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/c53d82af-9a04-4405-acc0-b626b92f0c0d/call-ldsc/inputs/562856190/ieu-b-33.vcf.gz \
--ref-ld-chr /data/ref/eur_w_ld_chr/ \
--out /data/igd/ieu-b-33/ldsc.txt \
--w-ld-chr /data/ref/eur_w_ld_chr/ 

Beginning analysis at Fri Aug 21 01:28:41 2020
Reading summary statistics from /data/cromwell-executions/qc/c53d82af-9a04-4405-acc0-b626b92f0c0d/call-ldsc/inputs/562856190/ieu-b-33.vcf.gz ...
Read summary statistics for 26775880 SNPs.
Dropped 126046 SNPs with duplicated rs numbers.
Reading reference panel LD Score from /data/ref/eur_w_ld_chr/[1-22] ...
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] ...
Read regression weight LD Scores for 1290028 SNPs.
After merging with reference panel LD, 1220779 SNPs remain.
After merging with regression SNP LD, 1220779 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.1865 (0.0132)
Lambda GC: 1.663
Mean Chi^2: 3.223
Intercept: 1.2795 (0.0259)
Ratio: 0.1257 (0.0116)
Analysis finished at Fri Aug 21 01:33:28 2020
Total time elapsed: 4.0m:47.5s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9663,
    "inflation_factor": 1.1799,
    "mean_EFFECT": -0.0021,
    "n": 474237,
    "n_snps": 26776111,
    "n_clumped_hits": 448,
    "n_p_sig": 98997,
    "n_mono": 0,
    "n_ns": 0,
    "n_mac": 22696,
    "is_snpid_unique": false,
    "n_miss_EFFECT": 0,
    "n_miss_SE": 0,
    "n_miss_PVAL": 0,
    "n_miss_AF": 0,
    "n_miss_AF_reference": 2114307,
    "n_est": 357770.9659,
    "ratio_se_n": 0.8686,
    "mean_diff": 0.0003,
    "ratio_diff": 1.9533,
    "sd_y_est1": 1.2472,
    "sd_y_est2": 1.0833,
    "r2_sum1": 0.1103,
    "r2_sum2": 0.0709,
    "r2_sum3": 0.094,
    "r2_sum4": 0.117,
    "ldsc_nsnp_merge_refpanel_ld": 1220779,
    "ldsc_nsnp_merge_regression_ld": 1220779,
    "ldsc_observed_scale_h2_beta": 0.1865,
    "ldsc_observed_scale_h2_se": 0.0132,
    "ldsc_intercept_beta": 1.2795,
    "ldsc_intercept_se": 0.0259,
    "ldsc_lambda_gc": 1.663,
    "ldsc_mean_chisq": 3.223,
    "ldsc_ratio": 0.1257
}

Flags

name value
af_correlation FALSE
inflation_factor FALSE
n FALSE
is_snpid_non_unique TRUE
mean_EFFECT_nonfinite FALSE
mean_EFFECT_05 FALSE
mean_EFFECT_01 FALSE
mean_chisq TRUE
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 numeric.mean numeric.sd numeric.p0 numeric.p25 numeric.p50 numeric.p75 numeric.p100 numeric.hist
character ID 47 0.9999982 3 64 0 26774317 0 NA NA NA NA NA NA NA NA
character REF 0 1.0000000 1 1 0 4 0 NA NA NA NA NA NA NA NA
character ALT 0 1.0000000 1 1 0 4 0 NA NA NA NA NA NA NA NA
numeric CHROM 0 1.0000000 NA NA NA NA NA 8.655324e+00 5.783754e+00 1.000000 4.000000e+00 8.000000e+00 1.300000e+01 2.200000e+01 ▇▅▃▂▂
numeric POS 0 1.0000000 NA NA NA NA NA 7.897199e+07 5.624013e+07 56.000000 3.282427e+07 6.963369e+07 1.148483e+08 2.492398e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA -2.059500e-03 1.264999e-01 -6.630690 -2.435000e-02 -1.870000e-04 2.098100e-02 7.742440e+00 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 8.052660e-02 9.514860e-02 0.001932 7.123000e-03 4.777700e-02 1.200860e-01 6.533380e+00 ▇▁▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.717137e-01 2.983301e-01 0.000000 2.064510e-01 4.637725e-01 7.305787e-01 1.000000e+00 ▇▆▆▆▆
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.717134e-01 2.983312e-01 0.000000 2.064711e-01 4.637601e-01 7.305680e-01 1.000000e+00 ▇▆▆▆▆
numeric AF 0 1.0000000 NA NA NA NA NA 7.929750e-02 1.931179e-01 0.000025 1.550000e-04 7.430000e-04 2.372200e-02 9.999750e-01 ▇▁▁▁▁
numeric AF_reference 2114307 0.9210376 NA NA NA NA NA 9.020570e-02 1.926426e-01 0.000000 1.397800e-03 7.388200e-03 5.391370e-02 1.000000e+00 ▇▁▁▁▁
numeric N 0 1.0000000 NA NA NA NA NA 4.217324e+05 1.102108e+05 436.000000 4.267300e+05 4.575980e+05 4.728380e+05 4.742370e+05 ▁▁▁▁▇

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 16141 rs529651976 C T -0.045364 0.212120 0.8306451 0.8306562 0.000525 0.0025958 36242
1 49298 rs200943160 T C -0.013948 0.011228 0.2141140 0.2141438 0.823640 0.7821490 36242
1 54353 rs140052487 C A 0.104084 0.099094 0.2935357 0.2935544 0.001868 0.0089856 36242
1 54564 rs558796213 G T 0.039101 0.114201 0.7320723 0.7320593 0.000142 0.0041933 406470
1 54591 rs561234294 A G 0.193191 0.119830 0.1069131 0.1069165 0.001553 0.0035942 36242
1 54712 rs552304420 T C 0.027348 0.043838 0.5327519 0.5327311 0.010447 0.0109824 36242
1 54815 rs568686875 T C 0.161670 0.185792 0.3842068 0.3842093 0.000481 0.0019968 36242
1 55326 rs3107975 T C -0.077139 0.033033 0.0195542 0.0195324 0.019678 0.0459265 36242
1 55351 rs531766459 T A 0.042569 0.060065 0.4785188 0.4785010 0.000504 0.0007987 406470
1 55405 rs372455836 C T 0.034255 0.055407 0.5364299 0.5364150 0.006936 0.0075879 36242
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51237137 rs534739169 A C 0.115865 0.088010 0.1879918 0.1880069 0.000215 0.0001997 442712
22 51237410 rs530437591 G A 0.001195 0.057277 0.9833480 0.9833545 0.000360 0.0017971 442712
22 51237486 rs149820726 G C -0.013092 0.158960 0.9343399 0.9343602 0.000538 0.0025958 36242
22 51238275 rs202031343 C T 0.088634 0.103530 0.3919286 0.3919320 0.001269 0.0009984 36242
22 51238307 rs577028785 A G -0.215218 0.233850 0.3573963 0.3574030 0.000248 0.0015974 36242
22 51238349 rs546389903 T C -0.010843 0.286340 0.9697799 0.9697933 0.000166 0.0013978 36242
22 51238660 rs569936315 A G -0.116814 0.152765 0.4444787 0.4444712 0.000066 0.0167732 442712
22 51239586 rs535432390 T G 0.016869 0.021463 0.4319087 0.4318925 0.002938 0.0001997 460882
22 51239678 rs573137567 G T 0.084570 0.084612 0.3175419 0.3175508 0.001904 0.0233626 36242
22 51244163 rs199560686 A G -0.236242 0.206365 0.2522813 0.2523014 0.000054 0.0077875 442712

bcf preview

1   16141   rs529651976 C   T   .   PASS    AF=0.000525 ES:SE:LP:AF:SS:ID   -0.045364:0.21212:0.0805845:0.000525:36242:rs529651976
1   49298   rs10399793  T   C   .   PASS    AF=0.82364  ES:SE:LP:AF:SS:ID   -0.013948:0.011228:0.669355:0.82364:36242:rs10399793
1   54353   rs140052487 C   A   .   PASS    AF=0.001868 ES:SE:LP:AF:SS:ID   0.104084:0.099094:0.532339:0.001868:36242:rs140052487
1   54564   rs558796213 G   T   .   PASS    AF=0.000142 ES:SE:LP:AF:SS:ID   0.039101:0.114201:0.135446:0.000142:406470:rs558796213
1   54591   rs561234294 A   G   .   PASS    AF=0.001553 ES:SE:LP:AF:SS:ID   0.193191:0.11983:0.970969:0.001553:36242:rs561234294
1   54712   rs573184866 T   C   .   PASS    AF=0.010447 ES:SE:LP:AF:SS:ID   0.027348:0.043838:0.273475:0.010447:36242:rs573184866
1   54815   rs568686875 T   C   .   PASS    AF=0.000481 ES:SE:LP:AF:SS:ID   0.16167:0.185792:0.415435:0.000481:36242:rs568686875
1   55326   rs3107975   T   C   .   PASS    AF=0.019678 ES:SE:LP:AF:SS:ID   -0.077139:0.033033:1.70876:0.019678:36242:rs3107975
1   55351   rs531766459 T   A   .   PASS    AF=0.000504 ES:SE:LP:AF:SS:ID   0.042569:0.060065:0.320101:0.000504:406470:rs531766459
1   55405   rs372455836 C   T   .   PASS    AF=0.006936 ES:SE:LP:AF:SS:ID   0.034255:0.055407:0.270487:0.006936:36242:rs372455836
1   55416   rs193242050 G   A   .   PASS    AF=9.4e-05  ES:SE:LP:AF:SS:ID   -0.253072:0.164035:0.910547:9.4e-05:442712:rs193242050
1   55427   rs183189405 T   C   .   PASS    AF=0.002351 ES:SE:LP:AF:SS:ID   -0.150898:0.109904:0.770226:0.002351:36242:rs183189405
1   56586   rs541979596 G   A   .   PASS    AF=0.001503 ES:SE:LP:AF:SS:ID   0.035734:0.13085:0.105249:0.001503:36242:rs541979596
1   57095   rs553759011 T   C   .   PASS    AF=3.6e-05  ES:SE:LP:AF:SS:ID   0.116796:0.223936:0.220404:3.6e-05:406470:rs553759011
1   57183   rs368339209 A   G   .   PASS    AF=2.8e-05  ES:SE:LP:AF:SS:ID   -0.023975:0.367905:0.0231811:2.8e-05:406470:rs368339209
1   61804   rs567421057 G   A   .   PASS    AF=7.4e-05  ES:SE:LP:AF:SS:ID   0.071332:0.164372:0.177615:7.4e-05:406470:rs567421057
1   61993   rs190553843 C   T   .   PASS    AF=9.4e-05  ES:SE:LP:AF:SS:ID   0.175816:0.160688:0.562452:9.4e-05:442712:rs190553843
1   62124   rs528478839 G   A   .   PASS    AF=0.000181 ES:SE:LP:AF:SS:ID   0.202101:0.396042:0.214768:0.000181:36242:rs528478839
1   62157   rs10399597  G   A   .   PASS    AF=0.000139 ES:SE:LP:AF:SS:ID   -0.012839:0.097279:0.0481872:0.000139:442712:rs10399597
1   62509   rs534313866 T   C   .   PASS    AF=0.000544 ES:SE:LP:AF:SS:ID   -0.1102:0.214247:0.216794:0.000544:36242:rs534313866
1   62617   rs543126209 T   G   .   PASS    AF=9.3e-05  ES:SE:LP:AF:SS:ID   -0.256681:0.163241:0.9361:9.3e-05:442712:rs543126209
1   64670   rs545257650 A   G   .   PASS    AF=0.000147 ES:SE:LP:AF:SS:ID   -0.030641:0.11767:0.0998749:0.000147:442712:rs545257650
1   64908   rs540391097 A   G   .   PASS    AF=0.000642 ES:SE:LP:AF:SS:ID   -0.039473:0.053874:0.333702:0.000642:442712:rs540391097
1   65009   rs563233355 G   A   .   PASS    AF=0.000292 ES:SE:LP:AF:SS:ID   0.048347:0.073712:0.290805:0.000292:442712:rs563233355
1   65974   rs531923826 A   G   .   PASS    AF=0.004642 ES:SE:LP:AF:SS:ID   -0.044385:0.068618:0.285875:0.004642:36242:rs531923826
1   67179   rs149952626 C   G   .   PASS    AF=0.000141 ES:SE:LP:AF:SS:ID   -0.741677:0.346578:1.48978:0.000141:36242:rs149952626
1   67223   rs78676975  C   T   .   PASS    AF=0.000486 ES:SE:LP:AF:SS:ID   0.10969:0.246631:0.182753:0.000486:36242:rs78676975
1   67224   rs566526215 G   A   .   PASS    AF=0.000161 ES:SE:LP:AF:SS:ID   0.088578:0.125194:0.319438:0.000161:442712:rs566526215
1   67631   rs533896527 G   C   .   PASS    AF=0.0002   ES:SE:LP:AF:SS:ID   -0.033348:0.096025:0.137634:0.0002:442712:rs533896527
1   69594   rs144967600 T   C   .   PASS    AF=0.000744 ES:SE:LP:AF:SS:ID   -0.24348:0.186984:0.714785:0.000744:36242:rs144967600
1   69610   rs376022826 C   T   .   PASS    AF=0.000217 ES:SE:LP:AF:SS:ID   -0.049688:0.381012:0.0475844:0.000217:36242:rs376022826
1   70317   rs570011908 G   A   .   PASS    AF=0.000639 ES:SE:LP:AF:SS:ID   0.267248:0.204572:0.718047:0.000639:36242:rs570011908
1   72526   rs547237130 A   G   .   PASS    AF=0.038202 ES:SE:LP:AF:SS:ID   0.059562:0.023215:1.98649:0.038202:36242:rs547237130
1   73093   rs535508237 G   A   .   PASS    AF=0.003983 ES:SE:LP:AF:SS:ID   0.027354:0.069264:0.159319:0.003983:36242:rs535508237
1   77763   rs557457745 G   A   .   PASS    AF=0.00538  ES:SE:LP:AF:SS:ID   -0.009079:0.062387:0.0534136:0.00538:36242:rs557457745
1   78942   rs372315362 C   G   .   PASS    AF=0.008006 ES:SE:LP:AF:SS:ID   0.00543:0.048838:0.0402705:0.008006:36242:rs372315362
1   79033   rs2462495   A   G   .   PASS    AF=0.998701 ES:SE:LP:AF:SS:ID   -0.089842:0.047373:1.23724:0.998701:406470:rs2462495
1   79137   rs143777184 A   T   .   PASS    AF=0.001022 ES:SE:LP:AF:SS:ID   -0.041218:0.04323:0.468077:0.001022:442712:rs143777184
1   79188   rs534350410 G   T   .   PASS    AF=0.001113 ES:SE:LP:AF:SS:ID   0.170325:0.14847:0.599846:0.001113:36242:rs534350410
1   82957   rs189774606 C   T   .   PASS    AF=0.000469 ES:SE:LP:AF:SS:ID   -0.017768:0.056625:0.122806:0.000469:442712:rs189774606
1   82961   rs537801787 C   T   .   PASS    AF=0.000515 ES:SE:LP:AF:SS:ID   -0.131714:0.212368:0.271536:0.000515:36242:rs537801787
1   82994   rs574556077 A   G   .   PASS    AF=0.000186 ES:SE:LP:AF:SS:ID   0.162459:0.318192:0.214901:0.000186:36242:rs574556077
1   83170   rs562997564 G   T   .   PASS    AF=0.001245 ES:SE:LP:AF:SS:ID   -0.17155:0.139052:0.66296:0.001245:36242:rs562997564
1   83771   rs189906733 T   G   .   PASS    AF=0.000664 ES:SE:LP:AF:SS:ID   -0.023535:0.049388:0.198111:0.000664:442712:rs189906733
1   84139   rs183605470 A   T   .   PASS    AF=0.020816 ES:SE:LP:AF:SS:ID   0.031553:0.031571:0.498145:0.020816:36242:rs183605470
1   84618   rs576633512 C   T   .   PASS    AF=0.000715 ES:SE:LP:AF:SS:ID   0.315785:0.185185:1.05477:0.000715:36242:rs576633512
1   85622   rs185273034 A   T   .   PASS    AF=0.001246 ES:SE:LP:AF:SS:ID   -0.085398:0.138764:0.268976:0.001246:36242:rs185273034
1   85892   rs147185795 A   G   .   PASS    AF=0.000456 ES:SE:LP:AF:SS:ID   -0.025048:0.064705:0.155715:0.000456:442712:rs147185795
1   86028   rs114608975 T   C   .   PASS    AF=0.061349 ES:SE:LP:AF:SS:ID   0.02997:0.018147:1.006:0.061349:36242:rs114608975
1   86192   rs548281277 G   A   .   PASS    AF=0.034551 ES:SE:LP:AF:SS:ID   0.051388:0.024365:1.45648:0.034551:36242:rs548281277