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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    "FORMAT.1": "<ID=SE,Number=A,Type=Float,Description=\"Standard error of effect size estimate\">",
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    "FORMAT.5": "<ID=EZ,Number=A,Type=Float,Description=\"Z-score provided if it was used to derive the EFFECT and SE fields\">",
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    "bcftools_viewCommand": "view -h /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukb-b-15590/ukb-b-15590.vcf.gz; Date=Sun May 10 05:54:34 2020"
}
 

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-15590/UKB-b-15590_data.vcf.gz \
--ref-ld-chr ../reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-15590/ldsc.txt \
--w-ld-chr ../reference/eur_w_ld_chr/ 

Beginning analysis at Thu Oct 17 14:44:12 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-15590/UKB-b-15590_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: 0.2058 (0.0065)
Lambda GC: 2.3205
Mean Chi^2: 3.0981
Intercept: 1.2002 (0.0174)
Ratio: 0.0954 (0.0083)
Analysis finished at Thu Oct 17 14:45:56 2019
Total time elapsed: 1.0m:44.32s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9499,
    "inflation_factor": 1.8418,
    "mean_EFFECT": 0,
    "n": "-Inf",
    "n_snps": 9851866,
    "n_clumped_hits": 420,
    "n_p_sig": 59115,
    "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": "NaN",
    "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": 0.2058,
    "ldsc_observed_scale_h2_se": 0.0065,
    "ldsc_intercept_beta": 1.2002,
    "ldsc_intercept_se": 0.0174,
    "ldsc_lambda_gc": 2.3205,
    "ldsc_mean_chisq": 3.0981,
    "ldsc_ratio": 0.0954
}
 

Flags

name value
af_correlation FALSE
inflation_factor TRUE
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 TRUE
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 ▇▅▃▂▂
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 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA NA NA 1.870000e-05 1.074070e-02 -0.2711480 -4.078300e-03 -1.800000e-06 4.088100e-03 1.765590e-01 ▁▁▃▇▁
numeric SE 0 1.0000000 NA NA NA NA NA NA NA 6.867300e-03 6.499700e-03 0.0019196 2.352600e-03 3.945100e-03 9.102200e-03 1.008860e-01 ▇▁▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA NA NA 4.032603e-01 3.109825e-01 0.0000000 1.100001e-01 3.599996e-01 6.700003e-01 1.000000e+00 ▇▅▃▃▃
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA NA NA 4.032633e-01 3.109608e-01 0.0000000 1.096150e-01 3.625554e-01 6.705089e-01 9.999997e-01 ▇▅▃▃▃
numeric AF 0 1.0000000 NA NA NA NA NA NA NA 2.035077e-01 2.568614e-01 0.0009930 1.317000e-02 7.791400e-02 3.164540e-01 9.990050e-01 ▇▂▁▁▁
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 ▇▂▁▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 49298 rs200943160 T C -0.0000659 0.0035280 0.9900000 0.9850883 0.623768 0.7821490 NA
1 54676 rs2462492 C T 0.0041639 0.0034951 0.2300001 0.2335150 0.400417 NA NA
1 86028 rs114608975 T C 0.0061539 0.0055882 0.2700001 0.2707950 0.103547 0.0277556 NA
1 91536 rs6702460 G T 0.0067186 0.0034413 0.0510000 0.0508954 0.456851 0.4207270 NA
1 234313 rs8179466 C T -0.0130916 0.0067871 0.0539995 0.0537429 0.074489 NA NA
1 534192 rs6680723 C T -0.0023206 0.0039310 0.5500004 0.5549669 0.240950 NA NA
1 546697 rs12025928 A G 0.0017907 0.0049031 0.7099994 0.7149465 0.913450 NA NA
1 693731 rs12238997 A G -0.0025230 0.0032948 0.4400003 0.4438294 0.116281 0.1417730 NA
1 705882 rs72631875 G A 0.0005843 0.0048268 0.9000000 0.9036471 0.067306 0.0315495 NA
1 706368 rs55727773 A G -0.0000562 0.0024402 0.9800000 0.9816233 0.515677 0.2751600 NA
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51219704 rs147475742 G A 0.0033892 0.0051487 0.5099998 0.5103660 0.041955 0.0473243 NA
22 51219766 rs182321900 C T -0.0212973 0.0239763 0.3700002 0.3743984 0.001939 NA NA
22 51220146 rs868950473 C T -0.0225304 0.0237500 0.3400001 0.3427995 0.001988 NA NA
22 51221190 rs369304721 G A 0.0086937 0.0051408 0.0909997 0.0908137 0.049730 NA NA
22 51221731 rs115055839 T C 0.0076426 0.0038447 0.0470002 0.0468322 0.073239 0.0625000 NA
22 51222100 rs114553188 G T 0.0004621 0.0045264 0.9199999 0.9186921 0.054465 0.0880591 NA
22 51223637 rs375798137 G A 0.0006006 0.0045483 0.8900000 0.8949507 0.054094 0.0788738 NA
22 51229805 rs9616985 T C 0.0073682 0.0038587 0.0560003 0.0561979 0.073073 0.0730831 NA
22 51232488 rs376461333 A G 0.0072454 0.0090890 0.4299995 0.4253588 0.020047 NA NA
22 51237063 rs3896457 T C 0.0020746 0.0023601 0.3800004 0.3794023 0.297931 0.2050720 NA

bcf preview

1   49298   rs10399793  T   C   .   PASS    AF=0.623768 ES:SE:LP:AF:ID  -6.59381e-05:0.00352796:0.00436481:0.623768:rs10399793
1   54676   rs2462492   C   T   .   PASS    AF=0.400417 ES:SE:LP:AF:ID  0.00416391:0.00349511:0.638272:0.400417:rs2462492
1   86028   rs114608975 T   C   .   PASS    AF=0.103547 ES:SE:LP:AF:ID  0.00615388:0.00558817:0.568636:0.103547:rs114608975
1   91536   rs6702460   G   T   .   PASS    AF=0.456851 ES:SE:LP:AF:ID  0.00671862:0.00344128:1.29243:0.456851:rs6702460
1   234313  rs8179466   C   T   .   PASS    AF=0.074489 ES:SE:LP:AF:ID  -0.0130916:0.00678707:1.26761:0.074489:rs8179466
1   534192  rs6680723   C   T   .   PASS    AF=0.24095  ES:SE:LP:AF:ID  -0.00232059:0.00393098:0.259637:0.24095:rs6680723
1   546697  rs12025928  A   G   .   PASS    AF=0.91345  ES:SE:LP:AF:ID  0.0017907:0.00490306:0.148742:0.91345:rs12025928
1   693731  rs12238997  A   G   .   PASS    AF=0.116281 ES:SE:LP:AF:ID  -0.002523:0.00329484:0.356547:0.116281:rs12238997
1   705882  rs72631875  G   A   .   PASS    AF=0.067306 ES:SE:LP:AF:ID  0.000584306:0.00482676:0.0457575:0.067306:rs72631875
1   706368  rs12029736  A   G   .   PASS    AF=0.515677 ES:SE:LP:AF:ID  -5.6206e-05:0.00244015:0.00877392:0.515677:rs12029736
1   714596  rs149887893 T   C   .   PASS    AF=0.032997 ES:SE:LP:AF:ID  -0.000388701:0.00615253:0.0222764:0.032997:rs149887893
1   715265  rs12184267  C   T   .   PASS    AF=0.036613 ES:SE:LP:AF:ID  -0.00105114:0.00558847:0.0705811:0.036613:rs12184267
1   715367  rs12184277  A   G   .   PASS    AF=0.03673  ES:SE:LP:AF:ID  -0.000657222:0.00556724:0.0409586:0.03673:rs12184277
1   717485  rs12184279  C   A   .   PASS    AF=0.036429 ES:SE:LP:AF:ID  -0.00213321:0.00560749:0.154902:0.036429:rs12184279
1   717587  rs144155419 G   A   .   PASS    AF=0.016397 ES:SE:LP:AF:ID  -0.00745576:0.0086364:0.408935:0.016397:rs144155419
1   720381  rs116801199 G   T   .   PASS    AF=0.036967 ES:SE:LP:AF:ID  -0.00147073:0.00554537:0.102373:0.036967:rs116801199
1   721290  rs12565286  G   C   .   PASS    AF=0.037064 ES:SE:LP:AF:ID  -0.00139913:0.00552637:0.09691:0.037064:rs12565286
1   722670  rs116030099 T   C   .   PASS    AF=0.101199 ES:SE:LP:AF:ID  0.00400344:0.00402608:0.49485:0.101199:rs116030099
1   723891  rs2977670   G   C   .   PASS    AF=0.959105 ES:SE:LP:AF:ID  0.00364818:0.00533019:0.309804:0.959105:rs2977670
1   724849  rs12126395  C   A   .   PASS    AF=0.031451 ES:SE:LP:AF:ID  -0.00174112:0.00967498:0.0655015:0.031451:rs12126395
1   725060  rs865924913 A   T   .   PASS    AF=0.053256 ES:SE:LP:AF:ID  0.0107166:0.0076968:0.79588:0.053256:rs865924913
1   726794  rs28454925  C   G   .   PASS    AF=0.036585 ES:SE:LP:AF:ID  -0.00246079:0.00556198:0.180456:0.036585:rs28454925
1   729632  rs116720794 C   T   .   PASS    AF=0.0369   ES:SE:LP:AF:ID  -0.00296605:0.0055114:0.229148:0.0369:rs116720794
1   729679  rs4951859   C   G   .   PASS    AF=0.843261 ES:SE:LP:AF:ID  0.00394965:0.00285524:0.769551:0.843261:rs4951859
1   730087  rs148120343 T   C   .   PASS    AF=0.055891 ES:SE:LP:AF:ID  -0.00806815:0.00462332:1.09151:0.055891:rs148120343
1   731718  rs58276399  T   C   .   PASS    AF=0.122261 ES:SE:LP:AF:ID  -0.0037637:0.00312545:0.638272:0.122261:rs58276399
1   732989  rs369030935 C   T   .   PASS    AF=0.02571  ES:SE:LP:AF:ID  -0.00760859:0.00768715:0.49485:0.02571:rs369030935
1   734349  rs141242758 T   C   .   PASS    AF=0.121504 ES:SE:LP:AF:ID  -0.00362687:0.00312676:0.60206:0.121504:rs141242758
1   736289  rs79010578  T   A   .   PASS    AF=0.132295 ES:SE:LP:AF:ID  -0.00350737:0.00308158:0.585027:0.132295:rs79010578
1   736689  rs181876450 T   C   .   PASS    AF=0.011138 ES:SE:LP:AF:ID  -0.00206538:0.0112015:0.0705811:0.011138:rs181876450
1   740284  rs61770167  C   T   .   PASS    AF=0.005691 ES:SE:LP:AF:ID  0.00800119:0.0144735:0.236572:0.005691:rs61770167
1   742813  rs112573343 C   T   .   PASS    AF=0.002272 ES:SE:LP:AF:ID  0.0113982:0.0243002:0.19382:0.002272:rs112573343
1   746189  rs139221807 A   G   .   PASS    AF=0.00103  ES:SE:LP:AF:ID  -0.000964774:0.0398006:0.00877392:0.00103:rs139221807
1   752478  rs146277091 G   A   .   PASS    AF=0.036815 ES:SE:LP:AF:ID  -0.00204673:0.00545564:0.148742:0.036815:rs146277091
1   752566  rs3094315   G   A   .   PASS    AF=0.839002 ES:SE:LP:AF:ID  0.00356303:0.00276509:0.69897:0.839002:rs3094315
1   752721  rs3131972   A   G   .   PASS    AF=0.838633 ES:SE:LP:AF:ID  0.0040218:0.00276211:0.823909:0.838633:rs3131972
1   753405  rs3115860   C   A   .   PASS    AF=0.869829 ES:SE:LP:AF:ID  0.0032044:0.00296399:0.552842:0.869829:rs3115860
1   753541  rs2073813   G   A   .   PASS    AF=0.129817 ES:SE:LP:AF:ID  -0.00408918:0.0029701:0.769551:0.129817:rs2073813
1   754063  rs12184312  G   T   .   PASS    AF=0.037327 ES:SE:LP:AF:ID  -0.00325875:0.00536314:0.267606:0.037327:rs12184312
1   754105  rs12184325  C   T   .   PASS    AF=0.03757  ES:SE:LP:AF:ID  -0.00310441:0.00532934:0.251812:0.03757:rs12184325
1   754182  rs3131969   A   G   .   PASS    AF=0.869175 ES:SE:LP:AF:ID  0.00358297:0.0029582:0.638272:0.869175:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.869273 ES:SE:LP:AF:ID  0.00354464:0.00295938:0.638272:0.869273:rs3131968
1   754211  rs12184313  G   A   .   PASS    AF=0.037526 ES:SE:LP:AF:ID  -0.00323358:0.00535252:0.259637:0.037526:rs12184313
1   754334  rs3131967   T   C   .   PASS    AF=0.869178 ES:SE:LP:AF:ID  0.00361728:0.00295814:0.657577:0.869178:rs3131967
1   754433  rs150578204 G   A   .   PASS    AF=0.005121 ES:SE:LP:AF:ID  -0.000780245:0.0151874:0.0177288:0.005121:rs150578204
1   754458  rs142682604 G   T   .   PASS    AF=0.005087 ES:SE:LP:AF:ID  -0.00112838:0.0152272:0.0268721:0.005087:rs142682604
1   754503  rs3115859   G   A   .   PASS    AF=0.838088 ES:SE:LP:AF:ID  0.00403234:0.00275448:0.853872:0.838088:rs3115859
1   754629  rs10454459  A   G   .   PASS    AF=0.037539 ES:SE:LP:AF:ID  -0.00366283:0.00536008:0.309804:0.037539:rs10454459
1   754964  rs3131966   C   T   .   PASS    AF=0.83872  ES:SE:LP:AF:ID  0.00402947:0.00276224:0.853872:0.83872:rs3131966
1   755240  rs181660517 T   G   .   PASS    AF=0.013769 ES:SE:LP:AF:ID  0.0106635:0.00964205:0.568636:0.013769:rs181660517