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/e0844a94-2add-455f-b114-888a1e457605/call-ldsc/inputs/-674580007/ieu-b-7.vcf.gz \
--ref-ld-chr /data/ref/eur_w_ld_chr/ \
--out /data/igd/ieu-b-7/ldsc.txt \
--w-ld-chr /data/ref/eur_w_ld_chr/ 

Beginning analysis at Tue Jun 23 15:55:19 2020
Reading summary statistics from /data/cromwell-executions/qc/e0844a94-2add-455f-b114-888a1e457605/call-ldsc/inputs/-674580007/ieu-b-7.vcf.gz ...
Read summary statistics for 17891839 SNPs.
Dropped 488494 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, 1217474 SNPs remain.
After merging with regression SNP LD, 1217474 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0155 (0.0013)
Lambda GC: 1.0847
Mean Chi^2: 1.1288
Intercept: 0.9884 (0.0059)
Ratio < 0 (usually indicates GC correction).
Analysis finished at Tue Jun 23 15:58:06 2020
Total time elapsed: 2.0m:46.81s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9622,
    "inflation_factor": 0.9028,
    "mean_EFFECT": -0.0253,
    "n": 482730,
    "n_snps": 17891936,
    "n_clumped_hits": 23,
    "n_p_sig": 3530,
    "n_mono": 0,
    "n_ns": 0,
    "n_mac": 2171844,
    "is_snpid_unique": false,
    "n_miss_EFFECT": 0,
    "n_miss_SE": 0,
    "n_miss_PVAL": 0,
    "n_miss_AF": 0,
    "n_miss_AF_reference": 2582376,
    "n_est": 379185.3044,
    "ratio_se_n": 0.8863,
    "mean_diff": 0.0239,
    "ratio_diff": 450.6671,
    "sd_y_est1": 19.7372,
    "sd_y_est2": 17.4928,
    "r2_sum1": 0.2059,
    "r2_sum2": 0.0005,
    "r2_sum3": 0.0007,
    "r2_sum4": 0.0027,
    "ldsc_nsnp_merge_refpanel_ld": 1217474,
    "ldsc_nsnp_merge_regression_ld": 1217474,
    "ldsc_observed_scale_h2_beta": 0.0155,
    "ldsc_observed_scale_h2_se": 0.0013,
    "ldsc_intercept_beta": 0.9884,
    "ldsc_intercept_se": 0.0059,
    "ldsc_lambda_gc": 1.0847,
    "ldsc_mean_chisq": 1.1288,
    "ldsc_ratio": -0.0901
}

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 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 numeric.mean numeric.sd numeric.p0 numeric.p25 numeric.p50 numeric.p75 numeric.p100 numeric.hist
character ID 45 0.9999975 3 64 0 17530232 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 8.625208e+00 5.761533e+00 1.000 4.000000e+00 8.000000e+00 1.300000e+01 2.200000e+01 ▇▅▃▂▂
numeric POS 0 1.0000000 NA NA NA NA NA 7.910828e+07 5.617392e+07 173.000 3.305852e+07 6.982141e+07 1.147497e+08 2.492385e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA -2.534450e-02 7.009912e-01 -5.000 -1.295000e-01 -5.100000e-03 6.650000e-02 5.000000e+00 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 5.109780e-01 1.296699e+00 0.016 3.680000e-02 2.241000e-01 6.792000e-01 1.491830e+03 ▇▁▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 5.159013e-01 2.825639e-01 0.000 2.775000e-01 5.216005e-01 7.582999e-01 1.000000e+00 ▆▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 5.159015e-01 2.825645e-01 0.000 2.774851e-01 5.215619e-01 7.583165e-01 1.000000e+00 ▆▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA 1.188529e-01 2.215974e-01 0.001 2.100000e-03 8.400000e-03 1.147000e-01 9.990000e-01 ▇▁▁▁▁
numeric AF_reference 2582376 0.8556682 NA NA NA NA NA 1.379419e-01 2.248656e-01 0.000 1.797100e-03 2.436100e-02 1.701280e-01 1.000000e+00 ▇▁▁▁▁
numeric N 0 1.0000000 NA NA NA NA NA 1.998644e+05 2.299328e+05 528.000 3.443000e+03 1.151800e+04 4.686920e+05 4.827300e+05 ▇▁▁▁▆

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 54591 rs561234294 A G 0.6797 0.8869 0.4435004 0.4434519 0.0062 0.0035942 999
1 54676 rs2462492 C T -0.0996 0.0656 0.1287001 0.1289406 0.3166 NA 2137
1 79188 rs534350410 G T 0.6704 0.8795 0.4458995 0.4459100 0.0062 0.0035942 999
1 82994 rs574556077 A G -1.2614 1.8502 0.4954000 0.4953881 0.0016 0.0019968 999
1 86028 rs114608975 T C 0.2158 0.1222 0.0774497 0.0774030 0.0655 0.0277556 2137
1 90231 rs553304094 C A -1.7603 1.8868 0.3508003 0.3508431 0.0017 0.0037939 999
1 91536 rs6702460 G T -0.1040 0.0625 0.0962698 0.0961124 0.3872 0.4207270 2137
1 234313 rs8179466 C T -0.1138 0.1413 0.4205000 0.4206012 0.0475 NA 2137
1 534192 rs6680723 C T -0.0316 0.0771 0.6815002 0.6819106 0.1804 NA 2137
1 544584 rs576404767 C T -0.6397 2.0828 0.7586999 0.7587409 0.0018 0.0003994 938
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51231424 rs539541647 A G -1.1451 1.2784 0.3704000 0.3703975 0.0015 0.0011981 3167
22 51232488 rs376461333 A G 0.1271 0.1670 0.4466003 0.4466106 0.0200 NA 11518
22 51233336 rs1322471824 A G -0.3659 2.4898 0.8832001 0.8831639 0.0011 NA 879
22 51234048 rs141330630 T C -0.3709 0.7974 0.6418004 0.6418336 0.0069 0.0095847 879
22 51234159 rs8138356 T A -0.9937 1.7318 0.5660998 0.5661058 0.0016 0.0215655 919
22 51234163 rs192982090 G A -1.5364 1.7089 0.3685997 0.3686218 0.0014 0.0007987 964
22 51234199 rs6010092 T C 0.1478 1.9246 0.9388000 0.9387865 0.0020 0.0313498 794
22 51237063 rs3896457 T C 0.0108 0.0457 0.8132001 0.8131814 0.2937 0.2050720 11518
22 51238513 rs1569214665 C G -1.8077 1.9812 0.3614997 0.3615441 0.0011 NA 938
22 51239586 rs535432390 T G -0.2659 0.3816 0.4859001 0.4859261 0.0036 0.0001997 11518

bcf preview

1   54591   rs561234294 A   G   .   PASS    AF=0.0062   ES:SE:LP:AF:SS:NC:ID    0.6797:0.8869:0.353106:0.0062:999:527:rs561234294
1   54676   rs2462492   C   T   .   PASS    AF=0.3166   ES:SE:LP:AF:SS:NC:ID    -0.0996:0.0656:0.890421:0.3166:2137:1169:rs2462492
1   79188   rs534350410 G   T   .   PASS    AF=0.0062   ES:SE:LP:AF:SS:NC:ID    0.6704:0.8795:0.350763:0.0062:999:527:rs534350410
1   82994   rs574556077 A   G   .   PASS    AF=0.0016   ES:SE:LP:AF:SS:NC:ID    -1.2614:1.8502:0.305044:0.0016:999:527:rs574556077
1   86028   rs114608975 T   C   .   PASS    AF=0.0655   ES:SE:LP:AF:SS:NC:ID    0.2158:0.1222:1.11098:0.0655:2137:1169:rs114608975
1   90231   rs553304094 C   A   .   PASS    AF=0.0017   ES:SE:LP:AF:SS:NC:ID    -1.7603:1.8868:0.45494:0.0017:999:527:rs553304094
1   91536   rs1251109649    G   T   .   PASS    AF=0.3872   ES:SE:LP:AF:SS:NC:ID    -0.104:0.0625:1.01651:0.3872:2137:1169:rs1251109649
1   234313  rs8179466   C   T   .   PASS    AF=0.0475   ES:SE:LP:AF:SS:NC:ID    -0.1138:0.1413:0.376234:0.0475:2137:1169:rs8179466
1   534192  rs6680723   C   T   .   PASS    AF=0.1804   ES:SE:LP:AF:SS:NC:ID    -0.0316:0.0771:0.166534:0.1804:2137:1169:rs6680723
1   544584  rs576404767 C   T   .   PASS    AF=0.0018   ES:SE:LP:AF:SS:NC:ID    -0.6397:2.0828:0.11993:0.0018:938:476:rs576404767
1   546697  rs12025928  A   G   .   PASS    AF=0.9244   ES:SE:LP:AF:SS:NC:ID    -0.0212:0.116:0.0679323:0.9244:2137:1169:rs12025928
1   565196  rs139723294 T   C   .   PASS    AF=0.0037   ES:SE:LP:AF:SS:NC:ID    0.0096:0.9084:0.00366348:0.0037:1487:582:rs139723294
1   567006  rs565235853 G   T   .   PASS    AF=0.0028   ES:SE:LP:AF:SS:NC:ID    0.0357:0.7092:0.0178193:0.0028:4308:2447:rs565235853
1   570161  rs572999760 G   A   .   PASS    AF=0.001    ES:SE:LP:AF:SS:NC:ID    3.5709:8.9314:0.161592:0.001:919:620:rs572999760
1   603482  rs865926247 T   C   .   PASS    AF=0.0021   ES:SE:LP:AF:SS:NC:ID    -0.618:1.5999:0.155336:0.0021:919:620:rs865926247
1   604070  rs560619932 G   A   .   PASS    AF=0.0016   ES:SE:LP:AF:SS:NC:ID    -0.3819:0.9047:0.172049:0.0016:3443:2110:rs560619932
1   615330  rs1275267063    C   T   .   PASS    AF=0.0013   ES:SE:LP:AF:SS:NC:ID    0.5173:2.0269:0.0977251:0.0013:919:620:rs1275267063
1   693731  rs12238997  A   G   .   PASS    AF=0.1206   ES:SE:LP:AF:SS:NC:ID    0.0182:0.0504:0.143694:0.1206:12776:7417:rs12238997
1   701131  rs185335630 A   C   .   PASS    AF=0.0036   ES:SE:LP:AF:SS:NC:ID    0.9666:1.3292:0.33059:0.0036:938:476:rs185335630
1   701747  rs561985667 G   A   .   PASS    AF=0.0016   ES:SE:LP:AF:SS:NC:ID    -0.3853:0.9059:0.173536:0.0016:3443:2110:rs561985667
1   705882  rs72631875  G   A   .   PASS    AF=0.0505   ES:SE:LP:AF:SS:NC:ID    -0.0919:0.1392:0.293197:0.0505:2137:1169:rs72631875
1   706368  rs963699400 A   G   .   PASS    AF=0.5054   ES:SE:LP:AF:SS:NC:ID    -0.0963:0.0837:0.602929:0.5054:3344:1678:rs963699400
1   710445  rs1334659872    A   G   .   PASS    AF=0.0045   ES:SE:LP:AF:SS:NC:ID    -0.0953:0.6431:0.0544822:0.0045:2406:1202:rs1334659872
1   713092  rs4565649   G   A   .   PASS    AF=0.0083   ES:SE:LP:AF:SS:NC:ID    0.0333:0.3157:0.0380571:0.0083:5849:3312:rs4565649
1   713977  rs74512038  C   T   .   PASS    AF=0.0032   ES:SE:LP:AF:SS:NC:ID    0.5202:0.9403:0.236497:0.0032:2901:1772:rs74512038
1   714439  rs74707816  G   A   .   PASS    AF=0.0025   ES:SE:LP:AF:SS:NC:ID    -0.3511:0.6878:0.214884:0.0025:5406:3406:rs74707816
1   714596  rs149887893 T   C   .   PASS    AF=0.0317   ES:SE:LP:AF:SS:NC:ID    0.0235:0.1458:0.059633:0.0317:5507:3140:rs149887893
1   715205  rs141090730 C   G   .   PASS    AF=0.0084   ES:SE:LP:AF:SS:NC:ID    -0.0308:0.308:0.0360706:0.0084:5849:3312:rs141090730
1   715265  rs12184267  C   T   .   PASS    AF=0.0342   ES:SE:LP:AF:SS:NC:ID    -0.0118:0.1081:0.0394341:0.0342:12776:7417:rs12184267
1   715367  rs12184277  A   G   .   PASS    AF=0.0342   ES:SE:LP:AF:SS:NC:ID    -0.022:0.1079:0.0764969:0.0342:12776:7417:rs12184277
1   715585  rs897133337 A   T   .   PASS    AF=0.0012   ES:SE:LP:AF:SS:NC:ID    -1.1187:2.4166:0.191519:0.0012:919:620:rs897133337
1   717474  rs141784362 C   T   .   PASS    AF=0.0081   ES:SE:LP:AF:SS:NC:ID    0.0438:0.308:0.0520764:0.0081:6787:3788:rs141784362
1   717485  rs12184279  C   A   .   PASS    AF=0.0337   ES:SE:LP:AF:SS:NC:ID    -0.0084:0.109:0.0273807:0.0337:12776:7417:rs12184279
1   717587  rs144155419 G   A   .   PASS    AF=0.0136   ES:SE:LP:AF:SS:NC:ID    -0.0099:0.1371:0.0257647:0.0136:463162:23259:rs144155419
1   718624  rs777092529 C   G   .   PASS    AF=0.0023   ES:SE:LP:AF:SS:NC:ID    -0.863:1.1423:0.346884:0.0023:1883:1389:rs777092529
1   718625  rs762187552 T   G   .   PASS    AF=0.0023   ES:SE:LP:AF:SS:NC:ID    -0.863:1.142:0.346981:0.0023:1883:1389:rs762187552
1   720381  rs116801199 G   T   .   PASS    AF=0.0346   ES:SE:LP:AF:SS:NC:ID    -0.0136:0.1074:0.0462886:0.0346:12776:7417:rs116801199
1   720583  rs551231909 G   A   .   PASS    AF=0.006    ES:SE:LP:AF:SS:NC:ID    0.0379:0.3868:0.0352691:0.006:5849:3312:rs551231909
1   720984  rs564367954 T   G   .   PASS    AF=0.0015   ES:SE:LP:AF:SS:NC:ID    -1.9172:1.489:0.703554:0.0015:3852:2460:rs564367954
1   721290  rs12565286  G   C   .   PASS    AF=0.0346   ES:SE:LP:AF:SS:NC:ID    -0.0143:0.107:0.0489054:0.0346:12776:7417:rs12565286
1   721538  rs569523401 A   C   .   PASS    AF=0.001    ES:SE:LP:AF:SS:NC:ID    2.7463:1.9236:0.814175:0.001:1487:582:rs569523401
1   722559  rs150361918 T   C   .   PASS    AF=0.0086   ES:SE:LP:AF:SS:NC:ID    -0.0073:0.3044:0.00841954:0.0086:5849:3312:rs150361918
1   722603  rs138029171 T   C   .   PASS    AF=0.0064   ES:SE:LP:AF:SS:NC:ID    0.0608:0.3758:0.0597326:0.0064:5849:3312:rs138029171
1   722670  rs116030099 T   C   .   PASS    AF=0.0959   ES:SE:LP:AF:SS:NC:ID    0.0617:0.0903:0.305834:0.0959:4543:2371:rs116030099
1   722980  rs114222710 C   T   .   PASS    AF=0.0082   ES:SE:LP:AF:SS:NC:ID    0.0196:0.3161:0.0219565:0.0082:5849:3312:rs114222710
1   723345  rs546176432 A   C   .   PASS    AF=0.0011   ES:SE:LP:AF:SS:NC:ID    -1.5948:2.5977:0.26817:0.0011:1487:582:rs546176432
1   723891  rs2977670   G   C   .   PASS    AF=0.9556   ES:SE:LP:AF:SS:NC:ID    -0.0139:0.0926:0.0552213:0.9556:12776:7417:rs2977670
1   723918  rs144434834 G   A   .   PASS    AF=0.0086   ES:SE:LP:AF:SS:NC:ID    0.0146:0.31:0.0165541:0.0086:5849:3312:rs144434834
1   724226  rs1029210216    G   A   .   PASS    AF=0.0013   ES:SE:LP:AF:SS:NC:ID    0.2618:3.0219:0.0310503:0.0013:964:769:rs1029210216
1   724849  rs12126395  C   A   .   PASS    AF=0.0178   ES:SE:LP:AF:SS:NC:ID    0.1412:0.2324:0.2648:0.0178:2137:1169:rs12126395