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/4277a9cd-ab5c-4b1f-989d-25c0e6171329/call-ldsc/inputs/562856191/ieu-b-34.vcf.gz \
--ref-ld-chr /data/ref/eur_w_ld_chr/ \
--out /data/igd/ieu-b-34/ldsc.txt \
--w-ld-chr /data/ref/eur_w_ld_chr/ 

Beginning analysis at Fri Aug 21 01:27:50 2020
Reading summary statistics from /data/cromwell-executions/qc/4277a9cd-ab5c-4b1f-989d-25c0e6171329/call-ldsc/inputs/562856191/ieu-b-34.vcf.gz ...
Read summary statistics for 26935511 SNPs.
Dropped 127346 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: 0.1543 (0.0126)
Lambda GC: 1.7433
Mean Chi^2: 2.9296
Intercept: 1.2522 (0.0233)
Ratio: 0.1307 (0.0121)
Analysis finished at Fri Aug 21 01:33:20 2020
Total time elapsed: 5.0m:30.56s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9666,
    "inflation_factor": 1.1799,
    "mean_EFFECT": -0.0003,
    "n": 519288,
    "n_snps": 26935743,
    "n_clumped_hits": 428,
    "n_p_sig": 89395,
    "n_mono": 0,
    "n_ns": 0,
    "n_mac": 45614,
    "is_snpid_unique": false,
    "n_miss_EFFECT": 0,
    "n_miss_SE": 0,
    "n_miss_PVAL": 0,
    "n_miss_AF": 0,
    "n_miss_AF_reference": 2114409,
    "n_est": 382131.9544,
    "ratio_se_n": 0.8578,
    "mean_diff": 0.0002,
    "ratio_diff": 1.1771,
    "sd_y_est1": 1.3322,
    "sd_y_est2": 1.1428,
    "r2_sum1": 0.0841,
    "r2_sum2": 0.0474,
    "r2_sum3": 0.0644,
    "r2_sum4": 0.0863,
    "ldsc_nsnp_merge_refpanel_ld": 1220779,
    "ldsc_nsnp_merge_regression_ld": 1220779,
    "ldsc_observed_scale_h2_beta": 0.1543,
    "ldsc_observed_scale_h2_se": 0.0126,
    "ldsc_intercept_beta": 1.2522,
    "ldsc_intercept_se": 0.0233,
    "ldsc_lambda_gc": 1.7433,
    "ldsc_mean_chisq": 2.9296,
    "ldsc_ratio": 0.1307
}

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 0.9999983 3 64 0 26933950 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 8.653330e+00 5.782462e+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 7.898009e+07 5.624919e+07 56.000000 3.282939e+07 6.963325e+07 1.148544e+08 2.492398e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA -2.713000e-04 1.628531e-01 -55.610300 -2.240000e-02 1.700000e-05 2.248400e-02 5.212860e+01 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 8.519200e-02 1.476297e-01 0.001088 7.024000e-03 4.734400e-02 1.198220e-01 9.680360e+01 ▇▁▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.714863e-01 2.984366e-01 0.000000 2.062192e-01 4.637736e-01 7.304324e-01 1.000000e+00 ▇▆▆▆▆
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.714859e-01 2.984378e-01 0.000000 2.062394e-01 4.637621e-01 7.304221e-01 1.000000e+00 ▇▆▆▆▆
numeric AF 0 1.0000000 NA NA NA NA NA 7.888420e-02 1.926403e-01 0.000025 1.650000e-04 7.860000e-04 2.306000e-02 9.999750e-01 ▇▁▁▁▁
numeric AF_reference 2114409 0.9215017 NA NA NA NA NA 8.967420e-02 1.921935e-01 0.000000 1.397800e-03 7.388200e-03 5.291530e-02 1.000000e+00 ▇▁▁▁▁
numeric N 0 1.0000000 NA NA NA NA NA 4.401245e+05 1.243355e+05 396.000000 4.420000e+05 4.639760e+05 5.178790e+05 5.192880e+05 ▁▁▁▂▇

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 16141 rs529651976 C T 0.100767 0.217058 0.6424968 0.6424758 0.000511 0.0025958 35212
1 49298 rs200943160 T C 0.012982 0.011322 0.2515290 0.2515399 0.823810 0.7821490 35212
1 54353 rs140052487 C A 0.101965 0.101925 0.3171071 0.3171206 0.001811 0.0089856 35212
1 54564 rs558796213 G T 0.035745 0.115360 0.7566761 0.7566704 0.000141 0.0041933 406788
1 54591 rs561234294 A G -0.140054 0.120983 0.2469932 0.2470135 0.001554 0.0035942 35212
1 54712 rs552304420 T C 0.075660 0.044370 0.0881576 0.0881560 0.010369 0.0109824 35212
1 54815 rs568686875 T C -0.012004 0.188002 0.9490690 0.9490894 0.000481 0.0019968 35212
1 55326 rs3107975 T C -0.010272 0.033415 0.7585269 0.7585337 0.019541 0.0459265 35212
1 55351 rs531766459 T A -0.048670 0.060646 0.4222552 0.4222487 0.000504 0.0007987 406788
1 55405 rs372455836 C T 0.022133 0.056528 0.6954133 0.6953978 0.006811 0.0075879 35212
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51237137 rs534739169 A C -0.074050 0.088839 0.4045517 0.4045457 0.000213 0.0001997 442000
22 51237410 rs530437591 G A 0.047558 0.057747 0.4101965 0.4101908 0.000352 0.0017971 442000
22 51237486 rs149820726 G C 0.119831 0.159984 0.4538559 0.4538460 0.000540 0.0025958 35212
22 51238275 rs202031343 C T 0.102475 0.103988 0.3243912 0.3244030 0.001278 0.0009984 35212
22 51238307 rs577028785 A G 0.054696 0.239065 0.8190251 0.8190311 0.000241 0.0015974 35212
22 51238349 rs546389903 T C -0.233553 0.284467 0.4116376 0.4116351 0.000170 0.0013978 35212
22 51238660 rs569936315 A G 0.038583 0.152092 0.7997379 0.7997413 0.000066 0.0167732 442000
22 51239586 rs535432390 T G -0.033768 0.021674 0.1192320 0.1192343 0.002942 0.0001997 460173
22 51239678 rs573137567 G T 0.023670 0.086614 0.7846356 0.7846369 0.001846 0.0233626 35212
22 51244163 rs199560686 A G 0.071638 0.205340 0.7271935 0.7271831 0.000054 0.0077875 442000

bcf preview

1   16141   rs529651976 C   T   .   PASS    AF=0.000511 ES:SE:LP:AF:SS:ID   0.100767:0.217058:0.192129:0.000511:35212:rs529651976
1   49298   rs10399793  T   C   .   PASS    AF=0.82381  ES:SE:LP:AF:SS:ID   0.012982:0.011322:0.599412:0.82381:35212:rs10399793
1   54353   rs140052487 C   A   .   PASS    AF=0.001811 ES:SE:LP:AF:SS:ID   0.101965:0.101925:0.498794:0.001811:35212:rs140052487
1   54564   rs558796213 G   T   .   PASS    AF=0.000141 ES:SE:LP:AF:SS:ID   0.035745:0.11536:0.12109:0.000141:406788:rs558796213
1   54591   rs561234294 A   G   .   PASS    AF=0.001554 ES:SE:LP:AF:SS:ID   -0.140054:0.120983:0.607315:0.001554:35212:rs561234294
1   54712   rs573184866 T   C   .   PASS    AF=0.010369 ES:SE:LP:AF:SS:ID   0.07566:0.04437:1.05474:0.010369:35212:rs573184866
1   54815   rs568686875 T   C   .   PASS    AF=0.000481 ES:SE:LP:AF:SS:ID   -0.012004:0.188002:0.0227022:0.000481:35212:rs568686875
1   55326   rs3107975   T   C   .   PASS    AF=0.019541 ES:SE:LP:AF:SS:ID   -0.010272:0.033415:0.120029:0.019541:35212:rs3107975
1   55351   rs531766459 T   A   .   PASS    AF=0.000504 ES:SE:LP:AF:SS:ID   -0.04867:0.060646:0.374425:0.000504:406788:rs531766459
1   55405   rs372455836 C   T   .   PASS    AF=0.006811 ES:SE:LP:AF:SS:ID   0.022133:0.056528:0.157757:0.006811:35212:rs372455836
1   55416   rs193242050 G   A   .   PASS    AF=9.1e-05  ES:SE:LP:AF:SS:ID   0.062079:0.167:0.148677:9.1e-05:442000:rs193242050
1   55427   rs183189405 T   C   .   PASS    AF=0.002323 ES:SE:LP:AF:SS:ID   0.04188:0.111982:0.149707:0.002323:35212:rs183189405
1   56586   rs541979596 G   A   .   PASS    AF=0.001468 ES:SE:LP:AF:SS:ID   -0.049964:0.13359:0.149713:0.001468:35212:rs541979596
1   57095   rs553759011 T   C   .   PASS    AF=3.6e-05  ES:SE:LP:AF:SS:ID   0.162705:0.22621:0.326067:3.6e-05:406788:rs553759011
1   57183   rs368339209 A   G   .   PASS    AF=2.8e-05  ES:SE:LP:AF:SS:ID   0.546728:0.37162:0.850092:2.8e-05:406788:rs368339209
1   61804   rs567421057 G   A   .   PASS    AF=7.4e-05  ES:SE:LP:AF:SS:ID   0.171681:0.16604:0.521242:7.4e-05:406788:rs567421057
1   61993   rs190553843 C   T   .   PASS    AF=9.4e-05  ES:SE:LP:AF:SS:ID   0.068215:0.160231:0.173715:9.4e-05:442000:rs190553843
1   62124   rs528478839 G   A   .   PASS    AF=0.000182 ES:SE:LP:AF:SS:ID   0.093716:0.394123:0.090421:0.000182:35212:rs528478839
1   62157   rs10399597  G   A   .   PASS    AF=0.000138 ES:SE:LP:AF:SS:ID   0.154703:0.098311:0.937147:0.000138:442000:rs10399597
1   62509   rs534313866 T   C   .   PASS    AF=0.000533 ES:SE:LP:AF:SS:ID   0.150417:0.219313:0.307312:0.000533:35212:rs534313866
1   62617   rs543126209 T   G   .   PASS    AF=9e-05    ES:SE:LP:AF:SS:ID   0.059865:0.166187:0.143457:9e-05:442000:rs543126209
1   64670   rs545257650 A   G   .   PASS    AF=0.000146 ES:SE:LP:AF:SS:ID   -0.085785:0.118592:0.328396:0.000146:442000:rs545257650
1   64908   rs540391097 A   G   .   PASS    AF=0.000642 ES:SE:LP:AF:SS:ID   -0.058185:0.054478:0.544412:0.000642:442000:rs540391097
1   65009   rs563233355 G   A   .   PASS    AF=0.000288 ES:SE:LP:AF:SS:ID   0.063149:0.074705:0.400181:0.000288:442000:rs563233355
1   65974   rs531923826 A   G   .   PASS    AF=0.00463  ES:SE:LP:AF:SS:ID   -0.091369:0.069273:0.727796:0.00463:35212:rs531923826
1   67179   rs149952626 C   G   .   PASS    AF=0.000128 ES:SE:LP:AF:SS:ID   -0.156209:0.368382:0.172918:0.000128:35212:rs149952626
1   67223   rs78676975  C   T   .   PASS    AF=0.000467 ES:SE:LP:AF:SS:ID   0.07835:0.262195:0.116294:0.000467:35212:rs78676975
1   67224   rs566526215 G   A   .   PASS    AF=0.000161 ES:SE:LP:AF:SS:ID   0.017726:0.125635:0.0516961:0.000161:442000:rs566526215
1   67631   rs533896527 G   C   .   PASS    AF=0.000196 ES:SE:LP:AF:SS:ID   -0.008982:0.097123:0.0332502:0.000196:442000:rs533896527
1   69594   rs144967600 T   C   .   PASS    AF=0.00076  ES:SE:LP:AF:SS:ID   -0.022606:0.185917:0.0442156:0.00076:35212:rs144967600
1   69610   rs376022826 C   T   .   PASS    AF=0.000222 ES:SE:LP:AF:SS:ID   -0.105112:0.378793:0.107125:0.000222:35212:rs376022826
1   70317   rs570011908 G   A   .   PASS    AF=0.000637 ES:SE:LP:AF:SS:ID   -0.021005:0.207988:0.0364303:0.000637:35212:rs570011908
1   72526   rs547237130 A   G   .   PASS    AF=0.038312 ES:SE:LP:AF:SS:ID   0.009496:0.023367:0.164636:0.038312:35212:rs547237130
1   73093   rs535508237 G   A   .   PASS    AF=0.003939 ES:SE:LP:AF:SS:ID   -0.077481:0.070483:0.56603:0.003939:35212:rs535508237
1   77763   rs557457745 G   A   .   PASS    AF=0.005336 ES:SE:LP:AF:SS:ID   -0.092448:0.063452:0.8383:0.005336:35212:rs557457745
1   78942   rs372315362 C   G   .   PASS    AF=0.007969 ES:SE:LP:AF:SS:ID   -0.016564:0.049488:0.13203:0.007969:35212:rs372315362
1   79033   rs2462495   A   G   .   PASS    AF=0.998702 ES:SE:LP:AF:SS:ID   -0.027428:0.04786:0.246718:0.998702:406788:rs2462495
1   79137   rs143777184 A   T   .   PASS    AF=0.001008 ES:SE:LP:AF:SS:ID   -0.032121:0.043689:0.335156:0.001008:442000:rs143777184
1   79188   rs534350410 G   T   .   PASS    AF=0.001118 ES:SE:LP:AF:SS:ID   -0.086265:0.149429:0.248907:0.001118:35212:rs534350410
1   82957   rs189774606 C   T   .   PASS    AF=0.000456 ES:SE:LP:AF:SS:ID   0.019831:0.057462:0.136664:0.000456:442000:rs189774606
1   82961   rs537801787 C   T   .   PASS    AF=0.000505 ES:SE:LP:AF:SS:ID   0.227101:0.217239:0.528967:0.000505:35212:rs537801787
1   82994   rs574556077 A   G   .   PASS    AF=0.000162 ES:SE:LP:AF:SS:ID   -0.073017:0.3551:0.0772372:0.000162:35212:rs574556077
1   83170   rs562997564 G   T   .   PASS    AF=0.001254 ES:SE:LP:AF:SS:ID   0.267503:0.138879:1.26681:0.001254:35212:rs562997564
1   83771   rs189906733 T   G   .   PASS    AF=0.000651 ES:SE:LP:AF:SS:ID   -0.004902:0.05006:0.0352837:0.000651:442000:rs189906733
1   84139   rs183605470 A   T   .   PASS    AF=0.020791 ES:SE:LP:AF:SS:ID   -0.017368:0.031861:0.232324:0.020791:35212:rs183605470
1   84618   rs576633512 C   T   .   PASS    AF=0.000715 ES:SE:LP:AF:SS:ID   -0.070697:0.1875:0.151104:0.000715:35212:rs576633512
1   85622   rs185273034 A   T   .   PASS    AF=0.001251 ES:SE:LP:AF:SS:ID   0.242524:0.138583:1.09626:0.001251:35212:rs185273034
1   85892   rs147185795 A   G   .   PASS    AF=0.000446 ES:SE:LP:AF:SS:ID   -0.100781:0.065319:0.910639:0.000446:442000:rs147185795
1   86028   rs114608975 T   C   .   PASS    AF=0.061275 ES:SE:LP:AF:SS:ID   -0.023029:0.018317:0.680592:0.061275:35212:rs114608975
1   86192   rs548281277 G   A   .   PASS    AF=0.034599 ES:SE:LP:AF:SS:ID   0.012038:0.024556:0.204822:0.034599:35212:rs548281277