs4970385
1   831909  rs9697642   C   T   .   PASS    AF=0.705442 ES:SE:LP:AF:ID  0.000108756:0.000168167:0.283997:0.705442:rs9697642
1   832066  rs9697380   G   C   .   PASS    AF=0.705627 ES:SE:LP:AF:ID  0.000108912:0.000168175:0.283997:0.705627:rs9697380
1   832318  rs4500250   C   A   .   PASS    AF=0.705655 ES:SE:LP:AF:ID  0.000108371:0.000168193:0.283997:0.705655:rs4500250
1   832398  rs4553118   T   C   .   PASS    AF=0.730129 ES:SE:LP:AF:ID  0.000277643:0.000172776:0.958607:0.730129:rs4553118
1   832918  rs28765502  T   C   .   PASS    AF=0.294377 ES:SE:LP:AF:ID  -0.000109353:0.000168185:0.283997:0.294377:rs28765502
1   833223  rs13303211  C   T   .   PASS    AF=0.236703 ES:SE:LP:AF:ID  1.2546e-06:0.000179059:0.00436481:0.236703:rs13303211
1   833302  rs28752186  C   T   .   PASS    AF=0.236691 ES:SE:LP:AF:ID  2.52618e-06:0.000179061:0.00436481:0.236691:rs28752186
1   833641  rs28594623  T   C   .   PASS    AF=0.23975  ES:SE:LP:AF:ID  -2.11915e-05:0.000178487:0.0409586:0.23975:rs28594623
1   833824  rs28484835  T   C   .   PASS    AF=0.236693 ES:SE:LP:AF:ID  2.39306e-06:0.000179059:0.00436481:0.236693:rs28484835
1   833927  rs28593608  T   C   .   PASS    AF=0.212421 ES:SE:LP:AF:ID  -0.000184059:0.000186108:0.49485:0.212421:rs28593608
1   834198  rs28385272  T   C   .   PASS    AF=0.212316 ES:SE:LP:AF:ID  -0.000182958:0.000186141:0.481486:0.212316:rs28385272
1   834832  rs4411087   G   C   .   PASS    AF=0.237178 ES:SE:LP:AF:ID  -1.75157e-06:0.000178922:0.00436481:0.237178:rs4411087
1   834928  rs4422949   A   G   .   PASS    AF=0.212962 ES:SE:LP:AF:ID  -0.000178024:0.000185876:0.468521:0.212962:rs4422949
1   834999  rs28570054  G   A   .   PASS    AF=0.212924 ES:SE:LP:AF:ID  -0.000187005:0.000185914:0.508638:0.212924:rs28570054
1   835499  rs4422948   A   G   .   PASS    AF=0.241162 ES:SE:LP:AF:ID  1.21811e-05:0.000177673:0.0222764:0.241162:rs4422948
1   836529  rs28731045  C   G   .   PASS    AF=0.213543 ES:SE:LP:AF:ID  -0.000177952:0.00018564:0.468521:0.213543:rs28731045
1   836896  rs28705752  T   C   .   PASS    AF=0.269511 ES:SE:LP:AF:ID  0.000162572:0.000171441:0.468521:0.269511:rs28705752
1   836924  rs72890788  G   A   .   PASS    AF=0.213513 ES:SE:LP:AF:ID  -0.000180588:0.000185662:0.481486:0.213513:rs72890788
1   838387  rs4970384   T   C   .   PASS    AF=0.214587 ES:SE:LP:AF:ID  -0.000150229:0.000185305:0.376751:0.214587:rs4970384
1   838555  rs4970383   C   A   .   PASS    AF=0.246204 ES:SE:LP:AF:ID  3.68251e-05:0.000176451:0.0809219:0.246204:rs4970383
1   839103  rs28562941  A   G   .   PASS    AF=0.270019 ES:SE:LP:AF:ID  0.000148854:0.000171562:0.408935:0.270019:rs28562941
1   840753  rs4970382   T   C   .   PASS    AF=0.400124 ES:SE:LP:AF:ID  -2.89172e-05:0.000155125:0.0705811:0.400124:rs4970382
1   841085  rs1574243   C   G   .   PASS    AF=0.237102 ES:SE:LP:AF:ID  7.86161e-05:0.000180184:0.180456:0.237102:rs1574243
1   842013  rs7419119   T   G   .   PASS    AF=0.215391 ES:SE:LP:AF:ID  -0.000175812:0.000185429:0.468521:0.215391:rs7419119
1   842362  rs28540380  C   T   .   PASS    AF=0.235323 ES:SE:LP:AF:ID  -0.000297582:0.000182883:1:0.235323:rs28540380
1   843405  rs11516185  A   G   .   PASS    AF=0.362606 ES:SE:LP:AF:ID  -0.000221648:0.000192566:0.60206:0.362606:rs11516185