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/5a9f7130-2f84-4ba7-ac4e-f2de9c65965e/call-ldsc/inputs/-261043424/ieu-b-4963.vcf.gz \
--ref-ld-chr /data/ref/eur_w_ld_chr/ \
--out /data/igd/ieu-b-4963/ldsc.txt \
--w-ld-chr /data/ref/eur_w_ld_chr/ 

Beginning analysis at Fri Mar  4 17:36:02 2022
Reading summary statistics from /data/cromwell-executions/qc/5a9f7130-2f84-4ba7-ac4e-f2de9c65965e/call-ldsc/inputs/-261043424/ieu-b-4963.vcf.gz ...
Read summary statistics for 9821218 SNPs.
Dropped 174563 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, 1211097 SNPs remain.
After merging with regression SNP LD, 1211097 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.001 (0.0022)
Lambda GC: 1.0132
Mean Chi^2: 1.0065
Intercept: 1.0025 (0.0063)
Ratio: 0.3831 (0.9735)
Analysis finished at Fri Mar  4 17:37:49 2022
Total time elapsed: 1.0m:47.33s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.941,
    "inflation_factor": 1,
    "mean_EFFECT": -7.6577e-07,
    "n": "-Inf",
    "n_snps": 9822229,
    "n_clumped_hits": 1,
    "n_p_sig": 1,
    "n_mono": 0,
    "n_ns": 1164810,
    "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": 1173219,
    "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": 1211097,
    "ldsc_nsnp_merge_regression_ld": 1211097,
    "ldsc_observed_scale_h2_beta": 0.001,
    "ldsc_observed_scale_h2_se": 0.0022,
    "ldsc_intercept_beta": 1.0025,
    "ldsc_intercept_se": 0.0063,
    "ldsc_lambda_gc": 1.0132,
    "ldsc_mean_chisq": 1.0065,
    "ldsc_ratio": 0.3846
}

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 661 0.9999327 3 58 0 9789033 0 NA NA NA NA NA NA NA NA NA NA
character REF 0 1.0000000 1 88 0 15603 0 NA NA NA NA NA NA NA NA NA NA
character ALT 0 1.0000000 1 662 0 64323 0 NA NA NA NA NA NA NA NA NA NA
logical N 9822229 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 8.828634e+00 5.930421e+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 7.849431e+07 5.639403e+07 302.0000000 3.212056e+07 6.889801e+07 1.144117e+08 2.492405e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA NA NA -8.000000e-07 5.569000e-04 -0.0069710 -2.715000e-04 -2.100000e-06 2.646000e-04 7.006700e-03 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA NA NA 4.842000e-04 2.741000e-04 0.0002375 2.721000e-04 3.629000e-04 6.203000e-04 2.852900e-03 ▇▂▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA NA NA 4.992490e-01 2.889798e-01 0.0000000 2.500000e-01 5.000000e-01 7.499995e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA NA NA 4.992480e-01 2.889535e-01 0.0000000 2.486710e-01 4.990733e-01 7.496739e-01 1.000000e+00 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA NA NA 3.083127e-01 2.967468e-01 0.0102630 5.109900e-02 1.968100e-01 5.133060e-01 9.897370e-01 ▇▂▂▂▂
numeric AF_reference 1173219 0.8805547 NA NA NA NA NA NA NA 2.608523e-01 2.546513e-01 0.0000000 4.892170e-02 1.727240e-01 4.127400e-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 0.0000401 0.0003675 0.9100000 0.9132253 0.601808 NA NA
1 10352 rs1557426776 TA T 0.0003512 0.0003782 0.3500000 0.3530799 0.606807 NA NA
1 11008 rs575272151 C G 0.0006381 0.0006310 0.3100002 0.3118831 0.085881 0.0880591 NA
1 11012 rs544419019 C G 0.0006381 0.0006310 0.3100002 0.3118831 0.085881 0.0880591 NA
1 13110 rs540538026 G A -0.0000358 0.0008355 0.9699999 0.9658433 0.058622 0.0267572 NA
1 13116 rs62635286 T G -0.0001309 0.0004946 0.7899998 0.7912576 0.189342 0.0970447 NA
1 13118 rs200579949 A G -0.0001309 0.0004946 0.7899998 0.7912576 0.189342 0.0970447 NA
1 13273 rs531730856 G C -0.0002158 0.0005798 0.7099994 0.7097235 0.133807 0.0950479 NA
1 14464 rs546169444 A T 0.0001627 0.0005255 0.7600007 0.7568930 0.157294 0.0958466 NA
1 14599 rs531646671 T A -0.0005310 0.0004804 0.2700001 0.2690226 0.191200 0.1475640 NA
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
23 154901936 rs697727 A G -1.76e-05 0.0002851 0.9500000 0.9507822 0.751335 0.643179 NA
23 154901964 rs697726 G A 5.31e-05 0.0003014 0.8600001 0.8600344 0.347085 0.117616 NA
23 154902105 rs696316 G T -1.42e-05 0.0002851 0.9599999 0.9601779 0.751265 0.636026 NA
23 154902889 rs697725 A T -2.94e-05 0.0002850 0.9199999 0.9179450 0.750899 0.584106 NA
23 154903118 rs479770 G A -1.86e-05 0.0002852 0.9500000 0.9480383 0.751390 0.643444 NA
23 154903224 rs480725 A T -1.86e-05 0.0002852 0.9500000 0.9480153 0.751393 0.643444 NA
23 154903937 rs674707 G A -1.91e-05 0.0002852 0.9500000 0.9466535 0.751407 0.643444 NA
23 154909055 rs473529 C G -5.96e-05 0.0002687 0.8200001 0.8244488 0.305641 0.463046 NA
23 154918266 rs642043 C T -7.92e-05 0.0002695 0.7700005 0.7688277 0.303462 0.478675 NA
23 154927581 rs644138 G A -7.56e-05 0.0002696 0.7800007 0.7791297 0.303313 0.463576 NA

bcf preview

1   10177   rs1264289758    AC  A   .   PASS    AF=0.601808 ES:SE:LP:AF:ID  4.00514e-05:0.000367541:0.0409586:0.601808:rs1264289758
1   10352   rs1557426776    TA  T   .   PASS    AF=0.606807 ES:SE:LP:AF:ID  0.000351229:0.000378222:0.455932:0.606807:rs1557426776
1   11008   rs575272151 C   G   .   PASS    AF=0.085881 ES:SE:LP:AF:ID  0.000638133:0.000631016:0.508638:0.085881:rs575272151
1   11012   rs544419019 C   G   .   PASS    AF=0.085881 ES:SE:LP:AF:ID  0.000638133:0.000631016:0.508638:0.085881:rs544419019
1   13110   rs540538026 G   A   .   PASS    AF=0.058622 ES:SE:LP:AF:ID  -3.57775e-05:0.000835491:0.0132283:0.058622:rs540538026
1   13116   rs62635286  T   G   .   PASS    AF=0.189342 ES:SE:LP:AF:ID  -0.000130911:0.000494605:0.102373:0.189342:rs62635286
1   13118   rs62028691  A   G   .   PASS    AF=0.189342 ES:SE:LP:AF:ID  -0.000130911:0.000494605:0.102373:0.189342:rs62028691
1   13273   rs531730856 G   C   .   PASS    AF=0.133807 ES:SE:LP:AF:ID  -0.0002158:0.000579753:0.148742:0.133807:rs531730856
1   14464   rs546169444 A   T   .   PASS    AF=0.157294 ES:SE:LP:AF:ID  0.000162674:0.000525495:0.119186:0.157294:rs546169444
1   14599   rs707680    T   A   .   PASS    AF=0.1912   ES:SE:LP:AF:ID  -0.000530963:0.000480372:0.568636:0.1912:rs707680
1   14604   rs1418508701    A   G   .   PASS    AF=0.1912   ES:SE:LP:AF:ID  -0.000530963:0.000480372:0.568636:0.1912:rs1418508701
1   14930   rs6682385   A   G   .   PASS    AF=0.473759 ES:SE:LP:AF:ID  -0.000117135:0.000372474:0.124939:0.473759:rs6682385
1   14933   rs199856693 G   A   .   PASS    AF=0.044899 ES:SE:LP:AF:ID  0.000792106:0.000918307:0.408935:0.044899:rs199856693
1   15211   rs3982632   T   G   .   PASS    AF=0.741321 ES:SE:LP:AF:ID  0.000517493:0.00043059:0.638272:0.741321:rs3982632
1   15820   rs1316988498    G   T   .   PASS    AF=0.275162 ES:SE:LP:AF:ID  -0.000135382:0.000442006:0.119186:0.275162:rs1316988498
1   15903   rs557514207 GC  G   .   PASS    AF=0.580988 ES:SE:LP:AF:ID  0.000111843:0.000363922:0.119186:0.580988:rs557514207
1   28590   rs1344649620    T   TTGG    .   PASS    AF=0.956596 ES:SE:LP:AF:ID  -0.000338788:0.00103709:0.130768:0.956596:rs1344649620
1   30923   rs1165072081    G   T   .   PASS    AF=0.91017  ES:SE:LP:AF:ID  0.000953127:0.000686991:0.769551:0.91017:rs1165072081
1   47159   rs540662756 T   C   .   PASS    AF=0.062691 ES:SE:LP:AF:ID  -0.000604174:0.000785629:0.356547:0.062691:rs540662756
1   49298   rs10399793  T   C   .   PASS    AF=0.623175 ES:SE:LP:AF:ID  0.00105786:0.0004376:1.79588:0.623175:rs10399793
1   49554   rs539322794 A   G   .   PASS    AF=0.093061 ES:SE:LP:AF:ID  -0.000759736:0.00067135:0.585027:0.093061:rs539322794
1   51479   rs116400033 T   A   .   PASS    AF=0.21357  ES:SE:LP:AF:ID  -5.99762e-05:0.00046717:0.0457575:0.21357:rs116400033
1   54490   rs141149254 G   A   .   PASS    AF=0.154486 ES:SE:LP:AF:ID  0.000155318:0.000524878:0.113509:0.154486:rs141149254
1   54676   rs2462492   C   T   .   PASS    AF=0.400994 ES:SE:LP:AF:ID  -0.000847509:0.00043261:1.30103:0.400994:rs2462492
1   54712   rs573184866 TTTTC   T   .   PASS    AF=0.414756 ES:SE:LP:AF:ID  0.000231349:0.000342559:0.30103:0.414756:rs573184866
1   54716   rs1166278911    C   T   .   PASS    AF=0.417026 ES:SE:LP:AF:ID  -0.000305958:0.000395242:0.356547:0.417026:rs1166278911
1   55545   rs28396308  C   T   .   PASS    AF=0.25392  ES:SE:LP:AF:ID  -0.000476537:0.000444926:0.552842:0.25392:rs28396308
1   58814   rs114420996 G   A   .   PASS    AF=0.090274 ES:SE:LP:AF:ID  -0.000745488:0.000676294:0.568636:0.090274:rs114420996
1   59040   rs62637815  T   C   .   PASS    AF=0.089027 ES:SE:LP:AF:ID  -0.000938307:0.000679317:0.769551:0.089027:rs62637815
1   60351   rs62637817  A   G   .   PASS    AF=0.081181 ES:SE:LP:AF:ID  -0.00106155:0.000704466:0.886057:0.081181:rs62637817
1   62777   rs3844233   A   T   .   PASS    AF=0.43849  ES:SE:LP:AF:ID  0.000652043:0.000376145:1.08092:0.43849:rs3844233
1   63268   rs28664618  T   C   .   PASS    AF=0.382435 ES:SE:LP:AF:ID  -0.000327281:0.00040379:0.376751:0.382435:rs28664618
1   63671   rs80011619  G   A   .   PASS    AF=0.159205 ES:SE:LP:AF:ID  -0.00116041:0.000514577:1.61979:0.159205:rs80011619
1   63735   rs61158452  C   CCTA    .   PASS    AF=0.684387 ES:SE:LP:AF:ID  0.000289161:0.000400621:0.327902:0.684387:rs61158452
1   64931   rs62639104  G   A   .   PASS    AF=0.079842 ES:SE:LP:AF:ID  -0.0010808:0.000712313:0.886057:0.079842:rs62639104
1   68082   rs367789441 T   C   .   PASS    AF=0.070752 ES:SE:LP:AF:ID  -0.000201777:0.00072537:0.107905:0.070752:rs367789441
1   69428   rs140739101 T   G   .   PASS    AF=0.032895 ES:SE:LP:AF:ID  -0.000288764:0.00109399:0.102373:0.032895:rs140739101
1   69761   rs200505207 A   T   .   PASS    AF=0.073885 ES:SE:LP:AF:ID  -0.000451615:0.000713201:0.275724:0.073885:rs200505207
1   69897   rs200676709 T   C   .   PASS    AF=0.750866 ES:SE:LP:AF:ID  0.000495135:0.000453537:0.568636:0.750866:rs200676709
1   74790   rs13328700  C   G   .   PASS    AF=0.034069 ES:SE:LP:AF:ID  0.00235554:0.00104409:1.61979:0.034069:rs13328700
1   74792   rs1335672253    G   A   .   PASS    AF=0.034069 ES:SE:LP:AF:ID  0.00235554:0.00104409:1.61979:0.034069:rs1335672253
1   76838   rs563953605 T   G   .   PASS    AF=0.077284 ES:SE:LP:AF:ID  -0.000718555:0.000726793:0.49485:0.077284:rs563953605
1   76854   rs367666799 A   G   .   PASS    AF=0.077285 ES:SE:LP:AF:ID  -0.000705986:0.000704075:0.49485:0.077285:rs367666799
1   77866   rs563593912 C   T   .   PASS    AF=0.077087 ES:SE:LP:AF:ID  -0.000709659:0.000727031:0.481486:0.077087:rs563593912
1   77874   rs62641297  G   A   .   PASS    AF=0.077087 ES:SE:LP:AF:ID  -0.000709659:0.000727031:0.481486:0.077087:rs62641297
1   81260   rs571136476 C   T   .   PASS    AF=0.04141  ES:SE:LP:AF:ID  -0.00142471:0.00101903:0.79588:0.04141:rs571136476
1   81587   rs536406113 C   T   .   PASS    AF=0.061021 ES:SE:LP:AF:ID  0.000284485:0.00077146:0.148742:0.061021:rs536406113
1   82163   rs139113303 G   A   .   PASS    AF=0.075299 ES:SE:LP:AF:ID  -0.000731162:0.000712602:0.522879:0.075299:rs139113303
1   82609   rs149189449 C   G   .   PASS    AF=0.075331 ES:SE:LP:AF:ID  -0.0007372:0.000712409:0.522879:0.075331:rs149189449
1   83514   rs201754587 C   T   .   PASS    AF=0.352715 ES:SE:LP:AF:ID  0.000126748:0.000407242:0.119186:0.352715:rs201754587