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/0ea68a6b-84fa-40c3-8038-154b12d095bc/call-ldsc/inputs/-261022214/ieu-b-5089.vcf.gz \
--ref-ld-chr /data/ref/eur_w_ld_chr/ \
--out /data/igd/ieu-b-5089/ldsc.txt \
--w-ld-chr /data/ref/eur_w_ld_chr/ 

Beginning analysis at Mon Nov 14 23:35:46 2022
Reading summary statistics from /data/cromwell-executions/qc/0ea68a6b-84fa-40c3-8038-154b12d095bc/call-ldsc/inputs/-261022214/ieu-b-5089.vcf.gz ...
Read summary statistics for 0 SNPs.
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.
Traceback (most recent call last):
  File "./ldsc/ldsc.py", line 647, in <module>
    sumstats.estimate_h2(args, log)
  File "/ldsc/ldscore/sumstats.py", line 330, in estimate_h2
    args, log, args.h2)
  File "/ldsc/ldscore/sumstats.py", line 252, in _read_ld_sumstats
    sumstats = _merge_and_log(ref_ld, sumstats, 'reference panel LD', log)
  File "/ldsc/ldscore/sumstats.py", line 238, in _merge_and_log
    raise ValueError(msg.format(N=len(sumstats), F=noun))
ValueError: After merging with reference panel LD, 0 SNPs remain.

Analysis finished at Mon Nov 14 23:36:58 2022
Total time elapsed: 1.0m:12.18s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9503,
    "inflation_factor": 1.1474,
    "mean_EFFECT": -0,
    "n": "-Inf",
    "n_snps": 12321875,
    "n_clumped_hits": 82,
    "n_p_sig": 14022,
    "n_mono": 0,
    "n_ns": 1293897,
    "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": 1423040,
    "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": 0,
    "ldsc_nsnp_merge_regression_ld": "NA",
    "ldsc_observed_scale_h2_beta": "NA",
    "ldsc_observed_scale_h2_se": "NA",
    "ldsc_intercept_beta": "NA",
    "ldsc_intercept_se": "NA",
    "ldsc_lambda_gc": "NA",
    "ldsc_mean_chisq": "NA",
    "ldsc_ratio": "NA"
}

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 NA
n_p_sig TRUE
miss_EFFECT FALSE
miss_SE FALSE
miss_PVAL FALSE
ldsc_ratio NA
ldsc_intercept_beta NA
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 675 0.9999452 3 58 0 12276232 0 NA NA NA NA NA NA NA NA NA NA
character REF 0 1.0000000 1 88 0 17566 0 NA NA NA NA NA NA NA NA NA NA
character ALT 0 1.0000000 1 662 0 71704 0 NA NA NA NA NA NA NA NA NA NA
logical N 12321875 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 8.757492e+00 5.885387e+00 1.0000000 4.000000e+00 8.000000e+00 1.300000e+01 2.300000e+01 ▇▅▅▂▂
numeric POS 0 1.0000000 NA NA NA NA NA NA NA 7.871202e+07 5.622121e+07 302.0000000 3.252510e+07 6.928045e+07 1.144492e+08 2.492405e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA NA NA -1.660000e-05 1.478740e-02 -0.4047140 -4.621100e-03 -1.480000e-05 4.605600e-03 3.809640e-01 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA NA NA 1.031680e-02 9.912200e-03 0.0021998 3.612800e-03 5.801500e-03 1.338820e-02 1.585320e-01 ▇▁▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA NA NA 4.756686e-01 2.959760e-01 0.0000000 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 4.756998e-01 2.959222e-01 0.0000000 2.135839e-01 4.677650e-01 7.318867e-01 9.999999e-01 ▇▇▆▆▆
numeric AF 0 1.0000000 NA NA NA NA NA NA NA 2.594005e-01 3.020432e-01 0.0008550 1.659900e-02 1.145450e-01 4.378850e-01 9.992590e-01 ▇▂▁▁▁
numeric AF_reference 1423040 0.8845111 NA NA NA NA NA NA NA 2.132160e-01 2.513550e-01 0.0000000 1.218050e-02 1.056310e-01 3.376600e-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 -0.0043316 0.0046377 0.3200000 0.3503149 0.600331 NA NA
1 10352 rs1557426776 TA T 0.0008633 0.0047802 0.7499995 0.8566788 0.607145 NA NA
1 11008 rs575272151 C G -0.0051071 0.0079063 0.5400003 0.5183067 0.086668 0.0880591 NA
1 11012 rs544419019 C G -0.0051071 0.0079063 0.5400003 0.5183067 0.086668 0.0880591 NA
1 13110 rs540538026 G A 0.0087056 0.0105670 0.3800004 0.4100239 0.058748 0.0267572 NA
1 13116 rs62635286 T G -0.0095856 0.0062527 0.1800002 0.1252698 0.189324 0.0970447 NA
1 13118 rs200579949 A G -0.0095856 0.0062527 0.1800002 0.1252698 0.189324 0.0970447 NA
1 13273 rs531730856 G C -0.0052869 0.0073370 0.5000000 0.4711660 0.134072 0.0950479 NA
1 14464 rs546169444 A T 0.0000549 0.0066715 0.8700001 0.9934346 0.156891 0.0958466 NA
1 14599 rs531646671 T A 0.0021571 0.0060582 0.8800001 0.7217876 0.192052 0.1475640 NA
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
23 154901936 rs697727 A G -0.0007604 0.0025497 0.9900000 0.7655426 0.752783 0.643179 NA
23 154901964 rs697726 G A 0.0008535 0.0026837 0.8000000 0.7504712 0.349025 0.117616 NA
23 154902105 rs696316 G T -0.0007302 0.0025496 1.0000000 0.7745762 0.752762 0.636026 NA
23 154902889 rs697725 A T -0.0006092 0.0025488 0.9599999 0.8110886 0.752468 0.584106 NA
23 154903118 rs479770 G A -0.0007849 0.0025499 0.9800000 0.7582272 0.752814 0.643444 NA
23 154903224 rs480725 A T -0.0007849 0.0025499 0.9800000 0.7582182 0.752816 0.643444 NA
23 154903937 rs674707 G A -0.0007822 0.0025500 0.9900000 0.7590341 0.752821 0.643444 NA
23 154909055 rs473529 C G -0.0000103 0.0023993 0.8900000 0.9965887 0.303505 0.463046 NA
23 154918266 rs642043 C T -0.0002340 0.0024068 0.8200001 0.9225447 0.301421 0.478675 NA
23 154927581 rs644138 G A -0.0001364 0.0024072 0.8499999 0.9548237 0.301323 0.463576 NA

bcf preview

1   10177   rs1264289758    AC  A   .   PASS    AF=0.600331 ES:SE:LP:AF:ID  -0.00433155:0.00463774:0.49485:0.600331:rs1264289758
1   10352   rs1557426776    TA  T   .   PASS    AF=0.607145 ES:SE:LP:AF:ID  0.000863317:0.00478018:0.124939:0.607145:rs1557426776
1   11008   rs575272151 C   G   .   PASS    AF=0.086668 ES:SE:LP:AF:ID  -0.00510713:0.00790629:0.267606:0.086668:rs575272151
1   11012   rs544419019 C   G   .   PASS    AF=0.086668 ES:SE:LP:AF:ID  -0.00510713:0.00790629:0.267606:0.086668:rs544419019
1   13110   rs540538026 G   A   .   PASS    AF=0.058748 ES:SE:LP:AF:ID  0.00870564:0.010567:0.420216:0.058748:rs540538026
1   13116   rs62635286  T   G   .   PASS    AF=0.189324 ES:SE:LP:AF:ID  -0.00958562:0.00625275:0.744727:0.189324:rs62635286
1   13118   rs62028691  A   G   .   PASS    AF=0.189324 ES:SE:LP:AF:ID  -0.00958562:0.00625275:0.744727:0.189324:rs62028691
1   13273   rs531730856 G   C   .   PASS    AF=0.134072 ES:SE:LP:AF:ID  -0.00528689:0.00733696:0.30103:0.134072:rs531730856
1   14464   rs546169444 A   T   .   PASS    AF=0.156891 ES:SE:LP:AF:ID  5.48975e-05:0.00667154:0.0604807:0.156891:rs546169444
1   14599   rs707680    T   A   .   PASS    AF=0.192052 ES:SE:LP:AF:ID  0.00215713:0.00605815:0.0555173:0.192052:rs707680
1   14604   rs1418508701    A   G   .   PASS    AF=0.192052 ES:SE:LP:AF:ID  0.00215713:0.00605815:0.0555173:0.192052:rs1418508701
1   14930   rs6682385   A   G   .   PASS    AF=0.473826 ES:SE:LP:AF:ID  0.00747669:0.00470917:1.01323:0.473826:rs6682385
1   14933   rs199856693 G   A   .   PASS    AF=0.045104 ES:SE:LP:AF:ID  0.0113862:0.0115608:0.431798:0.045104:rs199856693
1   15211   rs3982632   T   G   .   PASS    AF=0.741651 ES:SE:LP:AF:ID  -0.00550236:0.00544403:0.455932:0.741651:rs3982632
1   15820   rs1316988498    G   T   .   PASS    AF=0.275155 ES:SE:LP:AF:ID  -0.000697574:0.00558032:0.113509:0.275155:rs1316988498
1   15903   rs557514207 GC  G   .   PASS    AF=0.58116  ES:SE:LP:AF:ID  0.0106515:0.00460122:1.74473:0.58116:rs557514207
1   28590   rs1344649620    T   TTGG    .   PASS    AF=0.956486 ES:SE:LP:AF:ID  -0.0377325:0.0130953:2.56864:0.956486:rs1344649620
1   30923   rs1165072081    G   T   .   PASS    AF=0.910161 ES:SE:LP:AF:ID  -0.00553379:0.00868181:0.229148:0.910161:rs1165072081
1   47159   rs540662756 T   C   .   PASS    AF=0.0627   ES:SE:LP:AF:ID  -0.00231829:0.00989821:0.107905:0.0627:rs540662756
1   49298   rs10399793  T   C   .   PASS    AF=0.62404  ES:SE:LP:AF:ID  0.00619412:0.00550555:0.568636:0.62404:rs10399793
1   49554   rs539322794 A   G   .   PASS    AF=0.092798 ES:SE:LP:AF:ID  0.0012799:0.00850913:0.275724:0.092798:rs539322794
1   51479   rs116400033 T   A   .   PASS    AF=0.21342  ES:SE:LP:AF:ID  -0.000200782:0.00590326:0.05061:0.21342:rs116400033
1   54490   rs141149254 G   A   .   PASS    AF=0.1546   ES:SE:LP:AF:ID  0.00194567:0.00662991:0.0457575:0.1546:rs141149254
1   54676   rs2462492   C   T   .   PASS    AF=0.399716 ES:SE:LP:AF:ID  7.51749e-05:0.00546896:0.0409586:0.399716:rs2462492
1   54712   rs573184866 TTTTC   T   .   PASS    AF=0.414689 ES:SE:LP:AF:ID  0.000186951:0.0043186:0.0177288:0.414689:rs573184866
1   54716   rs1166278911    C   T   .   PASS    AF=0.417665 ES:SE:LP:AF:ID  -0.0105242:0.00499141:1.34679:0.417665:rs1166278911
1   55545   rs28396308  C   T   .   PASS    AF=0.25374  ES:SE:LP:AF:ID  -0.00485105:0.00561137:0.356547:0.25374:rs28396308
1   58814   rs114420996 G   A   .   PASS    AF=0.089707 ES:SE:LP:AF:ID  0.00572171:0.00857812:0.49485:0.089707:rs114420996
1   59040   rs62637815  T   C   .   PASS    AF=0.088587 ES:SE:LP:AF:ID  0.0026688:0.00860411:0.376751:0.088587:rs62637815
1   60351   rs62637817  A   G   .   PASS    AF=0.08075  ES:SE:LP:AF:ID  0.00491893:0.00892986:0.508638:0.08075:rs62637817
1   62777   rs3844233   A   T   .   PASS    AF=0.438311 ES:SE:LP:AF:ID  -0.000357571:0.00473947:0.0362122:0.438311:rs3844233
1   63268   rs28664618  T   C   .   PASS    AF=0.381764 ES:SE:LP:AF:ID  -0.00515098:0.00510116:0.443698:0.381764:rs28664618
1   63671   rs80011619  G   A   .   PASS    AF=0.158412 ES:SE:LP:AF:ID  -0.00201609:0.00649393:0.0655015:0.158412:rs80011619
1   63735   rs61158452  C   CCTA    .   PASS    AF=0.683607 ES:SE:LP:AF:ID  -1.94304e-05:0.00505591:0.05061:0.683607:rs61158452
1   64931   rs62639104  G   A   .   PASS    AF=0.079299 ES:SE:LP:AF:ID  0.00463851:0.00904864:0.481486:0.079299:rs62639104
1   68082   rs367789441 T   C   .   PASS    AF=0.070749 ES:SE:LP:AF:ID  0.00660116:0.00913551:0.318759:0.070749:rs367789441
1   69428   rs140739101 T   G   .   PASS    AF=0.032848 ES:SE:LP:AF:ID  -0.032834:0.0138678:1.82391:0.032848:rs140739101
1   69761   rs200505207 A   T   .   PASS    AF=0.073805 ES:SE:LP:AF:ID  0.00766993:0.00899995:0.420216:0.073805:rs200505207
1   69897   rs200676709 T   C   .   PASS    AF=0.751623 ES:SE:LP:AF:ID  0.00486656:0.00572995:0.236572:0.751623:rs200676709
1   74790   rs13328700  C   G   .   PASS    AF=0.034066 ES:SE:LP:AF:ID  -0.00359675:0.013098:0.221849:0.034066:rs13328700
1   74792   rs1335672253    G   A   .   PASS    AF=0.034066 ES:SE:LP:AF:ID  -0.00359675:0.013098:0.221849:0.034066:rs1335672253
1   76838   rs563953605 T   G   .   PASS    AF=0.076989 ES:SE:LP:AF:ID  0.00643066:0.00920823:0.619789:0.076989:rs563953605
1   76854   rs367666799 A   G   .   PASS    AF=0.077662 ES:SE:LP:AF:ID  -0.00456591:0.00884807:0.21467:0.077662:rs367666799
1   77866   rs563593912 C   T   .   PASS    AF=0.076794 ES:SE:LP:AF:ID  0.00685982:0.00920987:0.657577:0.076794:rs563593912
1   77874   rs62641297  G   A   .   PASS    AF=0.076794 ES:SE:LP:AF:ID  0.00685982:0.00920987:0.657577:0.076794:rs62641297
1   81260   rs571136476 C   T   .   PASS    AF=0.041605 ES:SE:LP:AF:ID  0.0133187:0.0127476:0.537602:0.041605:rs571136476
1   81587   rs536406113 C   T   .   PASS    AF=0.060854 ES:SE:LP:AF:ID  0.0125338:0.00975024:0.657577:0.060854:rs536406113
1   82163   rs139113303 G   A   .   PASS    AF=0.075567 ES:SE:LP:AF:ID  -0.00486319:0.00896356:0.229148:0.075567:rs139113303
1   82609   rs149189449 C   G   .   PASS    AF=0.075585 ES:SE:LP:AF:ID  -0.00490339:0.00896284:0.236572:0.075585:rs149189449
1   83514   rs201754587 C   T   .   PASS    AF=0.352722 ES:SE:LP:AF:ID  -0.00664508:0.00513373:0.721246:0.352722:rs201754587