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-1092/UKB-b-1092_data.vcf.gz \
--ref-ld-chr ../reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-1092/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-1092/UKB-b-1092_data.vcf.gz ...
Read summary statistics for 3623811 SNPs.
Dropped 599 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, 879986 SNPs remain.
After merging with regression SNP LD, 879986 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0007 (0.0012)
Lambda GC: 1.0517
Mean Chi^2: 1.0556
Intercept: 1.0483 (0.0087)
Ratio: 0.8674 (0.157)
Analysis finished at Thu Oct 17 14:41:05 2019
Total time elapsed: 46.87s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.8582,
    "inflation_factor": 1.0475,
    "mean_EFFECT": -8.6529e-08,
    "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": 29216,
    "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": 879986,
    "ldsc_nsnp_merge_regression_ld": 879986,
    "ldsc_observed_scale_h2_beta": 0.0007,
    "ldsc_observed_scale_h2_se": 0.0012,
    "ldsc_intercept_beta": 1.0483,
    "ldsc_intercept_se": 0.0087,
    "ldsc_lambda_gc": 1.0517,
    "ldsc_mean_chisq": 1.0556,
    "ldsc_ratio": 0.8687
}

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 3623215 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 3623811 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 8.661394e+00 5.771475e+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 7.854390e+07 5.675355e+07 828.0000000 3.158152e+07 6.888345e+07 1.147155e+08 2.492385e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA NA NA -1.000000e-07 1.772000e-04 -0.0009693 -1.183000e-04 -1.000000e-07 1.169000e-04 1.086600e-03 ▁▂▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA NA NA 1.715000e-04 1.910000e-05 0.0001456 1.548000e-04 1.654000e-04 1.849000e-04 5.325000e-04 ▇▁▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA NA NA 4.923325e-01 2.911999e-01 0.0000002 2.399999e-01 4.899999e-01 7.400005e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA NA NA 4.923311e-01 2.911713e-01 0.0000002 2.383658e-01 4.895938e-01 7.448736e-01 9.999997e-01 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA NA NA 4.100334e-01 2.000952e-01 0.1426830 2.348320e-01 3.689160e-01 5.613510e-01 8.573170e-01 ▇▅▃▃▂
numeric AF_reference 29216 0.9919378 NA NA NA NA NA NA NA 3.970275e-01 2.082214e-01 0.0000000 2.266370e-01 3.632190e-01 5.487220e-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 0.0002528 0.0002679 0.3500000 0.3454650 0.623765 0.782149 NA
1 54676 rs2462492 C T 0.0000199 0.0002654 0.9400001 0.9403468 0.400401 NA NA
1 91536 rs6702460 G T 0.0002107 0.0002614 0.4199997 0.4201280 0.456846 0.420727 NA
1 534192 rs6680723 C T -0.0003673 0.0002985 0.2200002 0.2185588 0.240959 NA NA
1 706368 rs55727773 A G 0.0001301 0.0001853 0.4799997 0.4826719 0.515645 0.275160 NA
1 729679 rs4951859 C G 0.0000001 0.0002168 1.0000000 0.9994944 0.843204 0.639976 NA
1 752566 rs3094315 G A -0.0000869 0.0002100 0.6800001 0.6790405 0.838945 0.718251 NA
1 752721 rs3131972 A G -0.0000863 0.0002097 0.6800001 0.6808132 0.838573 0.653355 NA
1 754503 rs3115859 G A -0.0001181 0.0002092 0.5700002 0.5724207 0.838026 0.663938 NA
1 754964 rs3131966 C T -0.0001150 0.0002098 0.5800000 0.5835220 0.838657 0.663339 NA
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51182485 rs6009961 A G -0.0003364 0.0001750 0.0549997 0.0545338 0.715502 0.6383790 NA
22 51186143 rs2879914 T C -0.0005067 0.0001622 0.0018000 0.0017900 0.381825 0.2733630 NA
22 51186228 rs3865766 C T -0.0004935 0.0001581 0.0018000 0.0018042 0.451061 0.4532750 NA
22 51192586 rs5771006 G A -0.0002841 0.0002131 0.1800002 0.1824168 0.167627 0.0848642 NA
22 51193227 rs34608236 T G 0.0005270 0.0002178 0.0160000 0.0155326 0.168490 0.0692891 NA
22 51197266 rs61290853 A G -0.0003324 0.0001633 0.0420001 0.0417662 0.386333 0.4229230 NA
22 51198027 rs34939255 A G 0.0003316 0.0001848 0.0729995 0.0727562 0.254562 0.0984425 NA
22 51211106 rs9628250 T C 0.0003208 0.0001832 0.0800000 0.0799783 0.271547 0.1671330 NA
22 51212875 rs2238837 A C -0.0003671 0.0001741 0.0350002 0.0350034 0.331457 0.3724040 NA
22 51237063 rs3896457 T C -0.0004225 0.0001782 0.0179999 0.0177653 0.297974 0.2050720 NA

bcf preview

1   49298   rs10399793  T   C   .   PASS    AF=0.623765 ES:SE:LP:AF:ID  0.000252773:0.000267932:0.455932:0.623765:rs10399793
1   54676   rs2462492   C   T   .   PASS    AF=0.400401 ES:SE:LP:AF:ID  1.98638e-05:0.000265438:0.0268721:0.400401:rs2462492
1   91536   rs6702460   G   T   .   PASS    AF=0.456846 ES:SE:LP:AF:ID  0.000210705:0.000261356:0.376751:0.456846:rs6702460
1   534192  rs6680723   C   T   .   PASS    AF=0.240959 ES:SE:LP:AF:ID  -0.000367312:0.000298538:0.657577:0.240959:rs6680723
1   706368  rs12029736  A   G   .   PASS    AF=0.515645 ES:SE:LP:AF:ID  0.000130101:0.000185326:0.318759:0.515645:rs12029736
1   729679  rs4951859   C   G   .   PASS    AF=0.843204 ES:SE:LP:AF:ID  1.37395e-07:0.000216816:-0:0.843204:rs4951859
1   752566  rs3094315   G   A   .   PASS    AF=0.838945 ES:SE:LP:AF:ID  -8.68807e-05:0.000209972:0.167491:0.838945:rs3094315
1   752721  rs3131972   A   G   .   PASS    AF=0.838573 ES:SE:LP:AF:ID  -8.62798e-05:0.000209746:0.167491:0.838573:rs3131972
1   754503  rs3115859   G   A   .   PASS    AF=0.838026 ES:SE:LP:AF:ID  -0.000118071:0.000209164:0.244125:0.838026:rs3115859
1   754964  rs3131966   C   T   .   PASS    AF=0.838657 ES:SE:LP:AF:ID  -0.000114996:0.000209752:0.236572:0.838657:rs3131966
1   755775  rs3131965   A   G   .   PASS    AF=0.83977  ES:SE:LP:AF:ID  -0.000122869:0.000212589:0.251812:0.83977:rs3131965
1   760912  rs1048488   C   T   .   PASS    AF=0.838306 ES:SE:LP:AF:ID  -0.000145416:0.000208767:0.309804:0.838306:rs1048488
1   761147  rs3115850   T   C   .   PASS    AF=0.838427 ES:SE:LP:AF:ID  -0.000139383:0.000208915:0.30103:0.838427:rs3115850
1   763394  rs3115847   G   A   .   PASS    AF=0.706753 ES:SE:LP:AF:ID  4.30367e-05:0.000217277:0.0757207:0.706753:rs3115847
1   768253  rs2977608   A   C   .   PASS    AF=0.761297 ES:SE:LP:AF:ID  -7.57109e-05:0.000177336:0.173925:0.761297:rs2977608
1   776546  rs12124819  A   G   .   PASS    AF=0.265385 ES:SE:LP:AF:ID  0.000105465:0.000198091:0.229148:0.265385:rs12124819
1   795988  rs59380221  C   T   .   PASS    AF=0.143053 ES:SE:LP:AF:ID  0.00014349:0.00023232:0.267606:0.143053:rs59380221
1   798400  rs10900604  A   G   .   PASS    AF=0.206591 ES:SE:LP:AF:ID  8.798e-05:0.000189181:0.19382:0.206591:rs10900604
1   798959  rs11240777  G   A   .   PASS    AF=0.20642  ES:SE:LP:AF:ID  9.35699e-05:0.000189262:0.207608:0.20642:rs11240777
1   808631  rs11240779  G   A   .   PASS    AF=0.772619 ES:SE:LP:AF:ID  -0.000139542:0.000180041:0.356547:0.772619:rs11240779
1   808928  rs11240780  C   T   .   PASS    AF=0.772847 ES:SE:LP:AF:ID  -0.000129606:0.000180345:0.327902:0.772847:rs11240780
1   814495  rs74461805  C   A   .   PASS    AF=0.340396 ES:SE:LP:AF:ID  0.000287555:0.000254114:0.585027:0.340396:rs74461805
1   830181  rs28444699  A   G   .   PASS    AF=0.697255 ES:SE:LP:AF:ID  9.34871e-05:0.000170016:0.236572:0.697255:rs28444699
1   831489  rs4970385   C   T   .   PASS    AF=0.705397 ES:SE:LP:AF:ID  8.057e-05:0.000166939:0.200659:0.705397:rs4970385
1   831909  rs9697642   C   T   .   PASS    AF=0.705442 ES:SE:LP:AF:ID  7.99076e-05:0.000166933:0.200659:0.705442:rs9697642
1   832066  rs9697380   G   C   .   PASS    AF=0.705627 ES:SE:LP:AF:ID  7.90316e-05:0.000166941:0.19382:0.705627:rs9697380
1   832318  rs4500250   C   A   .   PASS    AF=0.705655 ES:SE:LP:AF:ID  7.88118e-05:0.000166958:0.19382:0.705655:rs4500250
1   832398  rs4553118   T   C   .   PASS    AF=0.730129 ES:SE:LP:AF:ID  4.9707e-05:0.000171508:0.113509:0.730129:rs4553118
1   832918  rs28765502  T   C   .   PASS    AF=0.294377 ES:SE:LP:AF:ID  -8.08401e-05:0.000166951:0.200659:0.294377:rs28765502
1   833223  rs13303211  C   T   .   PASS    AF=0.236703 ES:SE:LP:AF:ID  -0.000115488:0.000177745:0.283997:0.236703:rs13303211
1   833302  rs28752186  C   T   .   PASS    AF=0.236691 ES:SE:LP:AF:ID  -0.000115333:0.000177747:0.283997:0.236691:rs28752186
1   833641  rs28594623  T   C   .   PASS    AF=0.23975  ES:SE:LP:AF:ID  -8.0092e-05:0.000177177:0.187087:0.23975:rs28594623
1   833824  rs28484835  T   C   .   PASS    AF=0.236693 ES:SE:LP:AF:ID  -0.000115369:0.000177745:0.283997:0.236693:rs28484835
1   833927  rs28593608  T   C   .   PASS    AF=0.212421 ES:SE:LP:AF:ID  -7.97043e-05:0.000184742:0.173925:0.212421:rs28593608
1   834198  rs28385272  T   C   .   PASS    AF=0.212316 ES:SE:LP:AF:ID  -7.59777e-05:0.000184774:0.167491:0.212316:rs28385272
1   834832  rs4411087   G   C   .   PASS    AF=0.237178 ES:SE:LP:AF:ID  -0.000122911:0.000177609:0.309804:0.237178:rs4411087
1   834928  rs4422949   A   G   .   PASS    AF=0.212962 ES:SE:LP:AF:ID  -9.28928e-05:0.000184511:0.21467:0.212962:rs4422949
1   834999  rs28570054  G   A   .   PASS    AF=0.212924 ES:SE:LP:AF:ID  -9.17878e-05:0.000184549:0.207608:0.212924:rs28570054
1   835499  rs4422948   A   G   .   PASS    AF=0.241162 ES:SE:LP:AF:ID  -0.000118647:0.000176369:0.30103:0.241162:rs4422948
1   836529  rs28731045  C   G   .   PASS    AF=0.213543 ES:SE:LP:AF:ID  -0.000105509:0.000184277:0.244125:0.213543:rs28731045
1   836896  rs28705752  T   C   .   PASS    AF=0.269511 ES:SE:LP:AF:ID  -0.000142668:0.000170182:0.39794:0.269511:rs28705752
1   836924  rs72890788  G   A   .   PASS    AF=0.213513 ES:SE:LP:AF:ID  -0.000104571:0.0001843:0.244125:0.213513:rs72890788
1   838387  rs4970384   T   C   .   PASS    AF=0.214587 ES:SE:LP:AF:ID  -0.000116578:0.000183945:0.275724:0.214587:rs4970384
1   838555  rs4970383   C   A   .   PASS    AF=0.246204 ES:SE:LP:AF:ID  -0.000109926:0.000175156:0.275724:0.246204:rs4970383
1   839103  rs28562941  A   G   .   PASS    AF=0.270019 ES:SE:LP:AF:ID  -0.000157831:0.000170303:0.455932:0.270019:rs28562941
1   840753  rs4970382   T   C   .   PASS    AF=0.400124 ES:SE:LP:AF:ID  -0.00020068:0.000153987:0.721246:0.400124:rs4970382
1   841085  rs1574243   C   G   .   PASS    AF=0.237102 ES:SE:LP:AF:ID  -0.000115591:0.000178861:0.283997:0.237102:rs1574243
1   842013  rs7419119   T   G   .   PASS    AF=0.215391 ES:SE:LP:AF:ID  -0.000104774:0.000184068:0.244125:0.215391:rs7419119
1   842362  rs28540380  C   T   .   PASS    AF=0.235323 ES:SE:LP:AF:ID  -0.00010624:0.00018154:0.251812:0.235323:rs28540380
1   843405  rs11516185  A   G   .   PASS    AF=0.362606 ES:SE:LP:AF:ID  -0.000122692:0.000191153:0.283997:0.362606:rs11516185