Summary

Summary {data-width=650}

Manhattan plot

manhattan_plot

QQ plot

qq_plot

AF plot

af_plot

P-Z plot

pz_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 /data/cromwell-executions/qc/88d0584c-dcb4-42f7-b295-1533ae4e5a9a/call-ldsc/inputs/-261043577/ieu-b-4915.vcf.gz \
--ref-ld-chr /data/ref/eur_w_ld_chr/ \
--out /data/igd/ieu-b-4915/ldsc.txt \
--w-ld-chr /data/ref/eur_w_ld_chr/ 

Beginning analysis at Fri Mar  4 03:51:51 2022
Reading summary statistics from /data/cromwell-executions/qc/88d0584c-dcb4-42f7-b295-1533ae4e5a9a/call-ldsc/inputs/-261043577/ieu-b-4915.vcf.gz ...
Read summary statistics for 7686828 SNPs.
Dropped 134205 SNPs with duplicated rs numbers.
Reading reference panel LD Score from /data/ref/eur_w_ld_chr/[1-22] ... (ldscore_fromlist)
Read reference panel LD Scores for 1290028 SNPs.
Removing partitioned LD Scores with zero variance.
Reading regression weight LD Score from /data/ref/eur_w_ld_chr/[1-22] ... (ldscore_fromlist)
Read regression weight LD Scores for 1290028 SNPs.
After merging with reference panel LD, 1144421 SNPs remain.
After merging with regression SNP LD, 1144421 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0006 (0.0012)
Lambda GC: 1.0146
Mean Chi^2: 1.0025
Intercept: 0.9981 (0.0065)
Ratio < 0 (usually indicates GC correction).
Analysis finished at Fri Mar  4 03:53:20 2022
Total time elapsed: 1.0m:29.35s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.923,
    "inflation_factor": 1,
    "mean_EFFECT": -3.3462e-08,
    "n": "-Inf",
    "n_snps": 7687713,
    "n_clumped_hits": 1,
    "n_p_sig": 8,
    "n_mono": 0,
    "n_ns": 977597,
    "n_mac": 0,
    "is_snpid_unique": false,
    "n_miss_EFFECT": 0,
    "n_miss_SE": 0,
    "n_miss_PVAL": 0,
    "n_miss_AF": 0,
    "n_miss_AF_reference": 971866,
    "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": 1144421,
    "ldsc_nsnp_merge_regression_ld": 1144421,
    "ldsc_observed_scale_h2_beta": 0.0006,
    "ldsc_observed_scale_h2_se": 0.0012,
    "ldsc_intercept_beta": 0.9981,
    "ldsc_intercept_se": 0.0065,
    "ldsc_lambda_gc": 1.0146,
    "ldsc_mean_chisq": 1.0025,
    "ldsc_ratio": -0.76
}

Flags

name value
af_correlation FALSE
inflation_factor FALSE
n TRUE
is_snpid_non_unique TRUE
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 575 0.9999252 3 58 0 7664545 0 NA NA NA NA NA NA NA NA NA NA
character REF 0 1.0000000 1 88 0 12945 0 NA NA NA NA NA NA NA NA NA NA
character ALT 0 1.0000000 1 662 0 53118 0 NA NA NA NA NA NA NA NA NA NA
logical N 7687713 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 8.877573e+00 5.963818e+00 1.0000000 4.000000e+00 8.00000e+00 1.300000e+01 2.300000e+01 ▇▅▅▂▂
numeric POS 0 1.0000000 NA NA NA NA NA NA NA 7.837341e+07 5.644403e+07 302.0000000 3.192739e+07 6.87943e+07 1.143364e+08 2.492405e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA NA NA 0.000000e+00 1.090000e-04 -0.0010110 -6.590000e-05 -7.00000e-07 6.450000e-05 9.785000e-04 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA NA NA 1.031000e-04 3.420000e-05 0.0000584 7.560000e-05 8.97000e-05 1.222000e-04 3.512000e-04 ▇▂▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA NA NA 4.974007e-01 2.889043e-01 0.0000000 2.500000e-01 5.00000e-01 7.499995e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA NA NA 4.974023e-01 2.888780e-01 0.0000000 2.467105e-01 4.95525e-01 7.477066e-01 1.000000e+00 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA NA NA 3.593836e-01 2.754722e-01 0.0357150 1.146620e-01 2.83261e-01 5.668430e-01 9.642850e-01 ▇▃▃▂▂
numeric AF_reference 971866 0.8735819 NA NA NA NA NA NA NA 3.180827e-01 2.464644e-01 0.0000000 1.136180e-01 2.51398e-01 4.828270e-01 1.000000e+00 ▇▅▃▂▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 10177 rs1264289758 AC A -0.0000566 0.0001060 0.5900000 0.5934730 0.601334 NA NA
1 10352 rs1557426776 TA T 0.0002539 0.0001092 0.0200000 0.0200881 0.607033 NA NA
1 11008 rs575272151 C G 0.0003641 0.0001815 0.0449997 0.0448680 0.086208 0.0880591 NA
1 11012 rs544419019 C G 0.0003641 0.0001815 0.0449997 0.0448680 0.086208 0.0880591 NA
1 13110 rs540538026 G A 0.0000514 0.0002412 0.8300000 0.8313534 0.058739 0.0267572 NA
1 13116 rs62635286 T G 0.0000007 0.0001428 1.0000000 0.9961709 0.189420 0.0970447 NA
1 13118 rs200579949 A G 0.0000007 0.0001428 1.0000000 0.9961709 0.189420 0.0970447 NA
1 13273 rs531730856 G C -0.0001440 0.0001674 0.3900004 0.3897260 0.133925 0.0950479 NA
1 14464 rs546169444 A T -0.0000280 0.0001521 0.8499999 0.8536660 0.157051 0.0958466 NA
1 14599 rs531646671 T A 0.0000306 0.0001386 0.8300000 0.8255035 0.191575 0.1475640 NA
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
23 154901936 rs697727 A G 7.00e-07 6.79e-05 0.9900000 0.9919588 0.751497 0.643179 NA
23 154901964 rs697726 G A 1.72e-05 7.17e-05 0.8100000 0.8107053 0.347477 0.117616 NA
23 154902105 rs696316 G T 8.00e-07 6.79e-05 0.9900000 0.9902810 0.751449 0.636026 NA
23 154902889 rs697725 A T 1.90e-06 6.79e-05 0.9800000 0.9778297 0.751121 0.584106 NA
23 154903118 rs479770 G A 6.00e-07 6.79e-05 0.9900000 0.9930193 0.751540 0.643444 NA
23 154903224 rs480725 A T 6.00e-07 6.79e-05 0.9900000 0.9931234 0.751542 0.643444 NA
23 154903937 rs674707 G A 6.00e-07 6.79e-05 0.9900000 0.9934773 0.751552 0.643444 NA
23 154909055 rs473529 C G 2.38e-05 6.39e-05 0.7099994 0.7102184 0.305122 0.463046 NA
23 154918266 rs642043 C T 2.57e-05 6.41e-05 0.6899999 0.6889904 0.302987 0.478675 NA
23 154927581 rs644138 G A 2.60e-05 6.41e-05 0.6899999 0.6856151 0.302860 0.463576 NA

bcf preview

1   10177   rs1264289758    AC  A   .   PASS    AF=0.601334 ES:SE:LP:AF:ID  -5.65956e-05:0.000106022:0.229148:0.601334:rs1264289758
1   10352   rs1557426776    TA  T   .   PASS    AF=0.607033 ES:SE:LP:AF:ID  0.000253871:0.000109206:1.69897:0.607033:rs1557426776
1   11008   rs575272151 C   G   .   PASS    AF=0.086208 ES:SE:LP:AF:ID  0.000364061:0.000181496:1.34679:0.086208:rs575272151
1   11012   rs544419019 C   G   .   PASS    AF=0.086208 ES:SE:LP:AF:ID  0.000364061:0.000181496:1.34679:0.086208:rs544419019
1   13110   rs540538026 G   A   .   PASS    AF=0.058739 ES:SE:LP:AF:ID  5.13604e-05:0.000241167:0.0809219:0.058739:rs540538026
1   13116   rs62635286  T   G   .   PASS    AF=0.18942  ES:SE:LP:AF:ID  6.85474e-07:0.000142834:-0:0.18942:rs62635286
1   13118   rs62028691  A   G   .   PASS    AF=0.18942  ES:SE:LP:AF:ID  6.85474e-07:0.000142834:-0:0.18942:rs62028691
1   13273   rs531730856 G   C   .   PASS    AF=0.133925 ES:SE:LP:AF:ID  -0.000144021:0.000167444:0.408935:0.133925:rs531730856
1   14464   rs546169444 A   T   .   PASS    AF=0.157051 ES:SE:LP:AF:ID  -2.80451e-05:0.000152053:0.0705811:0.157051:rs546169444
1   14599   rs707680    T   A   .   PASS    AF=0.191575 ES:SE:LP:AF:ID  3.05603e-05:0.000138613:0.0809219:0.191575:rs707680
1   14604   rs1418508701    A   G   .   PASS    AF=0.191575 ES:SE:LP:AF:ID  3.05603e-05:0.000138613:0.0809219:0.191575:rs1418508701
1   14930   rs6682385   A   G   .   PASS    AF=0.474007 ES:SE:LP:AF:ID  5.13412e-05:0.000107528:0.200659:0.474007:rs6682385
1   14933   rs199856693 G   A   .   PASS    AF=0.045013 ES:SE:LP:AF:ID  0.000295206:0.000264771:0.585027:0.045013:rs199856693
1   15211   rs3982632   T   G   .   PASS    AF=0.741404 ES:SE:LP:AF:ID  -0.00018161:0.000124339:0.853872:0.741404:rs3982632
1   15820   rs1316988498    G   T   .   PASS    AF=0.275206 ES:SE:LP:AF:ID  -0.000135702:0.00012751:0.537602:0.275206:rs1316988498
1   15903   rs557514207 GC  G   .   PASS    AF=0.581019 ES:SE:LP:AF:ID  -5.04795e-05:0.000105134:0.200659:0.581019:rs557514207
1   28590   rs1344649620    T   TTGG    .   PASS    AF=0.956493 ES:SE:LP:AF:ID  -0.00040001:0.000298767:0.744727:0.956493:rs1344649620
1   30923   rs1165072081    G   T   .   PASS    AF=0.910277 ES:SE:LP:AF:ID  -0.000139506:0.000198511:0.318759:0.910277:rs1165072081
1   47159   rs540662756 T   C   .   PASS    AF=0.062668 ES:SE:LP:AF:ID  -2.73249e-05:0.000226502:0.0457575:0.062668:rs540662756
1   49298   rs10399793  T   C   .   PASS    AF=0.623642 ES:SE:LP:AF:ID  7.28974e-05:0.000126142:0.251812:0.623642:rs10399793
1   49554   rs539322794 A   G   .   PASS    AF=0.092969 ES:SE:LP:AF:ID  -3.03958e-05:0.000194017:0.0555173:0.092969:rs539322794
1   51479   rs116400033 T   A   .   PASS    AF=0.213497 ES:SE:LP:AF:ID  6.16664e-05:0.000134841:0.187087:0.213497:rs116400033
1   54490   rs141149254 G   A   .   PASS    AF=0.154535 ES:SE:LP:AF:ID  9.69501e-05:0.000151504:0.283997:0.154535:rs141149254
1   54676   rs2462492   C   T   .   PASS    AF=0.40043  ES:SE:LP:AF:ID  0.000105964:0.000124959:0.39794:0.40043:rs2462492
1   54712   rs573184866 TTTTC   T   .   PASS    AF=0.414842 ES:SE:LP:AF:ID  6.64472e-06:9.87796e-05:0.0222764:0.414842:rs573184866
1   54716   rs1166278911    C   T   .   PASS    AF=0.417217 ES:SE:LP:AF:ID  -9.56279e-05:0.000114078:0.39794:0.417217:rs1166278911
1   55545   rs28396308  C   T   .   PASS    AF=0.253868 ES:SE:LP:AF:ID  1.68979e-05:0.000128329:0.0457575:0.253868:rs28396308
1   58814   rs114420996 G   A   .   PASS    AF=0.09004  ES:SE:LP:AF:ID  0.000162407:0.000195421:0.387216:0.09004:rs114420996
1   59040   rs62637815  T   C   .   PASS    AF=0.088874 ES:SE:LP:AF:ID  8.50138e-05:0.000196172:0.180456:0.088874:rs62637815
1   60351   rs62637817  A   G   .   PASS    AF=0.081028 ES:SE:LP:AF:ID  0.000164876:0.000203486:0.376751:0.081028:rs62637817
1   62777   rs3844233   A   T   .   PASS    AF=0.438469 ES:SE:LP:AF:ID  -0.000151207:0.000108458:0.79588:0.438469:rs3844233
1   63268   rs28664618  T   C   .   PASS    AF=0.382112 ES:SE:LP:AF:ID  -7.24472e-07:0.000116584:-0:0.382112:rs28664618
1   63671   rs80011619  G   A   .   PASS    AF=0.158848 ES:SE:LP:AF:ID  9.96756e-05:0.000148419:0.30103:0.158848:rs80011619
1   63735   rs61158452  C   CCTA    .   PASS    AF=0.683973 ES:SE:LP:AF:ID  -2.97409e-06:0.000115552:0.00877392:0.683973:rs61158452
1   64931   rs62639104  G   A   .   PASS    AF=0.079634 ES:SE:LP:AF:ID  0.000113942:0.000205968:0.236572:0.079634:rs62639104
1   68082   rs367789441 T   C   .   PASS    AF=0.070763 ES:SE:LP:AF:ID  0.000192969:0.000208878:0.443698:0.070763:rs367789441
1   69761   rs200505207 A   T   .   PASS    AF=0.073906 ES:SE:LP:AF:ID  0.000148164:0.00020547:0.327902:0.073906:rs200505207
1   69897   rs200676709 T   C   .   PASS    AF=0.751159 ES:SE:LP:AF:ID  7.16601e-05:0.000130882:0.236572:0.751159:rs200676709
1   76838   rs563953605 T   G   .   PASS    AF=0.0772   ES:SE:LP:AF:ID  -3.25009e-05:0.000209907:0.0555173:0.0772:rs563953605
1   76854   rs367666799 A   G   .   PASS    AF=0.077449 ES:SE:LP:AF:ID  4.44404e-05:0.000202713:0.0809219:0.077449:rs367666799
1   77866   rs563593912 C   T   .   PASS    AF=0.077004 ES:SE:LP:AF:ID  -2.95846e-05:0.000209962:0.05061:0.077004:rs563593912
1   77874   rs62641297  G   A   .   PASS    AF=0.077004 ES:SE:LP:AF:ID  -2.95846e-05:0.000209962:0.05061:0.077004:rs62641297
1   81260   rs571136476 C   T   .   PASS    AF=0.041516 ES:SE:LP:AF:ID  -0.000460968:0.000292687:0.920819:0.041516:rs571136476
1   81587   rs536406113 C   T   .   PASS    AF=0.060967 ES:SE:LP:AF:ID  6.13568e-05:0.000222552:0.107905:0.060967:rs536406113
1   82163   rs139113303 G   A   .   PASS    AF=0.07541  ES:SE:LP:AF:ID  7.69155e-05:0.000205271:0.148742:0.07541:rs139113303
1   82609   rs149189449 C   G   .   PASS    AF=0.075437 ES:SE:LP:AF:ID  7.69884e-05:0.00020523:0.148742:0.075437:rs149189449
1   83514   rs201754587 C   T   .   PASS    AF=0.352689 ES:SE:LP:AF:ID  -2.08307e-06:0.000117509:0.00436481:0.352689:rs201754587
1   86028   rs114608975 T   C   .   PASS    AF=0.103489 ES:SE:LP:AF:ID  -0.000117723:0.000199891:0.251812:0.103489:rs114608975
1   86065   rs116504101 G   C   .   PASS    AF=0.0761   ES:SE:LP:AF:ID  5.02429e-05:0.000205837:0.091515:0.0761:rs116504101
1   86331   rs115209712 A   G   .   PASS    AF=0.109607 ES:SE:LP:AF:ID  -0.000218235:0.00018107:0.638272:0.109607:rs115209712