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/29cb63f1-d2bc-46a4-8793-a1dd41ba95f9/call-ldsc/inputs/-261043604/ieu-b-4909.vcf.gz \
--ref-ld-chr /data/ref/eur_w_ld_chr/ \
--out /data/igd/ieu-b-4909/ldsc.txt \
--w-ld-chr /data/ref/eur_w_ld_chr/ 

Beginning analysis at Thu Mar  3 21:10:25 2022
Reading summary statistics from /data/cromwell-executions/qc/29cb63f1-d2bc-46a4-8793-a1dd41ba95f9/call-ldsc/inputs/-261043604/ieu-b-4909.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 21:11:13 2022
Total time elapsed: 47.62s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.5875,
    "inflation_factor": 0.9917,
    "mean_EFFECT": 0.0002,
    "n": "-Inf",
    "n_snps": 7247045,
    "n_clumped_hits": 0,
    "n_p_sig": 0,
    "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 2.333000e-04 1.415160e-01 -48.6654000 -5.225030e-02 -3.137000e-04 5.206750e-02 3.671970e+01 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA NA NA 9.902960e-02 1.245410e-01 0.0435152 5.190400e-02 7.212060e-02 1.270590e-01 9.069930e+01 ▇▁▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA NA NA 5.012275e-01 2.887856e-01 0.0000005 2.514299e-01 5.017796e-01 7.514516e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA NA NA 5.010609e-01 2.888859e-01 0.0000005 2.511424e-01 5.016165e-01 7.513817e-01 9.999995e-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 -0.0364031 0.195525 0.8523420 0.8523026 0.359860 0.7821490 NA
1 54676 rs2462492 C T -0.0337326 0.186849 0.8567721 0.8567334 0.388830 NA NA
1 86028 rs114608975 T C -0.5152540 0.343533 0.1339791 0.1336487 0.098238 0.0277556 NA
1 91536 rs6702460 G T 0.3488660 0.184182 0.0585100 0.0582068 0.453670 0.4207270 NA
1 234313 rs8179466 C T -0.1643860 0.321936 0.6097362 0.6096193 0.079244 NA NA
1 534192 rs6680723 C T -0.0225810 0.206698 0.9130299 0.9130071 0.240840 NA NA
1 546697 rs12025928 A G 0.0553198 0.249128 0.8243199 0.8242721 0.086871 NA NA
1 568800 rs375217967 G A -1.5552800 0.720835 0.0312076 0.0309583 0.016076 0.0778754 NA
1 569004 rs9285835 T C -0.0410916 0.424917 0.9229811 0.9229607 0.012532 NA NA
1 569624 rs6594035 T C 1.3055100 1.288990 0.3114039 0.3111479 0.011422 NA NA
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51219387 rs9616832 T C -0.0990246 0.1015930 0.3299476 0.3296998 0.073955 0.0654952 NA
22 51219704 rs147475742 G A -0.1735240 0.1466710 0.2370740 0.2367762 0.041917 0.0473243 NA
22 51220517 rs9616980 C G -0.1876150 0.2904980 0.5185397 0.5183835 0.011741 0.0027955 NA
22 51221190 rs369304721 G A -0.1845960 0.1394720 0.1859752 0.1856577 0.049718 NA NA
22 51221731 rs115055839 T C -0.1004370 0.1016240 0.3232503 0.3229961 0.073062 0.0625000 NA
22 51222100 rs114553188 G T 0.0347265 0.1009290 0.7308715 0.7307947 0.053551 0.0880591 NA
22 51223637 rs375798137 G A 0.0273375 0.1019370 0.7886186 0.7885605 0.053086 0.0788738 NA
22 51229805 rs9616985 T C -0.1010460 0.1017700 0.3210177 0.3207656 0.073123 0.0730831 NA
22 51232488 rs376461333 A G 0.1174930 0.2086500 0.5734915 0.5733597 0.020104 NA NA
22 51237063 rs3896457 T C 0.0857342 0.0571223 0.1337159 0.1333844 0.294910 0.2050720 NA

bcf preview

1   49298   rs10399793  T   C   .   PASS    AF=0.35986  ES:SE:LP:AF:ID  -0.0364031:0.195525:0.0693861:0.35986:rs10399793
1   54676   rs2462492   C   T   .   PASS    AF=0.38883  ES:SE:LP:AF:ID  -0.0337326:0.186849:0.0671347:0.38883:rs2462492
1   86028   rs114608975 T   C   .   PASS    AF=0.098238 ES:SE:LP:AF:ID  -0.515254:0.343533:0.872963:0.098238:rs114608975
1   91536   rs1251109649    G   T   .   PASS    AF=0.45367  ES:SE:LP:AF:ID  0.348866:0.184182:1.23277:0.45367:rs1251109649
1   234313  rs8179466   C   T   .   PASS    AF=0.079244 ES:SE:LP:AF:ID  -0.164386:0.321936:0.214858:0.079244:rs8179466
1   534192  rs6680723   C   T   .   PASS    AF=0.24084  ES:SE:LP:AF:ID  -0.022581:0.206698:0.039515:0.24084:rs6680723
1   546697  rs12025928  A   G   .   PASS    AF=0.086871 ES:SE:LP:AF:ID  0.0553198:0.249128:0.0839042:0.086871:rs12025928
1   568800  rs375217967 G   A   .   PASS    AF=0.016076 ES:SE:LP:AF:ID  -1.55528:0.720835:1.50574:0.016076:rs375217967
1   569004  rs9285835   T   C   .   PASS    AF=0.012532 ES:SE:LP:AF:ID  -0.0410916:0.424917:0.0348072:0.012532:rs9285835
1   569624  rs6594035   T   C   .   PASS    AF=0.011422 ES:SE:LP:AF:ID  1.30551:1.28899:0.506676:0.011422:rs6594035
1   693731  rs12238997  A   G   .   PASS    AF=0.12394  ES:SE:LP:AF:ID  0.119112:0.184622:0.284854:0.12394:rs12238997
1   705882  rs72631875  G   A   .   PASS    AF=0.071517 ES:SE:LP:AF:ID  -0.197747:0.259935:0.3497:0.071517:rs72631875
1   706368  rs963699400 A   G   .   PASS    AF=0.48937  ES:SE:LP:AF:ID  -0.135854:0.11029:0.660881:0.48937:rs963699400
1   714596  rs149887893 T   C   .   PASS    AF=0.036483 ES:SE:LP:AF:ID  -0.229174:0.492856:0.192435:0.036483:rs149887893
1   715265  rs12184267  C   T   .   PASS    AF=0.040536 ES:SE:LP:AF:ID  -0.277508:0.485901:0.245611:0.040536:rs12184267
1   715367  rs12184277  A   G   .   PASS    AF=0.040763 ES:SE:LP:AF:ID  -0.257395:0.486495:0.224119:0.040763:rs12184277
1   717485  rs12184279  C   A   .   PASS    AF=0.040352 ES:SE:LP:AF:ID  -0.259792:0.487391:0.226111:0.040352:rs12184279
1   717587  rs144155419 G   A   .   PASS    AF=0.016514 ES:SE:LP:AF:ID  -0.322222:0.556064:0.249948:0.016514:rs144155419
1   720381  rs116801199 G   T   .   PASS    AF=0.040909 ES:SE:LP:AF:ID  -0.240062:0.486214:0.206485:0.040909:rs116801199
1   721290  rs12565286  G   C   .   PASS    AF=0.041095 ES:SE:LP:AF:ID  -0.237752:0.486327:0.204089:0.041095:rs12565286
1   722670  rs116030099 T   C   .   PASS    AF=0.099265 ES:SE:LP:AF:ID  0.0288932:0.193403:0.0548886:0.099265:rs116030099
1   723891  rs2977670   G   C   .   PASS    AF=0.047367 ES:SE:LP:AF:ID  0.1521:0.382076:0.160739:0.047367:rs2977670
1   724849  rs12126395  C   A   .   PASS    AF=0.030038 ES:SE:LP:AF:ID  0.128428:0.528441:0.0925709:0.030038:rs12126395
1   725060  rs1445661281    A   T   .   PASS    AF=0.052781 ES:SE:LP:AF:ID  -0.641552:0.467632:0.7685:0.052781:rs1445661281
1   726794  rs28454925  C   G   .   PASS    AF=0.040513 ES:SE:LP:AF:ID  -0.271115:0.486364:0.238551:0.040513:rs28454925
1   729632  rs116720794 C   T   .   PASS    AF=0.040678 ES:SE:LP:AF:ID  -0.304207:0.487395:0.273534:0.040678:rs116720794
1   729679  rs4951859   C   G   .   PASS    AF=0.16855  ES:SE:LP:AF:ID  -0.0694594:0.16732:0.16868:0.16855:rs4951859
1   730087  rs148120343 T   C   .   PASS    AF=0.053483 ES:SE:LP:AF:ID  0.421692:0.320942:0.723102:0.053483:rs148120343
1   731453  rs186002080 G   A   .   PASS    AF=0.015304 ES:SE:LP:AF:ID  0.272755:0.522245:0.220691:0.015304:rs186002080
1   731718  rs58276399  T   C   .   PASS    AF=0.13048  ES:SE:LP:AF:ID  0.128267:0.176489:0.330176:0.13048:rs58276399
1   732989  rs369030935 C   T   .   PASS    AF=0.021775 ES:SE:LP:AF:ID  -0.154639:0.355909:0.177812:0.021775:rs369030935
1   734349  rs141242758 T   C   .   PASS    AF=0.12935  ES:SE:LP:AF:ID  0.126941:0.175984:0.327081:0.12935:rs141242758
1   736289  rs1254887344    T   A   .   PASS    AF=0.13925  ES:SE:LP:AF:ID  0.0931202:0.182022:0.215341:0.13925:rs1254887344
1   752478  rs146277091 G   A   .   PASS    AF=0.040427 ES:SE:LP:AF:ID  -0.300302:0.483993:0.271567:0.040427:rs146277091
1   752566  rs3094315   G   A   .   PASS    AF=0.17073  ES:SE:LP:AF:ID  -0.158198:0.161262:0.485661:0.17073:rs3094315
1   752721  rs3131972   A   G   .   PASS    AF=0.17249  ES:SE:LP:AF:ID  -0.137599:0.161288:0.404722:0.17249:rs3131972
1   753405  rs3115860   C   A   .   PASS    AF=0.13929  ES:SE:LP:AF:ID  -0.205231:0.164872:0.67057:0.13929:rs3115860
1   753541  rs1388595942    G   A   .   PASS    AF=0.13958  ES:SE:LP:AF:ID  0.1979:0.16443:0.640045:0.13958:rs1388595942
1   754063  rs12184312  G   T   .   PASS    AF=0.040063 ES:SE:LP:AF:ID  -0.437792:0.483455:0.437227:0.040063:rs12184312
1   754105  rs12184325  C   T   .   PASS    AF=0.040029 ES:SE:LP:AF:ID  -0.451754:0.483893:0.454995:0.040029:rs12184325
1   754182  rs3131969   A   G   .   PASS    AF=0.14121  ES:SE:LP:AF:ID  -0.204031:0.164542:0.666988:0.14121:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.14109  ES:SE:LP:AF:ID  -0.204435:0.164523:0.668927:0.14109:rs3131968
1   754211  rs12184313  G   A   .   PASS    AF=0.040203 ES:SE:LP:AF:ID  -0.437563:0.483759:0.436571:0.040203:rs12184313
1   754334  rs3131967   T   C   .   PASS    AF=0.14107  ES:SE:LP:AF:ID  -0.205225:0.164527:0.672496:0.14107:rs3131967
1   754503  rs3115859   G   A   .   PASS    AF=0.17227  ES:SE:LP:AF:ID  -0.13599:0.161752:0.397169:0.17227:rs3115859
1   754629  rs10454459  A   G   .   PASS    AF=0.040591 ES:SE:LP:AF:ID  -0.447268:0.48247:0.450823:0.040591:rs10454459
1   754964  rs3131966   C   T   .   PASS    AF=0.1717   ES:SE:LP:AF:ID  -0.134463:0.161814:0.391264:0.1717:rs3131966
1   755240  rs181660517 T   G   .   PASS    AF=0.011824 ES:SE:LP:AF:ID  -0.214264:0.767761:0.107768:0.011824:rs181660517
1   755775  rs3131965   A   G   .   PASS    AF=0.1692   ES:SE:LP:AF:ID  -0.138274:0.162228:0.404242:0.1692:rs3131965
1   755890  rs1280367067    A   T   .   PASS    AF=0.13948  ES:SE:LP:AF:ID  -0.202256:0.164764:0.657739:0.13948:rs1280367067