Summary

Summary {data-width=650}

Manhattan plot

manhattan_plot

manhattan_plot

QQ plot

qq_plot

qq_plot

AF plot

af_plot

af_plot

P-Z plot

pz_plot

pz_plot

beta_std 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 /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-12621/UKB-b-12621_data.vcf.gz \
--ref-ld-chr ../reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-12621/ldsc.txt \
--w-ld-chr ../reference/eur_w_ld_chr/ 

Beginning analysis at Thu Oct 17 14:42:05 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-12621/UKB-b-12621_data.vcf.gz ...
Read summary statistics for 8826928 SNPs.
Dropped 8018 SNPs with duplicated rs numbers.
Reading reference panel LD Score from ../reference/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 ../reference/eur_w_ld_chr/[1-22] ...
Read regression weight LD Scores for 1290028 SNPs.
After merging with reference panel LD, 1286506 SNPs remain.
After merging with regression SNP LD, 1286506 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0194 (0.0025)
Lambda GC: 1.1165
Mean Chi^2: 1.119
Intercept: 1.0251 (0.0076)
Ratio: 0.211 (0.0635)
Analysis finished at Thu Oct 17 14:43:43 2019
Total time elapsed: 1.0m:38.58s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.947,
    "inflation_factor": 1.0966,
    "mean_EFFECT": 0.0001,
    "n": "-Inf",
    "n_snps": 9851866,
    "n_clumped_hits": 0,
    "n_p_sig": 0,
    "n_mono": 0,
    "n_ns": 0,
    "n_mac": 0,
    "is_snpid_unique": true,
    "n_miss_EFFECT": 0,
    "n_miss_SE": 0,
    "n_miss_PVAL": 0,
    "n_miss_AF": 0,
    "n_miss_AF_reference": 87593,
    "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": 1286506,
    "ldsc_nsnp_merge_regression_ld": 1286506,
    "ldsc_observed_scale_h2_beta": 0.0194,
    "ldsc_observed_scale_h2_se": 0.0025,
    "ldsc_intercept_beta": 1.0251,
    "ldsc_intercept_se": 0.0076,
    "ldsc_lambda_gc": 1.1165,
    "ldsc_mean_chisq": 1.119,
    "ldsc_ratio": 0.2109
}

Flags

name value
af_correlation FALSE
inflation_factor FALSE
n TRUE
is_snpid_non_unique FALSE
mean_EFFECT_nonfinite FALSE
mean_EFFECT_05 FALSE
mean_EFFECT_01 FALSE
mean_chisq FALSE
n_p_sig FALSE
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 logical.mean logical.count numeric.mean numeric.sd numeric.p0 numeric.p25 numeric.p50 numeric.p75 numeric.p100 numeric.hist
character ID 0 1.0000000 3 58 0 8818947 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 8826928 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 8.648420e+00 5.760131e+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 7.877480e+07 5.634475e+07 828.0000000 3.240912e+07 6.932878e+07 1.145535e+08 2.492385e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA NA NA 5.690000e-05 4.240300e-03 -0.0434007 -1.703500e-03 2.580000e-05 1.769100e-03 4.307970e-02 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA NA NA 3.374700e-03 2.387200e-03 0.0012781 1.517100e-03 2.281800e-03 4.603300e-03 2.293240e-02 ▇▂▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA NA NA 4.861277e-01 2.924998e-01 0.0000005 2.300001e-01 4.799997e-01 7.400005e-01 1.000000e+00 ▇▇▇▇▆
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA NA NA 4.861285e-01 2.924736e-01 0.0000005 2.296690e-01 4.810607e-01 7.398244e-01 9.999999e-01 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA NA NA 2.242725e-01 2.589918e-01 0.0044280 2.260200e-02 1.071800e-01 3.543450e-01 9.955720e-01 ▇▂▁▁▁
numeric AF_reference 87593 0.9900766 NA NA NA NA NA NA NA 2.242624e-01 2.509356e-01 0.0000000 1.996810e-02 1.242010e-01 3.520370e-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 -0.0017455 0.0023563 0.4600002 0.4588314 0.623412 0.7821490 NA
1 54676 rs2462492 C T -0.0018993 0.0023292 0.4100001 0.4148341 0.401010 NA NA
1 86028 rs114608975 T C 0.0038042 0.0037364 0.3100002 0.3086099 0.103475 0.0277556 NA
1 91536 rs6702460 G T -0.0044573 0.0022949 0.0519996 0.0521016 0.457114 0.4207270 NA
1 234313 rs8179466 C T 0.0011096 0.0045380 0.8100000 0.8068322 0.074374 NA NA
1 534192 rs6680723 C T -0.0001613 0.0026224 0.9500000 0.9509690 0.241180 NA NA
1 546697 rs12025928 A G -0.0010990 0.0032707 0.7400005 0.7368544 0.913499 NA NA
1 693731 rs12238997 A G 0.0023716 0.0021948 0.2800000 0.2798807 0.116801 0.1417730 NA
1 705882 rs72631875 G A 0.0000780 0.0032235 0.9800000 0.9806877 0.067084 0.0315495 NA
1 706368 rs55727773 A G -0.0029949 0.0016274 0.0659994 0.0657296 0.515047 0.2751600 NA
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51219006 rs28729663 G A -0.0012853 0.0019678 0.5099998 0.5136506 0.137944 0.2052720 NA
22 51219387 rs9616832 T C -0.0003933 0.0025535 0.8800001 0.8775837 0.073607 0.0654952 NA
22 51219704 rs147475742 G A -0.0018140 0.0034214 0.5999997 0.5959866 0.041865 0.0473243 NA
22 51221190 rs369304721 G A -0.0034740 0.0034182 0.3100002 0.3094806 0.049591 NA NA
22 51221731 rs115055839 T C -0.0005014 0.0025544 0.8400000 0.8443942 0.073142 0.0625000 NA
22 51222100 rs114553188 G T -0.0023357 0.0030007 0.4400003 0.4363501 0.054671 0.0880591 NA
22 51223637 rs375798137 G A -0.0023462 0.0030151 0.4400003 0.4364830 0.054305 0.0788738 NA
22 51229805 rs9616985 T C -0.0002950 0.0025635 0.9100000 0.9083886 0.073010 0.0730831 NA
22 51232488 rs376461333 A G 0.0030247 0.0060322 0.6200004 0.6160739 0.020054 NA NA
22 51237063 rs3896457 T C -0.0019390 0.0015658 0.2200002 0.2156001 0.297872 0.2050720 NA

bcf preview

1   49298   rs10399793  T   C   .   PASS    AF=0.623412 ES:SE:LP:AF:ID  -0.00174546:0.00235627:0.337242:0.623412:rs10399793
1   54676   rs2462492   C   T   .   PASS    AF=0.40101  ES:SE:LP:AF:ID  -0.0018993:0.00232924:0.387216:0.40101:rs2462492
1   86028   rs114608975 T   C   .   PASS    AF=0.103475 ES:SE:LP:AF:ID  0.00380419:0.0037364:0.508638:0.103475:rs114608975
1   91536   rs6702460   G   T   .   PASS    AF=0.457114 ES:SE:LP:AF:ID  -0.00445731:0.00229487:1.284:0.457114:rs6702460
1   234313  rs8179466   C   T   .   PASS    AF=0.074374 ES:SE:LP:AF:ID  0.00110961:0.00453801:0.091515:0.074374:rs8179466
1   534192  rs6680723   C   T   .   PASS    AF=0.24118  ES:SE:LP:AF:ID  -0.000161252:0.00262241:0.0222764:0.24118:rs6680723
1   546697  rs12025928  A   G   .   PASS    AF=0.913499 ES:SE:LP:AF:ID  -0.00109902:0.00327068:0.130768:0.913499:rs12025928
1   693731  rs12238997  A   G   .   PASS    AF=0.116801 ES:SE:LP:AF:ID  0.00237163:0.00219476:0.552842:0.116801:rs12238997
1   705882  rs72631875  G   A   .   PASS    AF=0.067084 ES:SE:LP:AF:ID  7.80308e-05:0.00322351:0.00877392:0.067084:rs72631875
1   706368  rs12029736  A   G   .   PASS    AF=0.515047 ES:SE:LP:AF:ID  -0.0029949:0.00162743:1.18046:0.515047:rs12029736
1   714596  rs149887893 T   C   .   PASS    AF=0.032831 ES:SE:LP:AF:ID  0.00143182:0.00411505:0.136677:0.032831:rs149887893
1   715265  rs12184267  C   T   .   PASS    AF=0.036412 ES:SE:LP:AF:ID  0.00106989:0.00374006:0.113509:0.036412:rs12184267
1   715367  rs12184277  A   G   .   PASS    AF=0.036522 ES:SE:LP:AF:ID  0.000570228:0.00372663:0.0555173:0.036522:rs12184277
1   717485  rs12184279  C   A   .   PASS    AF=0.03621  ES:SE:LP:AF:ID  0.000523545:0.00375431:0.05061:0.03621:rs12184279
1   717587  rs144155419 G   A   .   PASS    AF=0.016368 ES:SE:LP:AF:ID  -0.00105245:0.00576436:0.0655015:0.016368:rs144155419
1   720381  rs116801199 G   T   .   PASS    AF=0.036744 ES:SE:LP:AF:ID  0.000446142:0.00371276:0.0457575:0.036744:rs116801199
1   721290  rs12565286  G   C   .   PASS    AF=0.036836 ES:SE:LP:AF:ID  0.000332018:0.00370037:0.0315171:0.036836:rs12565286
1   722670  rs116030099 T   C   .   PASS    AF=0.101124 ES:SE:LP:AF:ID  -0.00177964:0.00268723:0.29243:0.101124:rs116030099
1   723891  rs2977670   G   C   .   PASS    AF=0.959346 ES:SE:LP:AF:ID  -0.0017399:0.00356792:0.200659:0.959346:rs2977670
1   724849  rs12126395  C   A   .   PASS    AF=0.031442 ES:SE:LP:AF:ID  -0.00467432:0.00643177:0.327902:0.031442:rs12126395
1   725060  rs865924913 A   T   .   PASS    AF=0.05341  ES:SE:LP:AF:ID  0.000788422:0.00512203:0.0555173:0.05341:rs865924913
1   726794  rs28454925  C   G   .   PASS    AF=0.036382 ES:SE:LP:AF:ID  4.11049e-06:0.00372201:-0:0.036382:rs28454925
1   729632  rs116720794 C   T   .   PASS    AF=0.036705 ES:SE:LP:AF:ID  0.000429152:0.00368839:0.0409586:0.036705:rs116720794
1   729679  rs4951859   C   G   .   PASS    AF=0.842992 ES:SE:LP:AF:ID  -0.00218526:0.0019052:0.60206:0.842992:rs4951859
1   730087  rs148120343 T   C   .   PASS    AF=0.056043 ES:SE:LP:AF:ID  -0.00046632:0.00308259:0.0555173:0.056043:rs148120343
1   731718  rs58276399  T   C   .   PASS    AF=0.122786 ES:SE:LP:AF:ID  0.0022079:0.00208181:0.537602:0.122786:rs58276399
1   732989  rs369030935 C   T   .   PASS    AF=0.025546 ES:SE:LP:AF:ID  -0.00363862:0.00514522:0.318759:0.025546:rs369030935
1   734349  rs141242758 T   C   .   PASS    AF=0.122012 ES:SE:LP:AF:ID  0.00206271:0.00208269:0.49485:0.122012:rs141242758
1   736289  rs79010578  T   A   .   PASS    AF=0.132638 ES:SE:LP:AF:ID  0.00214047:0.00205433:0.522879:0.132638:rs79010578
1   736689  rs181876450 T   C   .   PASS    AF=0.011111 ES:SE:LP:AF:ID  -0.00816939:0.00748385:0.552842:0.011111:rs181876450
1   740284  rs61770167  C   T   .   PASS    AF=0.005775 ES:SE:LP:AF:ID  0.016052:0.00955862:1.03152:0.005775:rs61770167
1   752478  rs146277091 G   A   .   PASS    AF=0.036617 ES:SE:LP:AF:ID  0.000686193:0.00365151:0.0705811:0.036617:rs146277091
1   752566  rs3094315   G   A   .   PASS    AF=0.838708 ES:SE:LP:AF:ID  -0.00202065:0.00184422:0.568636:0.838708:rs3094315
1   752721  rs3131972   A   G   .   PASS    AF=0.83833  ES:SE:LP:AF:ID  -0.00224631:0.00184237:0.657577:0.83833:rs3131972
1   753405  rs3115860   C   A   .   PASS    AF=0.869358 ES:SE:LP:AF:ID  -0.00239644:0.00197498:0.657577:0.869358:rs3115860
1   753541  rs2073813   G   A   .   PASS    AF=0.130307 ES:SE:LP:AF:ID  0.00250701:0.00197922:0.677781:0.130307:rs2073813
1   754063  rs12184312  G   T   .   PASS    AF=0.037091 ES:SE:LP:AF:ID  -0.000275421:0.00359068:0.0268721:0.037091:rs12184312
1   754105  rs12184325  C   T   .   PASS    AF=0.037352 ES:SE:LP:AF:ID  -0.000439233:0.00356683:0.0457575:0.037352:rs12184325
1   754182  rs3131969   A   G   .   PASS    AF=0.868689 ES:SE:LP:AF:ID  -0.00258125:0.00197133:0.721246:0.868689:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.868764 ES:SE:LP:AF:ID  -0.00253986:0.00197204:0.69897:0.868764:rs3131968
1   754211  rs12184313  G   A   .   PASS    AF=0.0373   ES:SE:LP:AF:ID  -0.000461475:0.00358268:0.0457575:0.0373:rs12184313
1   754334  rs3131967   T   C   .   PASS    AF=0.868689 ES:SE:LP:AF:ID  -0.00257903:0.00197126:0.721246:0.868689:rs3131967
1   754433  rs150578204 G   A   .   PASS    AF=0.005072 ES:SE:LP:AF:ID  0.00629738:0.0101989:0.267606:0.005072:rs150578204
1   754458  rs142682604 G   T   .   PASS    AF=0.005041 ES:SE:LP:AF:ID  0.00594893:0.0102231:0.251812:0.005041:rs142682604
1   754503  rs3115859   G   A   .   PASS    AF=0.837777 ES:SE:LP:AF:ID  -0.00212805:0.00183715:0.60206:0.837777:rs3115859
1   754629  rs10454459  A   G   .   PASS    AF=0.037311 ES:SE:LP:AF:ID  -0.000374744:0.00358811:0.0362122:0.037311:rs10454459
1   754964  rs3131966   C   T   .   PASS    AF=0.838412 ES:SE:LP:AF:ID  -0.00216178:0.0018423:0.619789:0.838412:rs3131966
1   755240  rs181660517 T   G   .   PASS    AF=0.01384  ES:SE:LP:AF:ID  -0.00630661:0.00641508:0.481486:0.01384:rs181660517
1   755435  rs184270342 T   G   .   PASS    AF=0.005571 ES:SE:LP:AF:ID  0.0218885:0.00990973:1.56864:0.005571:rs184270342
1   755775  rs3131965   A   G   .   PASS    AF=0.839548 ES:SE:LP:AF:ID  -0.00213354:0.00186696:0.60206:0.839548:rs3131965