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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    "gwas_harmonisation_command": "--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/vcf_09_19b/bgzip_vcf/data.batch_100740.vcf.gz --id UKB-b:12901 --data /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/raw-output/data.batch_100740.txt.gz --cohort_controls 64944 --ref /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/human_g1k_v37.fasta --json /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/ukb_gwas.json; 1.1.1",
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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-12901/UKB-b-12901_data.vcf.gz \
--ref-ld-chr ../reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-12901/ldsc.txt \
--w-ld-chr ../reference/eur_w_ld_chr/ 

Beginning analysis at Thu Oct 17 14:42:07 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-12901/UKB-b-12901_data.vcf.gz ...
Read summary statistics for 8624973 SNPs.
Dropped 7372 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, 1285749 SNPs remain.
After merging with regression SNP LD, 1285749 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: -0.0076 (0.0064)
Lambda GC: 0.9941
Mean Chi^2: 0.9906
Intercept: 1.0003 (0.0055)
Ratio: NA (mean chi^2 < 1)
Analysis finished at Thu Oct 17 14:43:45 2019
Total time elapsed: 1.0m:37.83s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9462,
    "inflation_factor": 1,
    "mean_EFFECT": 9.0985e-06,
    "n": "-Inf",
    "n_snps": 9851866,
    "n_clumped_hits": 2,
    "n_p_sig": 24,
    "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": 83095,
    "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": 1285749,
    "ldsc_nsnp_merge_regression_ld": 1285749,
    "ldsc_observed_scale_h2_beta": "NA",
    "ldsc_observed_scale_h2_se": "NA",
    "ldsc_intercept_beta": 1.0003,
    "ldsc_intercept_se": 0.0055,
    "ldsc_lambda_gc": 0.9941,
    "ldsc_mean_chisq": 0.9906,
    "ldsc_ratio": -0.0319
}

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 8617635 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 8624973 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 8.650344e+00 5.760992e+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 7.877013e+07 5.637173e+07 828.0000000 3.238541e+07 6.929172e+07 1.145689e+08 2.492385e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA NA NA 9.100000e-06 4.419300e-03 -0.0435391 -1.874900e-03 -4.150000e-05 1.772400e-03 6.720440e-02 ▁▇▅▁▁
numeric SE 0 1.0000000 NA NA NA NA NA NA NA 3.651400e-03 2.492400e-03 0.0014502 1.707800e-03 2.518000e-03 4.935900e-03 2.499890e-02 ▇▂▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA NA NA 5.003493e-01 2.881794e-01 0.0000000 2.500000e-01 5.000000e-01 7.499995e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA NA NA 5.003484e-01 2.881556e-01 0.0000000 2.514761e-01 5.002916e-01 7.494386e-01 9.999996e-01 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA NA NA 2.291176e-01 2.594883e-01 0.0053900 2.519000e-02 1.138970e-01 3.626190e-01 9.946100e-01 ▇▂▁▁▁
numeric AF_reference 83095 0.9903658 NA NA NA NA NA NA NA 2.288668e-01 2.514590e-01 0.0000000 2.316290e-02 1.303910e-01 3.596250e-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 -0.0028724 0.0026727 0.2800000 0.2825129 0.623799 0.7821490 NA
1 54676 rs2462492 C T 0.0018783 0.0026649 0.4799997 0.4809194 0.399155 NA NA
1 86028 rs114608975 T C -0.0018228 0.0042420 0.6700003 0.6674164 0.103539 0.0277556 NA
1 91536 rs6702460 G T 0.0035354 0.0026213 0.1800002 0.1774232 0.455911 0.4207270 NA
1 234313 rs8179466 C T 0.0053610 0.0051834 0.2999998 0.3010141 0.074459 NA NA
1 534192 rs6680723 C T 0.0004340 0.0029855 0.8800001 0.8844093 0.242059 NA NA
1 546697 rs12025928 A G -0.0029113 0.0037042 0.4299995 0.4318955 0.912865 NA NA
1 693731 rs12238997 A G 0.0003317 0.0024893 0.8900000 0.8939830 0.117307 0.1417730 NA
1 705882 rs72631875 G A -0.0015198 0.0036282 0.6800001 0.6753100 0.067703 0.0315495 NA
1 706368 rs55727773 A G -0.0028318 0.0018476 0.1299999 0.1253514 0.513306 0.2751600 NA
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51219006 rs28729663 G A 0.0000033 0.0022476 1.0000000 0.9988188 0.136287 0.2052720 NA
22 51219387 rs9616832 T C -0.0005169 0.0029299 0.8600001 0.8599649 0.071764 0.0654952 NA
22 51219704 rs147475742 G A -0.0006217 0.0038967 0.8700001 0.8732297 0.041182 0.0473243 NA
22 51221190 rs369304721 G A -0.0006305 0.0039245 0.8700001 0.8723654 0.048357 NA NA
22 51221731 rs115055839 T C -0.0004379 0.0029306 0.8800001 0.8812165 0.071315 0.0625000 NA
22 51222100 rs114553188 G T 0.0015249 0.0033948 0.6499995 0.6532925 0.054855 0.0880591 NA
22 51223637 rs375798137 G A 0.0010557 0.0034125 0.7600007 0.7570493 0.054474 0.0788738 NA
22 51229805 rs9616985 T C -0.0008363 0.0029396 0.7800007 0.7760361 0.071220 0.0730831 NA
22 51232488 rs376461333 A G 0.0017659 0.0067683 0.7899998 0.7941613 0.020462 NA NA
22 51237063 rs3896457 T C -0.0005127 0.0017741 0.7700005 0.7726067 0.298401 0.2050720 NA

bcf preview

1   49298   rs10399793  T   C   .   PASS    AF=0.623799 ES:SE:LP:AF:ID  -0.00287236:0.00267273:0.552842:0.623799:rs10399793
1   54676   rs2462492   C   T   .   PASS    AF=0.399155 ES:SE:LP:AF:ID  0.00187828:0.00266489:0.318759:0.399155:rs2462492
1   86028   rs114608975 T   C   .   PASS    AF=0.103539 ES:SE:LP:AF:ID  -0.00182276:0.00424197:0.173925:0.103539:rs114608975
1   91536   rs6702460   G   T   .   PASS    AF=0.455911 ES:SE:LP:AF:ID  0.00353539:0.00262127:0.744727:0.455911:rs6702460
1   234313  rs8179466   C   T   .   PASS    AF=0.074459 ES:SE:LP:AF:ID  0.00536101:0.00518342:0.522879:0.074459:rs8179466
1   534192  rs6680723   C   T   .   PASS    AF=0.242059 ES:SE:LP:AF:ID  0.000434032:0.00298546:0.0555173:0.242059:rs6680723
1   546697  rs12025928  A   G   .   PASS    AF=0.912865 ES:SE:LP:AF:ID  -0.00291134:0.00370422:0.366532:0.912865:rs12025928
1   693731  rs12238997  A   G   .   PASS    AF=0.117307 ES:SE:LP:AF:ID  0.000331735:0.00248927:0.05061:0.117307:rs12238997
1   705882  rs72631875  G   A   .   PASS    AF=0.067703 ES:SE:LP:AF:ID  -0.00151975:0.0036282:0.167491:0.067703:rs72631875
1   706368  rs12029736  A   G   .   PASS    AF=0.513306 ES:SE:LP:AF:ID  -0.00283182:0.00184761:0.886057:0.513306:rs12029736
1   714596  rs149887893 T   C   .   PASS    AF=0.033673 ES:SE:LP:AF:ID  0.000370202:0.00460564:0.0268721:0.033673:rs149887893
1   715265  rs12184267  C   T   .   PASS    AF=0.037452 ES:SE:LP:AF:ID  0.000318836:0.00417716:0.0268721:0.037452:rs12184267
1   715367  rs12184277  A   G   .   PASS    AF=0.037639 ES:SE:LP:AF:ID  0.000154506:0.0041553:0.0132283:0.037639:rs12184277
1   717485  rs12184279  C   A   .   PASS    AF=0.037215 ES:SE:LP:AF:ID  -0.000502881:0.00419328:0.0457575:0.037215:rs12184279
1   717587  rs144155419 G   A   .   PASS    AF=0.016283 ES:SE:LP:AF:ID  -0.00701539:0.00657674:0.537602:0.016283:rs144155419
1   720381  rs116801199 G   T   .   PASS    AF=0.037856 ES:SE:LP:AF:ID  0.000120694:0.00414109:0.00877392:0.037856:rs116801199
1   721290  rs12565286  G   C   .   PASS    AF=0.03795  ES:SE:LP:AF:ID  8.91043e-05:0.00412795:0.00877392:0.03795:rs12565286
1   722670  rs116030099 T   C   .   PASS    AF=0.102733 ES:SE:LP:AF:ID  0.00297563:0.0030152:0.49485:0.102733:rs116030099
1   723891  rs2977670   G   C   .   PASS    AF=0.958094 ES:SE:LP:AF:ID  -0.000187788:0.00398695:0.0177288:0.958094:rs2977670
1   724849  rs12126395  C   A   .   PASS    AF=0.031684 ES:SE:LP:AF:ID  0.000502893:0.00730225:0.0222764:0.031684:rs12126395
1   725060  rs865924913 A   T   .   PASS    AF=0.052722 ES:SE:LP:AF:ID  0.00233836:0.00588027:0.161151:0.052722:rs865924913
1   726794  rs28454925  C   G   .   PASS    AF=0.037444 ES:SE:LP:AF:ID  -0.000601776:0.00415506:0.0555173:0.037444:rs28454925
1   729632  rs116720794 C   T   .   PASS    AF=0.037713 ES:SE:LP:AF:ID  -0.000573803:0.00412064:0.05061:0.037713:rs116720794
1   729679  rs4951859   C   G   .   PASS    AF=0.841444 ES:SE:LP:AF:ID  -0.00067987:0.00215272:0.124939:0.841444:rs4951859
1   730087  rs148120343 T   C   .   PASS    AF=0.056338 ES:SE:LP:AF:ID  0.00221821:0.00349686:0.275724:0.056338:rs148120343
1   731718  rs58276399  T   C   .   PASS    AF=0.123079 ES:SE:LP:AF:ID  0.000301476:0.00236446:0.0457575:0.123079:rs58276399
1   732989  rs369030935 C   T   .   PASS    AF=0.025131 ES:SE:LP:AF:ID  -0.00691872:0.00588813:0.619789:0.025131:rs369030935
1   734349  rs141242758 T   C   .   PASS    AF=0.122332 ES:SE:LP:AF:ID  0.00034812:0.00236522:0.0555173:0.122332:rs141242758
1   736289  rs79010578  T   A   .   PASS    AF=0.134134 ES:SE:LP:AF:ID  0.00198822:0.00232189:0.408935:0.134134:rs79010578
1   736689  rs181876450 T   C   .   PASS    AF=0.011558 ES:SE:LP:AF:ID  -0.00369833:0.00827493:0.187087:0.011558:rs181876450
1   740284  rs61770167  C   T   .   PASS    AF=0.006101 ES:SE:LP:AF:ID  0.0141693:0.0105081:0.744727:0.006101:rs61770167
1   752478  rs146277091 G   A   .   PASS    AF=0.037595 ES:SE:LP:AF:ID  -0.000883297:0.00408245:0.0809219:0.037595:rs146277091
1   752566  rs3094315   G   A   .   PASS    AF=0.837032 ES:SE:LP:AF:ID  -0.00143043:0.00208249:0.309804:0.837032:rs3094315
1   752721  rs3131972   A   G   .   PASS    AF=0.836736 ES:SE:LP:AF:ID  -0.00154079:0.00208096:0.337242:0.836736:rs3131972
1   753405  rs3115860   C   A   .   PASS    AF=0.86856  ES:SE:LP:AF:ID  -0.00132152:0.00223608:0.259637:0.86856:rs3115860
1   753541  rs2073813   G   A   .   PASS    AF=0.131007 ES:SE:LP:AF:ID  0.00116865:0.00224183:0.221849:0.131007:rs2073813
1   754063  rs12184312  G   T   .   PASS    AF=0.03804  ES:SE:LP:AF:ID  -0.0012526:0.00401839:0.119186:0.03804:rs12184312
1   754105  rs12184325  C   T   .   PASS    AF=0.038287 ES:SE:LP:AF:ID  -0.00141392:0.00399348:0.142668:0.038287:rs12184325
1   754182  rs3131969   A   G   .   PASS    AF=0.867973 ES:SE:LP:AF:ID  -0.00140439:0.00223249:0.275724:0.867973:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.868047 ES:SE:LP:AF:ID  -0.00142662:0.0022334:0.283997:0.868047:rs3131968
1   754211  rs12184313  G   A   .   PASS    AF=0.038195 ES:SE:LP:AF:ID  -0.00130797:0.00401193:0.130768:0.038195:rs12184313
1   754334  rs3131967   T   C   .   PASS    AF=0.867984 ES:SE:LP:AF:ID  -0.00139577:0.00223243:0.275724:0.867984:rs3131967
1   754433  rs150578204 G   A   .   PASS    AF=0.005397 ES:SE:LP:AF:ID  0.0227756:0.0111885:1.37675:0.005397:rs150578204
1   754503  rs3115859   G   A   .   PASS    AF=0.836162 ES:SE:LP:AF:ID  -0.00157647:0.00207487:0.346787:0.836162:rs3115859
1   754629  rs10454459  A   G   .   PASS    AF=0.038198 ES:SE:LP:AF:ID  -0.00105893:0.00401779:0.102373:0.038198:rs10454459
1   754964  rs3131966   C   T   .   PASS    AF=0.836796 ES:SE:LP:AF:ID  -0.00157933:0.00208056:0.346787:0.836796:rs3131966
1   755240  rs181660517 T   G   .   PASS    AF=0.013031 ES:SE:LP:AF:ID  -0.00689557:0.00752697:0.443698:0.013031:rs181660517
1   755435  rs184270342 T   G   .   PASS    AF=0.005662 ES:SE:LP:AF:ID  0.0085883:0.0111739:0.356547:0.005662:rs184270342
1   755775  rs3131965   A   G   .   PASS    AF=0.838112 ES:SE:LP:AF:ID  -0.00176862:0.00210985:0.39794:0.838112:rs3131965
1   755890  rs3115858   A   T   .   PASS    AF=0.868225 ES:SE:LP:AF:ID  -0.00129988:0.00222956:0.251812:0.868225:rs3115858