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/5d01dea6-f928-41da-8059-b229ba58cb87/call-ldsc/inputs/-261021503/ieu-b-5107.vcf.gz \
--ref-ld-chr /data/ref/eur_w_ld_chr/ \
--out /data/igd/ieu-b-5107/ldsc.txt \
--w-ld-chr /data/ref/eur_w_ld_chr/ 

Beginning analysis at Wed Aug 16 03:35:24 2023
Reading summary statistics from /data/cromwell-executions/qc/5d01dea6-f928-41da-8059-b229ba58cb87/call-ldsc/inputs/-261021503/ieu-b-5107.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 Wed Aug 16 03:36:51 2023
Total time elapsed: 1.0m:26.95s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9503,
    "inflation_factor": 1.557,
    "mean_EFFECT": -0,
    "n": "-Inf",
    "n_snps": 12321875,
    "n_clumped_hits": 231,
    "n_p_sig": 38165,
    "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 TRUE
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 -2.140000e-05 7.008400e-03 -0.1576310 -2.491600e-03 -1.110000e-05 2.471200e-03 1.668980e-01 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA NA NA 4.650500e-03 4.465300e-03 0.0011569 1.628400e-03 2.614800e-03 6.033800e-03 7.089450e-02 ▇▁▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA NA NA 4.303266e-01 3.067274e-01 0.0000000 1.499999e-01 4.000000e-01 6.999999e-01 1.000000e+00 ▇▅▅▅▅
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA NA NA 4.309273e-01 3.065366e-01 0.0000000 1.476792e-01 4.050666e-01 6.958646e-01 9.999999e-01 ▇▅▅▅▅
numeric AF 0 1.0000000 NA NA NA NA NA NA NA 2.593998e-01 3.020453e-01 0.0009790 1.659800e-02 1.145610e-01 4.379330e-01 9.990180e-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 0.0003278 0.0020872 0.8800001 0.8752106 0.601077 NA NA
1 10352 rs1557426776 TA T -0.0000557 0.0021487 0.9699999 0.9793019 0.606637 NA NA
1 11008 rs575272151 C G -0.0019704 0.0035726 0.5300002 0.5812773 0.086225 0.0880591 NA
1 11012 rs544419019 C G -0.0019704 0.0035726 0.5300002 0.5812773 0.086225 0.0880591 NA
1 13110 rs540538026 G A 0.0036355 0.0047534 0.3900004 0.4443722 0.058675 0.0267572 NA
1 13116 rs62635286 T G 0.0022655 0.0028119 0.4299995 0.4204273 0.189233 0.0970447 NA
1 13118 rs200579949 A G 0.0022655 0.0028119 0.4299995 0.4204273 0.189233 0.0970447 NA
1 13273 rs531730856 G C -0.0062546 0.0032916 0.0560003 0.0574093 0.134119 0.0950479 NA
1 14464 rs546169444 A T 0.0033549 0.0029978 0.2900000 0.2630995 0.156889 0.0958466 NA
1 14599 rs531646671 T A -0.0016269 0.0027288 0.6400000 0.5510584 0.191526 0.1475640 NA
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
23 154901936 rs697727 A G -0.0052872 0.0013458 5.0e-05 0.0000855 0.751858 0.643179 NA
23 154901964 rs697726 G A -0.0049918 0.0014193 5.3e-04 0.0004363 0.347921 0.117616 NA
23 154902105 rs696316 G T -0.0052743 0.0013458 5.3e-05 0.0000889 0.751813 0.636026 NA
23 154902889 rs697725 A T -0.0053160 0.0013453 4.4e-05 0.0000777 0.751497 0.584106 NA
23 154903118 rs479770 G A -0.0052722 0.0013460 5.3e-05 0.0000897 0.751902 0.643444 NA
23 154903224 rs480725 A T -0.0052713 0.0013460 5.3e-05 0.0000899 0.751905 0.643444 NA
23 154903937 rs674707 G A -0.0052674 0.0013460 5.4e-05 0.0000910 0.751914 0.643444 NA
23 154909055 rs473529 C G 0.0043564 0.0012672 4.6e-04 0.0005866 0.304753 0.463046 NA
23 154918266 rs642043 C T 0.0044148 0.0012713 4.0e-04 0.0005152 0.302610 0.478675 NA
23 154927581 rs644138 G A 0.0044123 0.0012715 4.0e-04 0.0005201 0.302486 0.463576 NA

bcf preview

1   10177   rs1264289758    AC  A   .   PASS    AF=0.601077 ES:SE:LP:AF:ID  0.000327781:0.0020872:0.0555173:0.601077:rs1264289758
1   10352   rs1557426776    TA  T   .   PASS    AF=0.606637 ES:SE:LP:AF:ID  -5.57449e-05:0.00214865:0.0132283:0.606637:rs1557426776
1   11008   rs575272151 C   G   .   PASS    AF=0.086225 ES:SE:LP:AF:ID  -0.00197036:0.0035726:0.275724:0.086225:rs575272151
1   11012   rs544419019 C   G   .   PASS    AF=0.086225 ES:SE:LP:AF:ID  -0.00197036:0.0035726:0.275724:0.086225:rs544419019
1   13110   rs540538026 G   A   .   PASS    AF=0.058675 ES:SE:LP:AF:ID  0.00363554:0.00475339:0.408935:0.058675:rs540538026
1   13116   rs62635286  T   G   .   PASS    AF=0.189233 ES:SE:LP:AF:ID  0.00226546:0.00281186:0.366532:0.189233:rs62635286
1   13118   rs62028691  A   G   .   PASS    AF=0.189233 ES:SE:LP:AF:ID  0.00226546:0.00281186:0.366532:0.189233:rs62028691
1   13273   rs531730856 G   C   .   PASS    AF=0.134119 ES:SE:LP:AF:ID  -0.00625458:0.00329157:1.25181:0.134119:rs531730856
1   14464   rs546169444 A   T   .   PASS    AF=0.156889 ES:SE:LP:AF:ID  0.00335488:0.00299785:0.537602:0.156889:rs546169444
1   14599   rs707680    T   A   .   PASS    AF=0.191526 ES:SE:LP:AF:ID  -0.00162686:0.00272883:0.19382:0.191526:rs707680
1   14604   rs1418508701    A   G   .   PASS    AF=0.191526 ES:SE:LP:AF:ID  -0.00162686:0.00272883:0.19382:0.191526:rs1418508701
1   14930   rs6682385   A   G   .   PASS    AF=0.473883 ES:SE:LP:AF:ID  -0.00357059:0.00211606:1.07572:0.473883:rs6682385
1   14933   rs199856693 G   A   .   PASS    AF=0.045108 ES:SE:LP:AF:ID  0.00439756:0.00520018:0.408935:0.045108:rs199856693
1   15211   rs3982632   T   G   .   PASS    AF=0.741381 ES:SE:LP:AF:ID  0.00380513:0.00244707:0.853872:0.741381:rs3982632
1   15820   rs1316988498    G   T   .   PASS    AF=0.275173 ES:SE:LP:AF:ID  0.0057806:0.00250996:1.74473:0.275173:rs1316988498
1   15903   rs557514207 GC  G   .   PASS    AF=0.581189 ES:SE:LP:AF:ID  0.00113481:0.00206914:0.259637:0.581189:rs557514207
1   28590   rs1344649620    T   TTGG    .   PASS    AF=0.956544 ES:SE:LP:AF:ID  -0.00342413:0.00588977:0.318759:0.956544:rs1344649620
1   30923   rs1165072081    G   T   .   PASS    AF=0.910223 ES:SE:LP:AF:ID  0.00314457:0.00390723:0.387216:0.910223:rs1165072081
1   47159   rs540662756 T   C   .   PASS    AF=0.062706 ES:SE:LP:AF:ID  0.00125808:0.00446179:0.124939:0.062706:rs540662756
1   49298   rs10399793  T   C   .   PASS    AF=0.623725 ES:SE:LP:AF:ID  -0.0030896:0.00248256:0.638272:0.623725:rs10399793
1   49554   rs539322794 A   G   .   PASS    AF=0.092919 ES:SE:LP:AF:ID  0.00230591:0.00382129:0.318759:0.092919:rs539322794
1   51479   rs116400033 T   A   .   PASS    AF=0.213248 ES:SE:LP:AF:ID  -0.00303847:0.00265681:0.69897:0.213248:rs116400033
1   54490   rs141149254 G   A   .   PASS    AF=0.154378 ES:SE:LP:AF:ID  -0.00510879:0.00298511:1.1549:0.154378:rs141149254
1   54676   rs2462492   C   T   .   PASS    AF=0.400468 ES:SE:LP:AF:ID  -0.00166396:0.00245926:0.346787:0.400468:rs2462492
1   54712   rs573184866 TTTTC   T   .   PASS    AF=0.414679 ES:SE:LP:AF:ID  -0.00150634:0.00194521:0.327902:0.414679:rs573184866
1   54716   rs1166278911    C   T   .   PASS    AF=0.417418 ES:SE:LP:AF:ID  0.000433989:0.00224591:0.0861861:0.417418:rs1166278911
1   55545   rs28396308  C   T   .   PASS    AF=0.253788 ES:SE:LP:AF:ID  0.00437638:0.00252701:1.16749:0.253788:rs28396308
1   58814   rs114420996 G   A   .   PASS    AF=0.089978 ES:SE:LP:AF:ID  0.00354018:0.00385172:0.49485:0.089978:rs114420996
1   59040   rs62637815  T   C   .   PASS    AF=0.088759 ES:SE:LP:AF:ID  0.0034815:0.00386738:0.508638:0.088759:rs62637815
1   60351   rs62637817  A   G   .   PASS    AF=0.080963 ES:SE:LP:AF:ID  0.00460046:0.00401101:0.677781:0.080963:rs62637817
1   62777   rs3844233   A   T   .   PASS    AF=0.438271 ES:SE:LP:AF:ID  -0.000328888:0.00213465:0.0132283:0.438271:rs3844233
1   63268   rs28664618  T   C   .   PASS    AF=0.382212 ES:SE:LP:AF:ID  0.00161986:0.00229483:0.455932:0.382212:rs28664618
1   63671   rs80011619  G   A   .   PASS    AF=0.158734 ES:SE:LP:AF:ID  0.00134473:0.0029223:0.167491:0.158734:rs80011619
1   63735   rs61158452  C   CCTA    .   PASS    AF=0.683954 ES:SE:LP:AF:ID  0.00501785:0.00227571:1.63827:0.683954:rs61158452
1   64931   rs62639104  G   A   .   PASS    AF=0.079554 ES:SE:LP:AF:ID  0.00424364:0.00406057:0.60206:0.079554:rs62639104
1   68082   rs367789441 T   C   .   PASS    AF=0.070758 ES:SE:LP:AF:ID  0.00432096:0.00411242:0.568636:0.070758:rs367789441
1   69428   rs140739101 T   G   .   PASS    AF=0.032923 ES:SE:LP:AF:ID  -0.00664574:0.00621944:0.468521:0.032923:rs140739101
1   69761   rs200505207 A   T   .   PASS    AF=0.073863 ES:SE:LP:AF:ID  0.00374125:0.00404757:0.468521:0.073863:rs200505207
1   69897   rs200676709 T   C   .   PASS    AF=0.751237 ES:SE:LP:AF:ID  -0.00310511:0.00257777:0.677781:0.751237:rs200676709
1   74790   rs13328700  C   G   .   PASS    AF=0.03409  ES:SE:LP:AF:ID  -0.000681597:0.00590976:0.0655015:0.03409:rs13328700
1   74792   rs1335672253    G   A   .   PASS    AF=0.03409  ES:SE:LP:AF:ID  -0.000681597:0.00590976:0.0655015:0.03409:rs1335672253
1   76838   rs563953605 T   G   .   PASS    AF=0.077094 ES:SE:LP:AF:ID  0.00334172:0.00413806:0.420216:0.077094:rs563953605
1   76854   rs367666799 A   G   .   PASS    AF=0.077484 ES:SE:LP:AF:ID  -0.000993508:0.00399191:0.05061:0.077484:rs367666799
1   77866   rs563593912 C   T   .   PASS    AF=0.076901 ES:SE:LP:AF:ID  0.00342495:0.00413902:0.431798:0.076901:rs563593912
1   77874   rs62641297  G   A   .   PASS    AF=0.076901 ES:SE:LP:AF:ID  0.00342495:0.00413902:0.431798:0.076901:rs62641297
1   81260   rs571136476 C   T   .   PASS    AF=0.041484 ES:SE:LP:AF:ID  -0.00346056:0.00576878:0.275724:0.041484:rs571136476
1   81587   rs536406113 C   T   .   PASS    AF=0.060912 ES:SE:LP:AF:ID  0.00738525:0.00438376:1.11351:0.060912:rs536406113
1   82163   rs139113303 G   A   .   PASS    AF=0.075429 ES:SE:LP:AF:ID  1.53079e-05:0.00404349:0.0409586:0.075429:rs139113303
1   82609   rs149189449 C   G   .   PASS    AF=0.075457 ES:SE:LP:AF:ID  -9.06959e-05:0.0040426:0.0315171:0.075457:rs149189449
1   83514   rs201754587 C   T   .   PASS    AF=0.35286  ES:SE:LP:AF:ID  0.000539233:0.00231137:0.0705811:0.35286:rs201754587