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/f258a69c-2038-485b-a2b2-f5fe740d52a6/call-ldsc/inputs/-261043421/ieu-b-4966.vcf.gz \
--ref-ld-chr /data/ref/eur_w_ld_chr/ \
--out /data/igd/ieu-b-4966/ldsc.txt \
--w-ld-chr /data/ref/eur_w_ld_chr/ 

Beginning analysis at Fri Mar  4 19:09:53 2022
Reading summary statistics from /data/cromwell-executions/qc/f258a69c-2038-485b-a2b2-f5fe740d52a6/call-ldsc/inputs/-261043421/ieu-b-4966.vcf.gz ...
Read summary statistics for 12320830 SNPs.
Dropped 206220 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, 1220578 SNPs remain.
After merging with regression SNP LD, 1220578 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0181 (0.0018)
Lambda GC: 1.1393
Mean Chi^2: 1.1972
Intercept: 1.0417 (0.0078)
Ratio: 0.2115 (0.0393)
Analysis finished at Fri Mar  4 19:12:08 2022
Total time elapsed: 2.0m:14.48s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9503,
    "inflation_factor": 1.0966,
    "mean_EFFECT": -0.0001,
    "n": "-Inf",
    "n_snps": 12321875,
    "n_clumped_hits": 35,
    "n_p_sig": 2459,
    "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": 1220578,
    "ldsc_nsnp_merge_regression_ld": 1220578,
    "ldsc_observed_scale_h2_beta": 0.0181,
    "ldsc_observed_scale_h2_se": 0.0018,
    "ldsc_intercept_beta": 1.0417,
    "ldsc_intercept_se": 0.0078,
    "ldsc_lambda_gc": 1.1393,
    "ldsc_mean_chisq": 1.1972,
    "ldsc_ratio": 0.2115
}

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 TRUE
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 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 -5.840000e-05 3.647300e-03 -0.0642006 -1.148900e-03 -1.920000e-05 1.090700e-03 7.172600e-02 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA NA NA 2.579300e-03 2.475400e-03 0.0006386 9.034000e-04 1.450600e-03 3.347200e-03 3.960510e-02 ▇▁▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA NA NA 4.837385e-01 2.936789e-01 0.0000000 2.300001e-01 4.799997e-01 7.400005e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA NA NA 4.837366e-01 2.936530e-01 0.0000000 2.257177e-01 4.786347e-01 7.379335e-01 1.000000e+00 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA NA NA 2.594008e-01 3.020414e-01 0.0009740 1.660000e-02 1.145700e-01 4.379320e-01 9.990140e-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 -0.0018407 0.0011592 0.1100001 0.1123051 0.601107 NA NA
1 10352 rs1557426776 TA T -0.0009707 0.0011940 0.4199997 0.4162443 0.606883 NA NA
1 11008 rs575272151 C G 0.0013007 0.0019846 0.5099998 0.5122275 0.086244 0.0880591 NA
1 11012 rs544419019 C G 0.0013007 0.0019846 0.5099998 0.5122275 0.086244 0.0880591 NA
1 13110 rs540538026 G A -0.0027283 0.0026409 0.2999998 0.3015630 0.058685 0.0267572 NA
1 13116 rs62635286 T G -0.0017813 0.0015622 0.2500000 0.2541684 0.189302 0.0970447 NA
1 13118 rs200579949 A G -0.0017813 0.0015622 0.2500000 0.2541684 0.189302 0.0970447 NA
1 13273 rs531730856 G C 0.0021790 0.0018291 0.2300001 0.2335412 0.134049 0.0950479 NA
1 14464 rs546169444 A T -0.0027983 0.0016652 0.0929994 0.0928783 0.156894 0.0958466 NA
1 14599 rs531646671 T A 0.0008776 0.0015152 0.5600000 0.5624547 0.191632 0.1475640 NA
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
23 154901936 rs697727 A G 0.0018552 0.0007430 0.0129999 0.0125260 0.752079 0.643179 NA
23 154901964 rs697726 G A 0.0012323 0.0007832 0.1199999 0.1156214 0.347849 0.117616 NA
23 154902105 rs696316 G T 0.0018643 0.0007429 0.0120000 0.0120939 0.752035 0.636026 NA
23 154902889 rs697725 A T 0.0018579 0.0007427 0.0120000 0.0123640 0.751711 0.584106 NA
23 154903118 rs479770 G A 0.0018590 0.0007430 0.0120000 0.0123564 0.752122 0.643444 NA
23 154903224 rs480725 A T 0.0018589 0.0007430 0.0120000 0.0123574 0.752125 0.643444 NA
23 154903937 rs674707 G A 0.0018585 0.0007431 0.0120000 0.0123805 0.752135 0.643444 NA
23 154909055 rs473529 C G -0.0015915 0.0006995 0.0230001 0.0228887 0.304558 0.463046 NA
23 154918266 rs642043 C T -0.0016571 0.0007017 0.0179999 0.0182033 0.302402 0.478675 NA
23 154927581 rs644138 G A -0.0016538 0.0007018 0.0179999 0.0184520 0.302278 0.463576 NA

bcf preview

1   10177   rs1264289758    AC  A   .   PASS    AF=0.601107 ES:SE:LP:AF:ID  -0.00184065:0.00115916:0.958607:0.601107:rs1264289758
1   10352   rs1557426776    TA  T   .   PASS    AF=0.606883 ES:SE:LP:AF:ID  -0.000970651:0.00119398:0.376751:0.606883:rs1557426776
1   11008   rs575272151 C   G   .   PASS    AF=0.086244 ES:SE:LP:AF:ID  0.00130068:0.00198464:0.29243:0.086244:rs575272151
1   11012   rs544419019 C   G   .   PASS    AF=0.086244 ES:SE:LP:AF:ID  0.00130068:0.00198464:0.29243:0.086244:rs544419019
1   13110   rs540538026 G   A   .   PASS    AF=0.058685 ES:SE:LP:AF:ID  -0.00272826:0.00264088:0.522879:0.058685:rs540538026
1   13116   rs62635286  T   G   .   PASS    AF=0.189302 ES:SE:LP:AF:ID  -0.00178135:0.0015622:0.60206:0.189302:rs62635286
1   13118   rs62028691  A   G   .   PASS    AF=0.189302 ES:SE:LP:AF:ID  -0.00178135:0.0015622:0.60206:0.189302:rs62028691
1   13273   rs531730856 G   C   .   PASS    AF=0.134049 ES:SE:LP:AF:ID  0.00217897:0.00182909:0.638272:0.134049:rs531730856
1   14464   rs546169444 A   T   .   PASS    AF=0.156894 ES:SE:LP:AF:ID  -0.00279828:0.00166524:1.03152:0.156894:rs546169444
1   14599   rs707680    T   A   .   PASS    AF=0.191632 ES:SE:LP:AF:ID  0.000877626:0.00151524:0.251812:0.191632:rs707680
1   14604   rs1418508701    A   G   .   PASS    AF=0.191632 ES:SE:LP:AF:ID  0.000877626:0.00151524:0.251812:0.191632:rs1418508701
1   14930   rs6682385   A   G   .   PASS    AF=0.473875 ES:SE:LP:AF:ID  -0.000959622:0.00117594:0.387216:0.473875:rs6682385
1   14933   rs199856693 G   A   .   PASS    AF=0.045061 ES:SE:LP:AF:ID  0.00192277:0.00289178:0.29243:0.045061:rs199856693
1   15211   rs3982632   T   G   .   PASS    AF=0.741476 ES:SE:LP:AF:ID  0.000224192:0.00135942:0.0604807:0.741476:rs3982632
1   15820   rs1316988498    G   T   .   PASS    AF=0.275197 ES:SE:LP:AF:ID  7.29396e-05:0.0013948:0.0177288:0.275197:rs1316988498
1   15903   rs557514207 GC  G   .   PASS    AF=0.581107 ES:SE:LP:AF:ID  0.000278906:0.0011493:0.091515:0.581107:rs557514207
1   28590   rs1344649620    T   TTGG    .   PASS    AF=0.956578 ES:SE:LP:AF:ID  0.00469503:0.00327684:0.823909:0.956578:rs1344649620
1   30923   rs1165072081    G   T   .   PASS    AF=0.910222 ES:SE:LP:AF:ID  -0.00182996:0.0021707:0.39794:0.910222:rs1165072081
1   47159   rs540662756 T   C   .   PASS    AF=0.062709 ES:SE:LP:AF:ID  0.00111877:0.00247707:0.187087:0.062709:rs540662756
1   49298   rs10399793  T   C   .   PASS    AF=0.623717 ES:SE:LP:AF:ID  0.00100263:0.00137925:0.327902:0.623717:rs10399793
1   49554   rs539322794 A   G   .   PASS    AF=0.092946 ES:SE:LP:AF:ID  -0.000465037:0.00212323:0.0809219:0.092946:rs539322794
1   51479   rs116400033 T   A   .   PASS    AF=0.213308 ES:SE:LP:AF:ID  -0.00241925:0.00147595:1:0.213308:rs116400033
1   54490   rs141149254 G   A   .   PASS    AF=0.154392 ES:SE:LP:AF:ID  -0.0023786:0.0016584:0.823909:0.154392:rs141149254
1   54676   rs2462492   C   T   .   PASS    AF=0.400408 ES:SE:LP:AF:ID  -0.000517584:0.00136629:0.154902:0.400408:rs2462492
1   54712   rs573184866 TTTTC   T   .   PASS    AF=0.414801 ES:SE:LP:AF:ID  3.07854e-06:0.00108076:-0:0.414801:rs573184866
1   54716   rs1166278911    C   T   .   PASS    AF=0.417433 ES:SE:LP:AF:ID  0.00143688:0.00124788:0.60206:0.417433:rs1166278911
1   55545   rs28396308  C   T   .   PASS    AF=0.253822 ES:SE:LP:AF:ID  -0.000355992:0.00140374:0.09691:0.253822:rs28396308
1   58814   rs114420996 G   A   .   PASS    AF=0.090044 ES:SE:LP:AF:ID  0.000415651:0.00213901:0.0705811:0.090044:rs114420996
1   59040   rs62637815  T   C   .   PASS    AF=0.088833 ES:SE:LP:AF:ID  -0.000975456:0.0021474:0.187087:0.088833:rs62637815
1   60351   rs62637817  A   G   .   PASS    AF=0.081024 ES:SE:LP:AF:ID  -5.61679e-05:0.00222704:0.00877392:0.081024:rs62637817
1   62777   rs3844233   A   T   .   PASS    AF=0.438321 ES:SE:LP:AF:ID  -0.00173104:0.00118596:0.853872:0.438321:rs3844233
1   63268   rs28664618  T   C   .   PASS    AF=0.382171 ES:SE:LP:AF:ID  0.000552106:0.00127487:0.180456:0.382171:rs28664618
1   63671   rs80011619  G   A   .   PASS    AF=0.158863 ES:SE:LP:AF:ID  0.000249891:0.00162311:0.0555173:0.158863:rs80011619
1   63735   rs61158452  C   CCTA    .   PASS    AF=0.684093 ES:SE:LP:AF:ID  0.000711139:0.00126407:0.244125:0.684093:rs61158452
1   64931   rs62639104  G   A   .   PASS    AF=0.079627 ES:SE:LP:AF:ID  -0.000186172:0.0022545:0.0315171:0.079627:rs62639104
1   68082   rs367789441 T   C   .   PASS    AF=0.070825 ES:SE:LP:AF:ID  0.00190009:0.00228329:0.387216:0.070825:rs367789441
1   69428   rs140739101 T   G   .   PASS    AF=0.032894 ES:SE:LP:AF:ID  -0.000381829:0.00345818:0.0409586:0.032894:rs140739101
1   69761   rs200505207 A   T   .   PASS    AF=0.073909 ES:SE:LP:AF:ID  0.000119178:0.00224796:0.0177288:0.073909:rs200505207
1   69897   rs200676709 T   C   .   PASS    AF=0.751154 ES:SE:LP:AF:ID  -0.000521269:0.00143193:0.142668:0.751154:rs200676709
1   74790   rs13328700  C   G   .   PASS    AF=0.034054 ES:SE:LP:AF:ID  0.000543621:0.0032873:0.0604807:0.034054:rs13328700
1   74792   rs1335672253    G   A   .   PASS    AF=0.034054 ES:SE:LP:AF:ID  0.000543621:0.0032873:0.0604807:0.034054:rs1335672253
1   76838   rs563953605 T   G   .   PASS    AF=0.077177 ES:SE:LP:AF:ID  -0.000698314:0.00229768:0.119186:0.077177:rs563953605
1   76854   rs367666799 A   G   .   PASS    AF=0.077496 ES:SE:LP:AF:ID  0.00106768:0.00221668:0.200659:0.077496:rs367666799
1   77866   rs563593912 C   T   .   PASS    AF=0.076982 ES:SE:LP:AF:ID  -0.000650104:0.00229824:0.107905:0.076982:rs563593912
1   77874   rs62641297  G   A   .   PASS    AF=0.076982 ES:SE:LP:AF:ID  -0.000650104:0.00229824:0.107905:0.076982:rs62641297
1   81260   rs571136476 C   T   .   PASS    AF=0.04151  ES:SE:LP:AF:ID  -0.000409971:0.00320303:0.0457575:0.04151:rs571136476
1   81587   rs536406113 C   T   .   PASS    AF=0.060987 ES:SE:LP:AF:ID  0.000734976:0.00243311:0.119186:0.060987:rs536406113
1   82163   rs139113303 G   A   .   PASS    AF=0.075441 ES:SE:LP:AF:ID  0.000710521:0.0022451:0.124939:0.075441:rs139113303
1   82609   rs149189449 C   G   .   PASS    AF=0.075468 ES:SE:LP:AF:ID  0.000708399:0.00224464:0.124939:0.075468:rs149189449
1   83514   rs201754587 C   T   .   PASS    AF=0.352678 ES:SE:LP:AF:ID  -0.00019628:0.00128455:0.0555173:0.352678:rs201754587