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 /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-4886/UKB-b-4886_data.vcf.gz \
--ref-ld-chr ../reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-4886/ldsc.txt \
--w-ld-chr ../reference/eur_w_ld_chr/ 

Beginning analysis at Thu Oct 17 14:44:47 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-4886/UKB-b-4886_data.vcf.gz ...
Read summary statistics for 9851866 SNPs.
Dropped 14738 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, 1289166 SNPs remain.
After merging with regression SNP LD, 1289166 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0406 (0.0019)
Lambda GC: 1.3123
Mean Chi^2: 1.3777
Intercept: 1.0211 (0.0077)
Ratio: 0.0558 (0.0203)
Analysis finished at Thu Oct 17 14:46:22 2019
Total time elapsed: 1.0m:35.66s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9499,
    "inflation_factor": 1.1999,
    "mean_EFFECT": -0.0001,
    "n": "-Inf",
    "n_snps": 9851866,
    "n_clumped_hits": 17,
    "n_p_sig": 609,
    "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": 184849,
    "n_est": "NA",
    "ratio_se_n": "NA",
    "mean_diff": "NaN",
    "ratio_diff": "NaN",
    "sd_y_est1": "NA",
    "sd_y_est2": "NA",
    "r2_sum1": 0,
    "r2_sum2": 0,
    "r2_sum3": 0,
    "r2_sum4": 0,
    "ldsc_nsnp_merge_refpanel_ld": 1289166,
    "ldsc_nsnp_merge_regression_ld": 1289166,
    "ldsc_observed_scale_h2_beta": 0.0406,
    "ldsc_observed_scale_h2_se": 0.0019,
    "ldsc_intercept_beta": 1.0211,
    "ldsc_intercept_se": 0.0077,
    "ldsc_lambda_gc": 1.3123,
    "ldsc_mean_chisq": 1.3777,
    "ldsc_ratio": 0.0559
}

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 TRUE
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 9837196 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 9851866 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 8.622825e+00 5.748290e+00 1.0000000 4.000000e+00 8.000000e+00 1.300000e+01 2.200000e+01 <U+2587><U+2585><U+2583><U+2582><U+2582>
numeric POS 0 1.0000000 NA NA NA NA NA NA NA 7.886027e+07 5.628334e+07 828.0000000 3.259061e+07 6.948835e+07 1.145912e+08 2.492385e+08 <U+2587><U+2586><U+2585><U+2582><U+2581>
numeric EFFECT 0 1.0000000 NA NA NA NA NA NA NA -7.040000e-05 1.972190e-02 -0.2962960 -6.410900e-03 -1.450000e-05 6.395900e-03 2.969910e-01 <U+2581><U+2581><U+2587><U+2581><U+2581>
numeric SE 0 1.0000000 NA NA NA NA NA NA NA 1.393760e-02 1.319350e-02 0.0038999 4.774200e-03 8.005700e-03 1.847250e-02 2.049010e-01 <U+2587><U+2581><U+2581><U+2581><U+2581>
numeric PVAL 0 1.0000000 NA NA NA NA NA NA NA 4.691626e-01 2.974908e-01 0.0000000 2.000000e-01 4.600002e-01 7.300002e-01 1.000000e+00 <U+2587><U+2586><U+2586><U+2586><U+2586>
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA NA NA 4.691646e-01 2.974650e-01 0.0000000 2.039588e-01 4.584229e-01 7.269586e-01 1.000000e+00 <U+2587><U+2586><U+2586><U+2586><U+2586>
numeric AF 0 1.0000000 NA NA NA NA NA NA NA 2.035074e-01 2.568625e-01 0.0009810 1.316800e-02 7.791200e-02 3.164520e-01 9.990120e-01 <U+2587><U+2582><U+2581><U+2581><U+2581>
numeric AF_reference 184849 0.9812372 NA NA NA NA NA NA NA 2.068392e-01 2.482924e-01 0.0000000 1.198080e-02 9.984030e-02 3.202880e-01 1.000000e+00 <U+2587><U+2582><U+2581><U+2581><U+2581>

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 49298 rs200943160 T C -0.0030830 0.0071767 0.6700003 0.6674965 0.623782 0.7821490 NA
1 54676 rs2462492 C T 0.0036964 0.0071070 0.5999997 0.6029925 0.400383 NA NA
1 86028 rs114608975 T C 0.0007837 0.0113640 0.9500000 0.9450164 0.103570 0.0277556 NA
1 91536 rs6702460 G T 0.0064390 0.0069992 0.3599996 0.3575889 0.456806 0.4207270 NA
1 234313 rs8179466 C T 0.0014539 0.0137977 0.9199999 0.9160813 0.074512 NA NA
1 534192 rs6680723 C T 0.0104354 0.0079947 0.1900002 0.1917942 0.240955 NA NA
1 546697 rs12025928 A G -0.0046682 0.0099713 0.6400000 0.6396696 0.913464 NA NA
1 693731 rs12238997 A G -0.0055197 0.0066974 0.4100001 0.4098555 0.116412 0.1417730 NA
1 705882 rs72631875 G A 0.0090912 0.0098152 0.3500000 0.3543225 0.067294 0.0315495 NA
1 706368 rs55727773 A G -0.0023222 0.0049622 0.6400000 0.6397983 0.515682 0.2751600 NA
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51219704 rs147475742 G A -0.0212637 0.0104191 0.0409996 0.0412669 0.041941 0.0473243 NA
22 51219766 rs182321900 C T -0.0416674 0.0484541 0.3900004 0.3898246 0.001942 NA NA
22 51220146 rs868950473 C T -0.0295953 0.0480156 0.5400003 0.5376514 0.001990 NA NA
22 51221190 rs369304721 G A -0.0227278 0.0104003 0.0290001 0.0288667 0.049729 NA NA
22 51221731 rs115055839 T C -0.0161877 0.0077798 0.0369999 0.0374584 0.073207 0.0625000 NA
22 51222100 rs114553188 G T 0.0038384 0.0091558 0.6800001 0.6750495 0.054463 0.0880591 NA
22 51223637 rs375798137 G A 0.0032799 0.0092002 0.7199992 0.7214638 0.054091 0.0788738 NA
22 51229805 rs9616985 T C -0.0162009 0.0078082 0.0379997 0.0379998 0.073041 0.0730831 NA
22 51232488 rs376461333 A G 0.0079025 0.0183880 0.6700003 0.6673689 0.020048 NA NA
22 51237063 rs3896457 T C 0.0002659 0.0047754 0.9599999 0.9555939 0.298005 0.2050720 NA

bcf preview

1   49298   rs10399793  T   C   .   PASS    AF=0.623782 ES:SE:LP:AF:ID  -0.003083:0.00717667:0.173925:0.623782:rs10399793
1   54676   rs2462492   C   T   .   PASS    AF=0.400383 ES:SE:LP:AF:ID  0.00369638:0.00710703:0.221849:0.400383:rs2462492
1   86028   rs114608975 T   C   .   PASS    AF=0.10357  ES:SE:LP:AF:ID  0.000783734:0.011364:0.0222764:0.10357:rs114608975
1   91536   rs6702460   G   T   .   PASS    AF=0.456806 ES:SE:LP:AF:ID  0.00643903:0.00699918:0.443698:0.456806:rs6702460
1   234313  rs8179466   C   T   .   PASS    AF=0.074512 ES:SE:LP:AF:ID  0.00145388:0.0137977:0.0362122:0.074512:rs8179466
1   534192  rs6680723   C   T   .   PASS    AF=0.240955 ES:SE:LP:AF:ID  0.0104354:0.0079947:0.721246:0.240955:rs6680723
1   546697  rs12025928  A   G   .   PASS    AF=0.913464 ES:SE:LP:AF:ID  -0.00466819:0.00997134:0.19382:0.913464:rs12025928
1   693731  rs12238997  A   G   .   PASS    AF=0.116412 ES:SE:LP:AF:ID  -0.00551969:0.00669745:0.387216:0.116412:rs12238997
1   705882  rs72631875  G   A   .   PASS    AF=0.067294 ES:SE:LP:AF:ID  0.00909119:0.00981518:0.455932:0.067294:rs72631875
1   706368  rs12029736  A   G   .   PASS    AF=0.515682 ES:SE:LP:AF:ID  -0.00232221:0.00496219:0.19382:0.515682:rs12029736
1   714596  rs149887893 T   C   .   PASS    AF=0.032977 ES:SE:LP:AF:ID  -0.00454381:0.0125161:0.142668:0.032977:rs149887893
1   715265  rs12184267  C   T   .   PASS    AF=0.036597 ES:SE:LP:AF:ID  -0.00282587:0.0113672:0.09691:0.036597:rs12184267
1   715367  rs12184277  A   G   .   PASS    AF=0.036715 ES:SE:LP:AF:ID  -0.00234781:0.0113239:0.0757207:0.036715:rs12184277
1   717485  rs12184279  C   A   .   PASS    AF=0.036417 ES:SE:LP:AF:ID  -0.00245785:0.011405:0.0809219:0.036417:rs12184279
1   717587  rs144155419 G   A   .   PASS    AF=0.016441 ES:SE:LP:AF:ID  -0.0159622:0.0175379:0.443698:0.016441:rs144155419
1   720381  rs116801199 G   T   .   PASS    AF=0.036955 ES:SE:LP:AF:ID  -0.00388816:0.0112789:0.136677:0.036955:rs116801199
1   721290  rs12565286  G   C   .   PASS    AF=0.037051 ES:SE:LP:AF:ID  -0.00493584:0.0112404:0.180456:0.037051:rs12565286
1   722670  rs116030099 T   C   .   PASS    AF=0.101222 ES:SE:LP:AF:ID  0.0132489:0.00818702:0.958607:0.101222:rs116030099
1   723891  rs2977670   G   C   .   PASS    AF=0.959115 ES:SE:LP:AF:ID  0.000412909:0.0108412:0.0132283:0.959115:rs2977670
1   724849  rs12126395  C   A   .   PASS    AF=0.031429 ES:SE:LP:AF:ID  -0.0056263:0.0196902:0.107905:0.031429:rs12126395
1   725060  rs865924913 A   T   .   PASS    AF=0.053261 ES:SE:LP:AF:ID  -0.0257282:0.0156511:1:0.053261:rs865924913
1   726794  rs28454925  C   G   .   PASS    AF=0.036572 ES:SE:LP:AF:ID  -0.00372411:0.0113127:0.130768:0.036572:rs28454925
1   729632  rs116720794 C   T   .   PASS    AF=0.036888 ES:SE:LP:AF:ID  -0.0018547:0.0112099:0.0604807:0.036888:rs116720794
1   729679  rs4951859   C   G   .   PASS    AF=0.84314  ES:SE:LP:AF:ID  0.00566048:0.00580505:0.481486:0.84314:rs4951859
1   730087  rs148120343 T   C   .   PASS    AF=0.055971 ES:SE:LP:AF:ID  -0.00534528:0.00939596:0.244125:0.055971:rs148120343
1   731718  rs58276399  T   C   .   PASS    AF=0.1224   ES:SE:LP:AF:ID  -0.00690574:0.00635316:0.552842:0.1224:rs58276399
1   732989  rs369030935 C   T   .   PASS    AF=0.025687 ES:SE:LP:AF:ID  -0.00805083:0.0156411:0.21467:0.025687:rs369030935
1   734349  rs141242758 T   C   .   PASS    AF=0.121645 ES:SE:LP:AF:ID  -0.00663464:0.00635575:0.522879:0.121645:rs141242758
1   736289  rs79010578  T   A   .   PASS    AF=0.132373 ES:SE:LP:AF:ID  -0.00483212:0.00626533:0.356547:0.132373:rs79010578
1   736689  rs181876450 T   C   .   PASS    AF=0.011139 ES:SE:LP:AF:ID  0.0406972:0.0227762:1.13077:0.011139:rs181876450
1   740284  rs61770167  C   T   .   PASS    AF=0.005704 ES:SE:LP:AF:ID  0.0147692:0.0293955:0.207608:0.005704:rs61770167
1   742813  rs112573343 C   T   .   PASS    AF=0.002272 ES:SE:LP:AF:ID  0.0241939:0.0494203:0.207608:0.002272:rs112573343
1   746189  rs139221807 A   G   .   PASS    AF=0.001031 ES:SE:LP:AF:ID  -0.116537:0.0809004:0.823909:0.001031:rs139221807
1   752478  rs146277091 G   A   .   PASS    AF=0.036802 ES:SE:LP:AF:ID  -0.00232125:0.011097:0.0809219:0.036802:rs146277091
1   752566  rs3094315   G   A   .   PASS    AF=0.838877 ES:SE:LP:AF:ID  0.00215243:0.00562163:0.154902:0.838877:rs3094315
1   752721  rs3131972   A   G   .   PASS    AF=0.83851  ES:SE:LP:AF:ID  0.00217378:0.00561569:0.154902:0.83851:rs3131972
1   753405  rs3115860   C   A   .   PASS    AF=0.86968  ES:SE:LP:AF:ID  0.00150084:0.00602516:0.09691:0.86968:rs3115860
1   753541  rs2073813   G   A   .   PASS    AF=0.129957 ES:SE:LP:AF:ID  -0.00214068:0.00603771:0.142668:0.129957:rs2073813
1   754063  rs12184312  G   T   .   PASS    AF=0.037306 ES:SE:LP:AF:ID  -0.00267444:0.0109098:0.091515:0.037306:rs12184312
1   754105  rs12184325  C   T   .   PASS    AF=0.037549 ES:SE:LP:AF:ID  -0.00203097:0.0108409:0.0705811:0.037549:rs12184325
1   754182  rs3131969   A   G   .   PASS    AF=0.86903  ES:SE:LP:AF:ID  0.00172462:0.00601348:0.113509:0.86903:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.869128 ES:SE:LP:AF:ID  0.00119531:0.00601589:0.0757207:0.869128:rs3131968
1   754211  rs12184313  G   A   .   PASS    AF=0.03751  ES:SE:LP:AF:ID  -0.00238577:0.0108875:0.0809219:0.03751:rs12184313
1   754334  rs3131967   T   C   .   PASS    AF=0.869032 ES:SE:LP:AF:ID  0.00175325:0.00601337:0.113509:0.869032:rs3131967
1   754433  rs150578204 G   A   .   PASS    AF=0.005129 ES:SE:LP:AF:ID  0.057499:0.0308682:1.20066:0.005129:rs150578204
1   754458  rs142682604 G   T   .   PASS    AF=0.005095 ES:SE:LP:AF:ID  0.0562659:0.0309482:1.16115:0.005095:rs142682604
1   754503  rs3115859   G   A   .   PASS    AF=0.83796  ES:SE:LP:AF:ID  0.00225432:0.00560009:0.161151:0.83796:rs3115859
1   754629  rs10454459  A   G   .   PASS    AF=0.037523 ES:SE:LP:AF:ID  -0.00227914:0.0109028:0.0809219:0.037523:rs10454459
1   754964  rs3131966   C   T   .   PASS    AF=0.838592 ES:SE:LP:AF:ID  0.00255192:0.00561587:0.187087:0.838592:rs3131966
1   755240  rs181660517 T   G   .   PASS    AF=0.013782 ES:SE:LP:AF:ID  -0.0170371:0.0195972:0.420216:0.013782:rs181660517