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-16209/UKB-b-16209_data.vcf.gz \
--ref-ld-chr ../reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-16209/ldsc.txt \
--w-ld-chr ../reference/eur_w_ld_chr/ 

Beginning analysis at Thu Oct 17 14:44:57 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-16209/UKB-b-16209_data.vcf.gz ...
Read summary statistics for 3807533 SNPs.
Dropped 667 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, 916230 SNPs remain.
After merging with regression SNP LD, 916230 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0039 (0.0012)
Lambda GC: 1.0465
Mean Chi^2: 1.0424
Intercept: 1.0034 (0.0087)
Ratio: 0.0809 (0.205)
Analysis finished at Thu Oct 17 14:45:46 2019
Total time elapsed: 48.44s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.867,
    "inflation_factor": 1.0475,
    "mean_EFFECT": 1.077e-06,
    "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": 30873,
    "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": 916230,
    "ldsc_nsnp_merge_regression_ld": 916230,
    "ldsc_observed_scale_h2_beta": 0.0039,
    "ldsc_observed_scale_h2_se": 0.0012,
    "ldsc_intercept_beta": 1.0034,
    "ldsc_intercept_se": 0.0087,
    "ldsc_lambda_gc": 1.0465,
    "ldsc_mean_chisq": 1.0424,
    "ldsc_ratio": 0.0802
}

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 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 3806869 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 3807533 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 8.661454e+00 5.769103e+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 7.856454e+07 5.676662e+07 828.0000000 3.160703e+07 6.889456e+07 1.147178e+08 2.492385e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA NA NA 1.100000e-06 1.872000e-04 -0.0010931 -1.230000e-04 1.100000e-06 1.249000e-04 1.126800e-03 ▁▂▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA NA NA 1.820000e-04 2.250000e-05 0.0001524 1.624000e-04 1.747000e-04 1.976000e-04 5.574000e-04 ▇▁▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA NA NA 4.935221e-01 2.907662e-01 0.0000004 2.399999e-01 4.899999e-01 7.499995e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA NA NA 4.935201e-01 2.907380e-01 0.0000004 2.398954e-01 4.907939e-01 7.454413e-01 9.999998e-01 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA NA NA 4.022284e-01 2.064712e-01 0.1301600 2.219890e-01 3.578430e-01 5.568110e-01 8.698400e-01 ▇▅▃▃▂
numeric AF_reference 30873 0.9918916 NA NA NA NA NA NA NA 3.902605e-01 2.124893e-01 0.0000000 2.158550e-01 3.532350e-01 5.443290e-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 -0.0001934 0.0002805 0.4899999 0.4904985 0.623765 0.782149 NA
1 54676 rs2462492 C T 0.0001241 0.0002778 0.6600001 0.6552246 0.400401 NA NA
1 91536 rs6702460 G T 0.0002715 0.0002736 0.3200000 0.3210039 0.456846 0.420727 NA
1 534192 rs6680723 C T -0.0002577 0.0003125 0.4100001 0.4095827 0.240959 NA NA
1 706368 rs55727773 A G -0.0001097 0.0001940 0.5700002 0.5716528 0.515645 0.275160 NA
1 729679 rs4951859 C G -0.0001507 0.0002270 0.5099998 0.5066211 0.843204 0.639976 NA
1 736289 rs79010578 T A 0.0000889 0.0002449 0.7199992 0.7166006 0.132335 0.139577 NA
1 752566 rs3094315 G A -0.0001122 0.0002198 0.6100002 0.6096926 0.838945 0.718251 NA
1 752721 rs3131972 A G -0.0001051 0.0002196 0.6300007 0.6320873 0.838573 0.653355 NA
1 753405 rs3115860 C A -0.0000369 0.0002356 0.8800001 0.8754423 0.869776 0.751797 NA
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51186228 rs3865766 C T 0.0000073 0.0001655 0.9599999 0.9646391 0.451061 0.4532750 NA
22 51192586 rs5771006 G A -0.0002085 0.0002230 0.3500000 0.3499073 0.167627 0.0848642 NA
22 51193227 rs34608236 T G 0.0001484 0.0002280 0.5199996 0.5150702 0.168490 0.0692891 NA
22 51197266 rs61290853 A G -0.0001524 0.0001709 0.3700002 0.3724435 0.386333 0.4229230 NA
22 51198027 rs34939255 A G 0.0000923 0.0001935 0.6300007 0.6334190 0.254562 0.0984425 NA
22 51211106 rs9628250 T C 0.0001034 0.0001918 0.5900000 0.5898286 0.271547 0.1671330 NA
22 51211392 rs3888396 T C -0.0002477 0.0002552 0.3300000 0.3318356 0.132638 0.1641370 NA
22 51212875 rs2238837 A C 0.0000837 0.0001823 0.6499995 0.6460630 0.331457 0.3724040 NA
22 51219006 rs28729663 G A 0.0003525 0.0002340 0.1299999 0.1319927 0.137950 0.2052720 NA
22 51237063 rs3896457 T C -0.0001523 0.0001866 0.4100001 0.4141768 0.297974 0.2050720 NA

bcf preview

1   49298   rs10399793  T   C   .   PASS    AF=0.623765 ES:SE:LP:AF:ID  -0.000193381:0.000280459:0.309804:0.623765:rs10399793
1   54676   rs2462492   C   T   .   PASS    AF=0.400401 ES:SE:LP:AF:ID  0.000124064:0.000277849:0.180456:0.400401:rs2462492
1   91536   rs6702460   G   T   .   PASS    AF=0.456846 ES:SE:LP:AF:ID  0.000271495:0.000273575:0.49485:0.456846:rs6702460
1   534192  rs6680723   C   T   .   PASS    AF=0.240959 ES:SE:LP:AF:ID  -0.000257693:0.000312496:0.387216:0.240959:rs6680723
1   706368  rs12029736  A   G   .   PASS    AF=0.515645 ES:SE:LP:AF:ID  -0.000109725:0.000193991:0.244125:0.515645:rs12029736
1   729679  rs4951859   C   G   .   PASS    AF=0.843204 ES:SE:LP:AF:ID  -0.000150722:0.000226954:0.29243:0.843204:rs4951859
1   736289  rs79010578  T   A   .   PASS    AF=0.132335 ES:SE:LP:AF:ID  8.89168e-05:0.000244946:0.142668:0.132335:rs79010578
1   752566  rs3094315   G   A   .   PASS    AF=0.838945 ES:SE:LP:AF:ID  -0.000112205:0.000219789:0.21467:0.838945:rs3094315
1   752721  rs3131972   A   G   .   PASS    AF=0.838573 ES:SE:LP:AF:ID  -0.00010512:0.000219553:0.200659:0.838573:rs3131972
1   753405  rs3115860   C   A   .   PASS    AF=0.869776 ES:SE:LP:AF:ID  -3.69283e-05:0.000235588:0.0555173:0.869776:rs3115860
1   754182  rs3131969   A   G   .   PASS    AF=0.869117 ES:SE:LP:AF:ID  -1.8553e-05:0.000235126:0.0268721:0.869117:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.869215 ES:SE:LP:AF:ID  -2.44489e-05:0.000235219:0.0362122:0.869215:rs3131968
1   754334  rs3131967   T   C   .   PASS    AF=0.869121 ES:SE:LP:AF:ID  -1.89618e-05:0.000235122:0.0268721:0.869121:rs3131967
1   754503  rs3115859   G   A   .   PASS    AF=0.838026 ES:SE:LP:AF:ID  -8.39528e-05:0.000218943:0.154902:0.838026:rs3115859
1   754964  rs3131966   C   T   .   PASS    AF=0.838657 ES:SE:LP:AF:ID  -8.15068e-05:0.000219559:0.148742:0.838657:rs3131966
1   755775  rs3131965   A   G   .   PASS    AF=0.83977  ES:SE:LP:AF:ID  -6.23846e-05:0.000222528:0.107905:0.83977:rs3131965
1   755890  rs3115858   A   T   .   PASS    AF=0.8694   ES:SE:LP:AF:ID  -1.9423e-05:0.00023485:0.0315171:0.8694:rs3115858
1   756604  rs3131962   A   G   .   PASS    AF=0.868947 ES:SE:LP:AF:ID  -1.69341e-05:0.000234259:0.0268721:0.868947:rs3131962
1   757640  rs3115853   G   A   .   PASS    AF=0.867898 ES:SE:LP:AF:ID  -2.88754e-05:0.00023381:0.0457575:0.867898:rs3115853
1   757734  rs4951929   C   T   .   PASS    AF=0.86909  ES:SE:LP:AF:ID  -2.31145e-05:0.000234451:0.0362122:0.86909:rs4951929
1   757936  rs4951862   C   A   .   PASS    AF=0.869098 ES:SE:LP:AF:ID  -2.29715e-05:0.000234469:0.0362122:0.869098:rs4951862
1   758144  rs3131956   A   G   .   PASS    AF=0.869106 ES:SE:LP:AF:ID  -2.35071e-05:0.000234474:0.0362122:0.869106:rs3131956
1   758626  rs3131954   C   T   .   PASS    AF=0.869584 ES:SE:LP:AF:ID  -2.07955e-05:0.000235118:0.0315171:0.869584:rs3131954
1   760912  rs1048488   C   T   .   PASS    AF=0.838306 ES:SE:LP:AF:ID  -7.23835e-05:0.000218528:0.130768:0.838306:rs1048488
1   761147  rs3115850   T   C   .   PASS    AF=0.838427 ES:SE:LP:AF:ID  -7.47263e-05:0.000218682:0.136677:0.838427:rs3115850
1   761732  rs2286139   C   T   .   PASS    AF=0.862254 ES:SE:LP:AF:ID  -5.41904e-05:0.000233626:0.0861861:0.862254:rs2286139
1   763394  rs3115847   G   A   .   PASS    AF=0.706753 ES:SE:LP:AF:ID  -0.000380542:0.000227436:1.02687:0.706753:rs3115847
1   768253  rs2977608   A   C   .   PASS    AF=0.761297 ES:SE:LP:AF:ID  4.16089e-05:0.000185628:0.0861861:0.761297:rs2977608
1   771823  rs2977605   T   C   .   PASS    AF=0.868906 ES:SE:LP:AF:ID  -4.56736e-05:0.000234669:0.0705811:0.868906:rs2977605
1   772755  rs2905039   A   C   .   PASS    AF=0.868916 ES:SE:LP:AF:ID  -4.61346e-05:0.000234673:0.0757207:0.868916:rs2905039
1   776546  rs12124819  A   G   .   PASS    AF=0.265385 ES:SE:LP:AF:ID  8.30859e-05:0.000207353:0.161151:0.265385:rs12124819
1   780785  rs2977612   T   A   .   PASS    AF=0.86878  ES:SE:LP:AF:ID  -3.12631e-07:0.000234525:-0:0.86878:rs2977612
1   785050  rs2905062   G   A   .   PASS    AF=0.868533 ES:SE:LP:AF:ID  -2.08329e-05:0.00023447:0.0315171:0.868533:rs2905062
1   785989  rs2980300   T   C   .   PASS    AF=0.868474 ES:SE:LP:AF:ID  -1.87775e-05:0.000234616:0.0268721:0.868474:rs2980300
1   787399  rs2905055   G   T   .   PASS    AF=0.860776 ES:SE:LP:AF:ID  -5.99073e-05:0.000234456:0.09691:0.860776:rs2905055
1   787685  rs2905054   G   T   .   PASS    AF=0.861487 ES:SE:LP:AF:ID  -0.000119894:0.000234609:0.21467:0.861487:rs2905054
1   787844  rs2905053   C   T   .   PASS    AF=0.869224 ES:SE:LP:AF:ID  -1.98119e-05:0.000235474:0.0315171:0.869224:rs2905053
1   795988  rs59380221  C   T   .   PASS    AF=0.143053 ES:SE:LP:AF:ID  8.73601e-05:0.000243182:0.142668:0.143053:rs59380221
1   798400  rs10900604  A   G   .   PASS    AF=0.206591 ES:SE:LP:AF:ID  1.37568e-05:0.000198027:0.0268721:0.206591:rs10900604
1   798959  rs11240777  G   A   .   PASS    AF=0.20642  ES:SE:LP:AF:ID  1.36025e-05:0.000198111:0.0222764:0.20642:rs11240777
1   808631  rs11240779  G   A   .   PASS    AF=0.772619 ES:SE:LP:AF:ID  -4.55975e-05:0.000188459:0.091515:0.772619:rs11240779
1   808928  rs11240780  C   T   .   PASS    AF=0.772847 ES:SE:LP:AF:ID  -4.87259e-05:0.000188776:0.09691:0.772847:rs11240780
1   814495  rs74461805  C   A   .   PASS    AF=0.340396 ES:SE:LP:AF:ID  0.000131895:0.000265995:0.207608:0.340396:rs74461805
1   824398  rs7538305   A   C   .   PASS    AF=0.138699 ES:SE:LP:AF:ID  5.61426e-05:0.000234902:0.091515:0.138699:rs7538305
1   830181  rs28444699  A   G   .   PASS    AF=0.697255 ES:SE:LP:AF:ID  0.000144511:0.000177965:0.376751:0.697255:rs28444699
1   831489  rs4970385   C   T   .   PASS    AF=0.705397 ES:SE:LP:AF:ID  0.000108608:0.000174744:0.275724:0.705397:rs4970385
1   831909  rs9697642   C   T   .   PASS    AF=0.705442 ES:SE:LP:AF:ID  0.000113145:0.000174738:0.283997:0.705442:rs9697642
1   832066  rs9697380   G   C   .   PASS    AF=0.705627 ES:SE:LP:AF:ID  0.000115524:0.000174746:0.29243:0.705627:rs9697380
1   832318  rs4500250   C   A   .   PASS    AF=0.705655 ES:SE:LP:AF:ID  0.000114674:0.000174764:0.29243:0.705655:rs4500250
1   832398  rs4553118   T   C   .   PASS    AF=0.730129 ES:SE:LP:AF:ID  0.000208664:0.000179526:0.60206:0.730129:rs4553118