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-9937/UKB-b-9937_data.vcf.gz \
--ref-ld-chr ../reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-9937/ldsc.txt \
--w-ld-chr ../reference/eur_w_ld_chr/ 

Beginning analysis at Thu Oct 17 14:43:10 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-9937/UKB-b-9937_data.vcf.gz ...
Read summary statistics for 9238368 SNPs.
Dropped 9928 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, 1287796 SNPs remain.
After merging with regression SNP LD, 1287796 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.021 (0.0027)
Lambda GC: 1.0948
Mean Chi^2: 1.1047
Intercept: 1.0181 (0.007)
Ratio: 0.1728 (0.0665)
Analysis finished at Thu Oct 17 14:44:55 2019
Total time elapsed: 1.0m:44.8s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9484,
    "inflation_factor": 1.0475,
    "mean_EFFECT": -0,
    "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": 107281,
    "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": 1287796,
    "ldsc_nsnp_merge_regression_ld": 1287796,
    "ldsc_observed_scale_h2_beta": 0.021,
    "ldsc_observed_scale_h2_se": 0.0027,
    "ldsc_intercept_beta": 1.0181,
    "ldsc_intercept_se": 0.007,
    "ldsc_lambda_gc": 1.0948,
    "ldsc_mean_chisq": 1.1047,
    "ldsc_ratio": 0.1729
}

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 9228490 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 9238368 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 8.637127e+00 5.754923e+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 7.880265e+07 5.631203e+07 828.0000000 3.248748e+07 6.938477e+07 1.145294e+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 -2.600000e-05 5.348300e-03 -0.0701293 -2.021900e-03 -6.400000e-06 2.001500e-03 6.387210e-02 <U+2581><U+2581><U+2587><U+2581><U+2581>
numeric SE 0 1.0000000 NA NA NA NA NA NA NA 4.174600e-03 3.238000e-03 0.0014263 1.713000e-03 2.686200e-03 5.726400e-03 3.636350e-02 <U+2587><U+2581><U+2581><U+2581><U+2581>
numeric PVAL 0 1.0000000 NA NA NA NA NA NA NA 4.889020e-01 2.917001e-01 0.0000001 2.300001e-01 4.899999e-01 7.400005e-01 1.000000e+00 <U+2587><U+2587><U+2587><U+2586><U+2587>
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA NA NA 4.889027e-01 2.916741e-01 0.0000001 2.331396e-01 4.850782e-01 7.416925e-01 1.000000e+00 <U+2587><U+2587><U+2587><U+2587><U+2587>
numeric AF 0 1.0000000 NA NA NA NA NA NA NA 2.151544e-01 2.579625e-01 0.0025940 1.811500e-02 9.439450e-02 3.382642e-01 9.974060e-01 <U+2587><U+2582><U+2581><U+2581><U+2581>
numeric AF_reference 107281 0.9883875 NA NA NA NA NA NA NA 2.159539e-01 2.497935e-01 0.0000000 1.537540e-02 1.126200e-01 3.376600e-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 0.0019801 0.0026239 0.4500005 0.4504650 0.624267 0.7821490 NA
1 54676 rs2462492 C T 0.0024261 0.0026056 0.3500000 0.3518020 0.399717 NA NA
1 86028 rs114608975 T C 0.0001648 0.0041472 0.9699999 0.9683006 0.103698 0.0277556 NA
1 91536 rs6702460 G T 0.0022025 0.0025638 0.3900004 0.3903104 0.456566 0.4207270 NA
1 234313 rs8179466 C T -0.0081211 0.0050422 0.1100001 0.1072609 0.074612 NA NA
1 534192 rs6680723 C T 0.0009931 0.0029267 0.7300002 0.7343785 0.240659 NA NA
1 546697 rs12025928 A G 0.0000499 0.0036494 0.9900000 0.9890999 0.913319 NA NA
1 693731 rs12238997 A G -0.0004884 0.0024553 0.8400000 0.8423270 0.115984 0.1417730 NA
1 705882 rs72631875 G A -0.0026612 0.0035914 0.4600002 0.4586951 0.067543 0.0315495 NA
1 706368 rs55727773 A G 0.0010751 0.0018176 0.5500004 0.5541931 0.516316 0.2751600 NA
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51219006 rs28729663 G A 0.0001365 0.0021880 0.9500000 0.9502416 0.137903 0.2052720 NA
22 51219387 rs9616832 T C 0.0005840 0.0028418 0.8400000 0.8371701 0.073846 0.0654952 NA
22 51219704 rs147475742 G A 0.0016821 0.0038083 0.6600001 0.6587062 0.042045 0.0473243 NA
22 51221190 rs369304721 G A -0.0011970 0.0037998 0.7499995 0.7527450 0.049852 NA NA
22 51221731 rs115055839 T C 0.0004124 0.0028445 0.8800001 0.8847302 0.073286 0.0625000 NA
22 51222100 rs114553188 G T -0.0015706 0.0033556 0.6400000 0.6397488 0.054213 0.0880591 NA
22 51223637 rs375798137 G A -0.0016942 0.0033721 0.6200004 0.6153827 0.053835 0.0788738 NA
22 51229805 rs9616985 T C 0.0000919 0.0028550 0.9699999 0.9743091 0.073083 0.0730831 NA
22 51232488 rs376461333 A G -0.0044126 0.0067303 0.5099998 0.5120610 0.020028 NA NA
22 51237063 rs3896457 T C 0.0002841 0.0017484 0.8700001 0.8709000 0.298065 0.2050720 NA

bcf preview

1   49298   rs10399793  T   C   .   PASS    AF=0.624267 ES:SE:LP:AF:ID  0.00198007:0.00262386:0.346787:0.624267:rs10399793
1   54676   rs2462492   C   T   .   PASS    AF=0.399717 ES:SE:LP:AF:ID  0.00242612:0.00260565:0.455932:0.399717:rs2462492
1   86028   rs114608975 T   C   .   PASS    AF=0.103698 ES:SE:LP:AF:ID  0.00016481:0.00414723:0.0132283:0.103698:rs114608975
1   91536   rs6702460   G   T   .   PASS    AF=0.456566 ES:SE:LP:AF:ID  0.00220247:0.00256383:0.408935:0.456566:rs6702460
1   234313  rs8179466   C   T   .   PASS    AF=0.074612 ES:SE:LP:AF:ID  -0.00812109:0.00504219:0.958607:0.074612:rs8179466
1   534192  rs6680723   C   T   .   PASS    AF=0.240659 ES:SE:LP:AF:ID  0.000993053:0.00292671:0.136677:0.240659:rs6680723
1   546697  rs12025928  A   G   .   PASS    AF=0.913319 ES:SE:LP:AF:ID  4.98563e-05:0.00364937:0.00436481:0.913319:rs12025928
1   693731  rs12238997  A   G   .   PASS    AF=0.115984 ES:SE:LP:AF:ID  -0.000488403:0.0024553:0.0757207:0.115984:rs12238997
1   705882  rs72631875  G   A   .   PASS    AF=0.067543 ES:SE:LP:AF:ID  -0.00266124:0.00359143:0.337242:0.067543:rs72631875
1   706368  rs12029736  A   G   .   PASS    AF=0.516316 ES:SE:LP:AF:ID  0.00107506:0.00181755:0.259637:0.516316:rs12029736
1   714596  rs149887893 T   C   .   PASS    AF=0.033154 ES:SE:LP:AF:ID  -0.00964586:0.00457071:1.45593:0.033154:rs149887893
1   715265  rs12184267  C   T   .   PASS    AF=0.036821 ES:SE:LP:AF:ID  -0.00745225:0.00414769:1.14267:0.036821:rs12184267
1   715367  rs12184277  A   G   .   PASS    AF=0.036946 ES:SE:LP:AF:ID  -0.00735359:0.00413104:1.12494:0.036946:rs12184277
1   717485  rs12184279  C   A   .   PASS    AF=0.036657 ES:SE:LP:AF:ID  -0.00794825:0.00415991:1.25181:0.036657:rs12184279
1   717587  rs144155419 G   A   .   PASS    AF=0.016475 ES:SE:LP:AF:ID  0.00661445:0.00641886:0.522879:0.016475:rs144155419
1   720381  rs116801199 G   T   .   PASS    AF=0.037207 ES:SE:LP:AF:ID  -0.00721371:0.0041132:1.10237:0.037207:rs116801199
1   721290  rs12565286  G   C   .   PASS    AF=0.037307 ES:SE:LP:AF:ID  -0.00767308:0.00409892:1.21467:0.037307:rs12565286
1   722670  rs116030099 T   C   .   PASS    AF=0.101356 ES:SE:LP:AF:ID  0.000340573:0.00299558:0.0409586:0.101356:rs116030099
1   723891  rs2977670   G   C   .   PASS    AF=0.958856 ES:SE:LP:AF:ID  0.00914637:0.00395472:1.67778:0.958856:rs2977670
1   724849  rs12126395  C   A   .   PASS    AF=0.031499 ES:SE:LP:AF:ID  -8.90696e-05:0.00722504:0.00436481:0.031499:rs12126395
1   725060  rs865924913 A   T   .   PASS    AF=0.053093 ES:SE:LP:AF:ID  -0.00738956:0.00574522:0.69897:0.053093:rs865924913
1   726794  rs28454925  C   G   .   PASS    AF=0.036796 ES:SE:LP:AF:ID  -0.00733727:0.00412839:1.11919:0.036796:rs28454925
1   729632  rs116720794 C   T   .   PASS    AF=0.037094 ES:SE:LP:AF:ID  -0.00749241:0.00409097:1.17393:0.037094:rs116720794
1   729679  rs4951859   C   G   .   PASS    AF=0.843341 ES:SE:LP:AF:ID  0.00249311:0.00212516:0.619789:0.843341:rs4951859
1   730087  rs148120343 T   C   .   PASS    AF=0.055796 ES:SE:LP:AF:ID  0.000184088:0.00344396:0.0177288:0.055796:rs148120343
1   731718  rs58276399  T   C   .   PASS    AF=0.121927 ES:SE:LP:AF:ID  -2.41866e-05:0.00232995:0.00436481:0.121927:rs58276399
1   732989  rs369030935 C   T   .   PASS    AF=0.025851 ES:SE:LP:AF:ID  0.00653001:0.00570687:0.60206:0.025851:rs369030935
1   734349  rs141242758 T   C   .   PASS    AF=0.121196 ES:SE:LP:AF:ID  0.000266917:0.00233084:0.0409586:0.121196:rs141242758
1   736289  rs79010578  T   A   .   PASS    AF=0.132104 ES:SE:LP:AF:ID  -0.00325182:0.00229574:0.79588:0.132104:rs79010578
1   736689  rs181876450 T   C   .   PASS    AF=0.011108 ES:SE:LP:AF:ID  -0.00303202:0.00834817:0.142668:0.011108:rs181876450
1   740284  rs61770167  C   T   .   PASS    AF=0.005619 ES:SE:LP:AF:ID  0.00370764:0.0108795:0.136677:0.005619:rs61770167
1   752478  rs146277091 G   A   .   PASS    AF=0.037017 ES:SE:LP:AF:ID  -0.00780772:0.00404898:1.26761:0.037017:rs146277091
1   752566  rs3094315   G   A   .   PASS    AF=0.839146 ES:SE:LP:AF:ID  0.00190381:0.00205949:0.443698:0.839146:rs3094315
1   752721  rs3131972   A   G   .   PASS    AF=0.838777 ES:SE:LP:AF:ID  0.00196162:0.00205704:0.468521:0.838777:rs3131972
1   753405  rs3115860   C   A   .   PASS    AF=0.870153 ES:SE:LP:AF:ID  -0.000175878:0.00220958:0.0268721:0.870153:rs3115860
1   753541  rs2073813   G   A   .   PASS    AF=0.129498 ES:SE:LP:AF:ID  0.000481858:0.00221356:0.0809219:0.129498:rs2073813
1   754063  rs12184312  G   T   .   PASS    AF=0.037575 ES:SE:LP:AF:ID  -0.00720943:0.0039784:1.1549:0.037575:rs12184312
1   754105  rs12184325  C   T   .   PASS    AF=0.037794 ES:SE:LP:AF:ID  -0.00700567:0.00395507:1.11351:0.037794:rs12184325
1   754182  rs3131969   A   G   .   PASS    AF=0.869507 ES:SE:LP:AF:ID  -0.000165912:0.00220494:0.0268721:0.869507:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.869635 ES:SE:LP:AF:ID  -9.94249e-05:0.00220593:0.0177288:0.869635:rs3131968
1   754211  rs12184313  G   A   .   PASS    AF=0.037765 ES:SE:LP:AF:ID  -0.00723359:0.00397149:1.16115:0.037765:rs12184313
1   754334  rs3131967   T   C   .   PASS    AF=0.869512 ES:SE:LP:AF:ID  -0.000168937:0.00220493:0.0268721:0.869512:rs3131967
1   754433  rs150578204 G   A   .   PASS    AF=0.005174 ES:SE:LP:AF:ID  0.00420439:0.0112278:0.148742:0.005174:rs150578204
1   754458  rs142682604 G   T   .   PASS    AF=0.005136 ES:SE:LP:AF:ID  0.00415089:0.0112606:0.148742:0.005136:rs142682604
1   754503  rs3115859   G   A   .   PASS    AF=0.838236 ES:SE:LP:AF:ID  0.0018522:0.00205144:0.431798:0.838236:rs3115859
1   754629  rs10454459  A   G   .   PASS    AF=0.037779 ES:SE:LP:AF:ID  -0.00723265:0.00397664:1.16115:0.037779:rs10454459
1   754964  rs3131966   C   T   .   PASS    AF=0.83886  ES:SE:LP:AF:ID  0.00185738:0.00205718:0.431798:0.83886:rs3131966
1   755240  rs181660517 T   G   .   PASS    AF=0.01367  ES:SE:LP:AF:ID  -0.0120508:0.00720664:1.02687:0.01367:rs181660517
1   755435  rs184270342 T   G   .   PASS    AF=0.005502 ES:SE:LP:AF:ID  -0.00692215:0.0111172:0.275724:0.005502:rs184270342
1   755775  rs3131965   A   G   .   PASS    AF=0.839942 ES:SE:LP:AF:ID  0.00192454:0.00208529:0.443698:0.839942:rs3131965