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/dda97465-709c-4b94-8cfe-d54bb66356b5/call-ldsc/inputs/-261043606/ieu-b-4907.vcf.gz \
--ref-ld-chr /data/ref/eur_w_ld_chr/ \
--out /data/igd/ieu-b-4907/ldsc.txt \
--w-ld-chr /data/ref/eur_w_ld_chr/ 

Beginning analysis at Thu Mar  3 20:57:58 2022
Reading summary statistics from /data/cromwell-executions/qc/dda97465-709c-4b94-8cfe-d54bb66356b5/call-ldsc/inputs/-261043606/ieu-b-4907.vcf.gz ...
Read summary statistics for 0 SNPs.
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.
Traceback (most recent call last):
  File "./ldsc/ldsc.py", line 647, in <module>
    sumstats.estimate_h2(args, log)
  File "/ldsc/ldscore/sumstats.py", line 330, in estimate_h2
    args, log, args.h2)
  File "/ldsc/ldscore/sumstats.py", line 252, in _read_ld_sumstats
    sumstats = _merge_and_log(ref_ld, sumstats, 'reference panel LD', log)
  File "/ldsc/ldscore/sumstats.py", line 238, in _merge_and_log
    raise ValueError(msg.format(N=len(sumstats), F=noun))
ValueError: After merging with reference panel LD, 0 SNPs remain.

Analysis finished at Thu Mar  3 20:58:47 2022
Total time elapsed: 49.03s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.5875,
    "inflation_factor": 1.01,
    "mean_EFFECT": -0.0003,
    "n": "-Inf",
    "n_snps": 7247045,
    "n_clumped_hits": 2,
    "n_p_sig": 17,
    "n_mono": 0,
    "n_ns": 0,
    "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": 75735,
    "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": 0,
    "ldsc_nsnp_merge_regression_ld": "NA",
    "ldsc_observed_scale_h2_beta": "NA",
    "ldsc_observed_scale_h2_se": "NA",
    "ldsc_intercept_beta": "NA",
    "ldsc_intercept_se": "NA",
    "ldsc_lambda_gc": "NA",
    "ldsc_mean_chisq": "NA",
    "ldsc_ratio": "NA"
}

Flags

name value
af_correlation TRUE
inflation_factor FALSE
n TRUE
is_snpid_non_unique TRUE
mean_EFFECT_nonfinite FALSE
mean_EFFECT_05 FALSE
mean_EFFECT_01 FALSE
mean_chisq NA
n_p_sig FALSE
miss_EFFECT FALSE
miss_SE FALSE
miss_PVAL FALSE
ldsc_ratio NA
ldsc_intercept_beta NA
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 132 0.9999818 3 58 0 7242977 0 NA NA 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 NA NA
character ALT 0 1.0000000 1 1 0 4 0 NA NA NA NA NA NA NA NA NA NA
logical N 7247045 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 8.656779e+00 5.769716e+00 1.0000000 4.000000e+00 8.000000e+00 1.300000e+01 2.200000e+01 ▇▅▅▂▂
numeric POS 0 1.0000000 NA NA NA NA NA NA NA 7.891593e+07 5.635127e+07 828.0000000 3.250802e+07 6.937929e+07 1.147034e+08 2.492385e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA NA NA -2.684000e-04 2.013050e-01 -52.0888000 -6.814260e-02 1.443000e-04 6.769030e-02 1.175380e+02 ▁▇▁▁▁
numeric SE 0 1.0000000 NA NA NA NA NA NA NA 1.284430e-01 1.661830e-01 0.0549365 6.686720e-02 9.290230e-02 1.636230e-01 1.125050e+02 ▇▁▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA NA NA 4.988785e-01 2.885376e-01 0.0000000 2.489958e-01 4.978689e-01 7.484538e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA NA NA 4.985698e-01 2.887226e-01 0.0000000 2.484630e-01 4.975659e-01 7.483226e-01 9.999998e-01 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA NA NA 1.683323e-01 1.474397e-01 0.0096754 3.631300e-02 1.193500e-01 2.811500e-01 5.000000e-01 ▇▃▂▂▂
numeric AF_reference 75735 0.9895495 NA NA NA NA NA NA NA 2.455140e-01 2.513943e-01 0.0000000 4.053510e-02 1.529550e-01 3.829870e-01 1.000000e+00 ▇▃▂▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 49298 rs200943160 T C -0.1103960 0.263136 0.6749972 0.6748217 0.359860 0.7821490 NA
1 54676 rs2462492 C T -0.1379940 0.276247 0.6176167 0.6174052 0.388830 NA NA
1 86028 rs114608975 T C 0.4612370 0.402975 0.2529117 0.2523833 0.098238 0.0277556 NA
1 91536 rs6702460 G T 0.0612125 0.252241 0.8083531 0.8082574 0.453670 0.4207270 NA
1 234313 rs8179466 C T -0.8195760 0.540956 0.1303701 0.1297595 0.079244 NA NA
1 534192 rs6680723 C T -0.4739710 0.308502 0.1250610 0.1244494 0.240840 NA NA
1 546697 rs12025928 A G -0.3862510 0.323809 0.2334812 0.2329336 0.086871 NA NA
1 568800 rs375217967 G A 0.9182330 0.586375 0.1179720 0.1173607 0.016076 0.0778754 NA
1 569004 rs9285835 T C 1.1596300 1.648320 0.4820455 0.4817303 0.012532 NA NA
1 569624 rs6594035 T C -0.8456200 2.154940 0.6949171 0.6947553 0.011422 NA NA
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51219387 rs9616832 T C -0.1020350 0.1385640 0.4618362 0.4615028 0.073955 0.0654952 NA
22 51219704 rs147475742 G A -0.2500140 0.1854250 0.1781439 0.1775524 0.041917 0.0473243 NA
22 51220517 rs9616980 C G -0.1036080 0.4012010 0.7963211 0.7962181 0.011741 0.0027955 NA
22 51221190 rs369304721 G A -0.1707170 0.1828030 0.3507979 0.3503632 0.049718 NA NA
22 51221731 rs115055839 T C -0.1066740 0.1388070 0.4425374 0.4421867 0.073062 0.0625000 NA
22 51222100 rs114553188 G T -0.0185057 0.1318700 0.8884510 0.8883970 0.053551 0.0880591 NA
22 51223637 rs375798137 G A -0.0339172 0.1332510 0.7991820 0.7990814 0.053086 0.0788738 NA
22 51229805 rs9616985 T C -0.1081110 0.1390340 0.4371696 0.4368127 0.073123 0.0730831 NA
22 51232488 rs376461333 A G 0.2732280 0.2658980 0.3046337 0.3041536 0.020104 NA NA
22 51237063 rs3896457 T C 0.0016740 0.0748836 0.9821740 0.9821652 0.294910 0.2050720 NA

bcf preview

1   49298   rs10399793  T   C   .   PASS    AF=0.35986  ES:SE:LP:AF:ID  -0.110396:0.263136:0.170698:0.35986:rs10399793
1   54676   rs2462492   C   T   .   PASS    AF=0.38883  ES:SE:LP:AF:ID  -0.137994:0.276247:0.209281:0.38883:rs2462492
1   86028   rs114608975 T   C   .   PASS    AF=0.098238 ES:SE:LP:AF:ID  0.461237:0.402975:0.597031:0.098238:rs114608975
1   91536   rs1251109649    G   T   .   PASS    AF=0.45367  ES:SE:LP:AF:ID  0.0612125:0.252241:0.0923989:0.45367:rs1251109649
1   234313  rs8179466   C   T   .   PASS    AF=0.079244 ES:SE:LP:AF:ID  -0.819576:0.540956:0.884822:0.079244:rs8179466
1   534192  rs6680723   C   T   .   PASS    AF=0.24084  ES:SE:LP:AF:ID  -0.473971:0.308502:0.902878:0.24084:rs6680723
1   546697  rs12025928  A   G   .   PASS    AF=0.086871 ES:SE:LP:AF:ID  -0.386251:0.323809:0.631748:0.086871:rs12025928
1   568800  rs375217967 G   A   .   PASS    AF=0.016076 ES:SE:LP:AF:ID  0.918233:0.586375:0.928221:0.016076:rs375217967
1   569004  rs9285835   T   C   .   PASS    AF=0.012532 ES:SE:LP:AF:ID  1.15963:1.64832:0.316912:0.012532:rs9285835
1   569624  rs6594035   T   C   .   PASS    AF=0.011422 ES:SE:LP:AF:ID  -0.84562:2.15494:0.158067:0.011422:rs6594035
1   693731  rs12238997  A   G   .   PASS    AF=0.12394  ES:SE:LP:AF:ID  -0.0155442:0.224117:0.0246914:0.12394:rs12238997
1   705882  rs72631875  G   A   .   PASS    AF=0.071517 ES:SE:LP:AF:ID  0.0916394:0.31414:0.113159:0.071517:rs72631875
1   706368  rs963699400 A   G   .   PASS    AF=0.48937  ES:SE:LP:AF:ID  0.00765467:0.146483:0.0184781:0.48937:rs963699400
1   714596  rs149887893 T   C   .   PASS    AF=0.036483 ES:SE:LP:AF:ID  -1.00351:0.978715:0.514727:0.036483:rs149887893
1   715265  rs12184267  C   T   .   PASS    AF=0.040536 ES:SE:LP:AF:ID  -0.981787:0.916201:0.54606:0.040536:rs12184267
1   715367  rs12184277  A   G   .   PASS    AF=0.040763 ES:SE:LP:AF:ID  -0.826432:0.91864:0.433282:0.040763:rs12184277
1   717485  rs12184279  C   A   .   PASS    AF=0.040352 ES:SE:LP:AF:ID  -0.847784:0.915064:0.450222:0.040352:rs12184279
1   717587  rs144155419 G   A   .   PASS    AF=0.016514 ES:SE:LP:AF:ID  1.68761:0.893374:1.22587:0.016514:rs144155419
1   720381  rs116801199 G   T   .   PASS    AF=0.040909 ES:SE:LP:AF:ID  -0.902552:0.916713:0.487709:0.040909:rs116801199
1   721290  rs12565286  G   C   .   PASS    AF=0.041095 ES:SE:LP:AF:ID  -0.96135:0.920952:0.527192:0.041095:rs12565286
1   722670  rs116030099 T   C   .   PASS    AF=0.099265 ES:SE:LP:AF:ID  0.022022:0.278953:0.0282108:0.099265:rs116030099
1   723891  rs2977670   G   C   .   PASS    AF=0.047367 ES:SE:LP:AF:ID  -0.462048:0.550366:0.396248:0.047367:rs2977670
1   724849  rs12126395  C   A   .   PASS    AF=0.030038 ES:SE:LP:AF:ID  0.162691:0.635268:0.0980096:0.030038:rs12126395
1   725060  rs1445661281    A   T   .   PASS    AF=0.052781 ES:SE:LP:AF:ID  0.379049:0.809319:0.194005:0.052781:rs1445661281
1   726794  rs28454925  C   G   .   PASS    AF=0.040513 ES:SE:LP:AF:ID  -0.843794:0.913827:0.448246:0.040513:rs28454925
1   729632  rs116720794 C   T   .   PASS    AF=0.040678 ES:SE:LP:AF:ID  -1.18082:0.929252:0.689523:0.040678:rs116720794
1   729679  rs4951859   C   G   .   PASS    AF=0.16855  ES:SE:LP:AF:ID  -0.0216091:0.216614:0.0359408:0.16855:rs4951859
1   730087  rs148120343 T   C   .   PASS    AF=0.053483 ES:SE:LP:AF:ID  -0.320961:0.383296:0.394942:0.053483:rs148120343
1   731453  rs186002080 G   A   .   PASS    AF=0.015304 ES:SE:LP:AF:ID  0.132253:0.645656:0.076869:0.015304:rs186002080
1   731718  rs58276399  T   C   .   PASS    AF=0.13048  ES:SE:LP:AF:ID  -0.0483972:0.224352:0.081293:0.13048:rs58276399
1   732989  rs369030935 C   T   .   PASS    AF=0.021775 ES:SE:LP:AF:ID  -0.29806:0.344411:0.412052:0.021775:rs369030935
1   734349  rs141242758 T   C   .   PASS    AF=0.12935  ES:SE:LP:AF:ID  -0.0318984:0.224165:0.0521253:0.12935:rs141242758
1   736289  rs1254887344    T   A   .   PASS    AF=0.13925  ES:SE:LP:AF:ID  -0.249301:0.226323:0.566744:0.13925:rs1254887344
1   752478  rs146277091 G   A   .   PASS    AF=0.040427 ES:SE:LP:AF:ID  -0.794175:0.927484:0.406441:0.040427:rs146277091
1   752566  rs3094315   G   A   .   PASS    AF=0.17073  ES:SE:LP:AF:ID  -0.118833:0.207713:0.246032:0.17073:rs3094315
1   752721  rs3131972   A   G   .   PASS    AF=0.17249  ES:SE:LP:AF:ID  -0.101699:0.20801:0.204044:0.17249:rs3131972
1   753405  rs3115860   C   A   .   PASS    AF=0.13929  ES:SE:LP:AF:ID  -0.177966:0.207673:0.406858:0.13929:rs3115860
1   753541  rs1388595942    G   A   .   PASS    AF=0.13958  ES:SE:LP:AF:ID  0.114658:0.208765:0.234262:0.13958:rs1388595942
1   754063  rs12184312  G   T   .   PASS    AF=0.040063 ES:SE:LP:AF:ID  -0.944349:0.936222:0.503625:0.040063:rs12184312
1   754105  rs12184325  C   T   .   PASS    AF=0.040029 ES:SE:LP:AF:ID  -1.06643:0.938793:0.590911:0.040029:rs12184325
1   754182  rs3131969   A   G   .   PASS    AF=0.14121  ES:SE:LP:AF:ID  -0.169415:0.208251:0.380596:0.14121:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.14109  ES:SE:LP:AF:ID  -0.169569:0.20825:0.381039:0.14109:rs3131968
1   754211  rs12184313  G   A   .   PASS    AF=0.040203 ES:SE:LP:AF:ID  -0.91995:0.93859:0.484821:0.040203:rs12184313
1   754334  rs3131967   T   C   .   PASS    AF=0.14107  ES:SE:LP:AF:ID  -0.168055:0.208273:0.376652:0.14107:rs3131967
1   754503  rs3115859   G   A   .   PASS    AF=0.17227  ES:SE:LP:AF:ID  -0.106179:0.207318:0.215552:0.17227:rs3115859
1   754629  rs10454459  A   G   .   PASS    AF=0.040591 ES:SE:LP:AF:ID  -0.835193:0.934755:0.429444:0.040591:rs10454459
1   754964  rs3131966   C   T   .   PASS    AF=0.1717   ES:SE:LP:AF:ID  -0.117707:0.207195:0.243962:0.1717:rs3131966
1   755240  rs181660517 T   G   .   PASS    AF=0.011824 ES:SE:LP:AF:ID  -1.6361:0.912039:1.13422:0.011824:rs181660517
1   755775  rs3131965   A   G   .   PASS    AF=0.1692   ES:SE:LP:AF:ID  -0.118384:0.207905:0.244641:0.1692:rs3131965
1   755890  rs1280367067    A   T   .   PASS    AF=0.13948  ES:SE:LP:AF:ID  -0.17506:0.206967:0.400078:0.13948:rs1280367067