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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    "gwas_harmonisation_command": "--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/vcf_09_19b/bgzip_vcf/data.batch_101510.vcf.gz --id UKB-b:2183 --data /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/raw-output/data.batch_101510.txt.gz --cohort_controls 64949 --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-2183/UKB-b-2183_data.vcf.gz \
--ref-ld-chr ../reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-2183/ldsc.txt \
--w-ld-chr ../reference/eur_w_ld_chr/ 

Beginning analysis at Thu Oct 17 14:42:18 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-2183/UKB-b-2183_data.vcf.gz ...
Read summary statistics for 8625255 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, 1285751 SNPs remain.
After merging with regression SNP LD, 1285751 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 3.1521e-05 (0.0069)
Lambda GC: 1.0133
Mean Chi^2: 1.0088
Intercept: 1.0088 (0.0058)
Ratio: 0.9959 (0.6539)
Analysis finished at Thu Oct 17 14:43:53 2019
Total time elapsed: 1.0m:34.43s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9462,
    "inflation_factor": 1,
    "mean_EFFECT": -6.338e-06,
    "n": "-Inf",
    "n_snps": 9851866,
    "n_clumped_hits": 4,
    "n_p_sig": 11,
    "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": 83101,
    "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": 1285751,
    "ldsc_nsnp_merge_regression_ld": 1285751,
    "ldsc_observed_scale_h2_beta": "NA",
    "ldsc_observed_scale_h2_se": "NA",
    "ldsc_intercept_beta": 1.0088,
    "ldsc_intercept_se": 0.0058,
    "ldsc_lambda_gc": 1.0133,
    "ldsc_mean_chisq": 1.0088,
    "ldsc_ratio": 1
}

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 TRUE
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 8617917 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 8625255 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 8.650335e+00 5.760993e+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 7.877026e+07 5.637169e+07 828.0000000 3.238547e+07 6.929218e+07 1.145689e+08 2.492385e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA NA NA -6.300000e-06 4.962600e-03 -0.0471616 -2.146800e-03 -6.510000e-05 1.982500e-03 6.221980e-02 ▁▂▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA NA NA 4.092700e-03 2.793800e-03 0.0016254 1.914100e-03 2.822200e-03 5.532500e-03 2.801970e-02 ▇▂▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA NA NA 4.979529e-01 2.881776e-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 4.979540e-01 2.881502e-01 0.0000000 2.482326e-01 4.965959e-01 7.466067e-01 9.999997e-01 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA NA NA 2.291107e-01 2.594876e-01 0.0053890 2.518600e-02 1.138890e-01 3.626125e-01 9.946110e-01 ▇▂▁▁▁
numeric AF_reference 83101 0.9903654 NA NA NA NA NA NA NA 2.288600e-01 2.514584e-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 -0.0006511 0.0029954 0.8300000 0.8279283 0.623812 0.7821490 NA
1 54676 rs2462492 C T -0.0024143 0.0029867 0.4199997 0.4188897 0.399144 NA NA
1 86028 rs114608975 T C -0.0037049 0.0047544 0.4400003 0.4358308 0.103536 0.0277556 NA
1 91536 rs6702460 G T -0.0038567 0.0029377 0.1900002 0.1892389 0.455916 0.4207270 NA
1 234313 rs8179466 C T -0.0054581 0.0058096 0.3500000 0.3474749 0.074455 NA NA
1 534192 rs6680723 C T -0.0031291 0.0033458 0.3500000 0.3496667 0.242057 NA NA
1 546697 rs12025928 A G 0.0040744 0.0041514 0.3300000 0.3263805 0.912862 NA NA
1 693731 rs12238997 A G 0.0027848 0.0027899 0.3200000 0.3181908 0.117313 0.1417730 NA
1 705882 rs72631875 G A -0.0056205 0.0040665 0.1700000 0.1669287 0.067698 0.0315495 NA
1 706368 rs55727773 A G -0.0026504 0.0020708 0.2000000 0.2005812 0.513304 0.2751600 NA
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51219006 rs28729663 G A 0.0038706 0.0025188 0.1199999 0.1243633 0.136315 0.2052720 NA
22 51219387 rs9616832 T C 0.0019198 0.0032829 0.5600000 0.5586813 0.071797 0.0654952 NA
22 51219704 rs147475742 G A -0.0017304 0.0043672 0.6899999 0.6919296 0.041190 0.0473243 NA
22 51221190 rs369304721 G A 0.0014306 0.0043981 0.7400005 0.7449796 0.048372 NA NA
22 51221731 rs115055839 T C 0.0018154 0.0032836 0.5800000 0.5803505 0.071348 0.0625000 NA
22 51222100 rs114553188 G T 0.0087450 0.0038050 0.0219999 0.0215454 0.054850 0.0880591 NA
22 51223637 rs375798137 G A 0.0088538 0.0038249 0.0210000 0.0206236 0.054470 0.0788738 NA
22 51229805 rs9616985 T C 0.0016492 0.0032938 0.6200004 0.6165749 0.071253 0.0730831 NA
22 51232488 rs376461333 A G 0.0139019 0.0075862 0.0669993 0.0668722 0.020460 NA NA
22 51237063 rs3896457 T C 0.0003022 0.0019885 0.8800001 0.8791921 0.298393 0.2050720 NA

bcf preview

1   49298   rs10399793  T   C   .   PASS    AF=0.623812 ES:SE:LP:AF:ID  -0.000651087:0.00299544:0.0809219:0.623812:rs10399793
1   54676   rs2462492   C   T   .   PASS    AF=0.399144 ES:SE:LP:AF:ID  -0.00241432:0.00298673:0.376751:0.399144:rs2462492
1   86028   rs114608975 T   C   .   PASS    AF=0.103536 ES:SE:LP:AF:ID  -0.00370488:0.0047544:0.356547:0.103536:rs114608975
1   91536   rs6702460   G   T   .   PASS    AF=0.455916 ES:SE:LP:AF:ID  -0.00385666:0.00293766:0.721246:0.455916:rs6702460
1   234313  rs8179466   C   T   .   PASS    AF=0.074455 ES:SE:LP:AF:ID  -0.00545811:0.0058096:0.455932:0.074455:rs8179466
1   534192  rs6680723   C   T   .   PASS    AF=0.242057 ES:SE:LP:AF:ID  -0.00312915:0.00334584:0.455932:0.242057:rs6680723
1   546697  rs12025928  A   G   .   PASS    AF=0.912862 ES:SE:LP:AF:ID  0.00407436:0.00415145:0.481486:0.912862:rs12025928
1   693731  rs12238997  A   G   .   PASS    AF=0.117313 ES:SE:LP:AF:ID  0.00278479:0.00278986:0.49485:0.117313:rs12238997
1   705882  rs72631875  G   A   .   PASS    AF=0.067698 ES:SE:LP:AF:ID  -0.0056205:0.00406652:0.769551:0.067698:rs72631875
1   706368  rs12029736  A   G   .   PASS    AF=0.513304 ES:SE:LP:AF:ID  -0.00265045:0.00207083:0.69897:0.513304:rs12029736
1   714596  rs149887893 T   C   .   PASS    AF=0.033677 ES:SE:LP:AF:ID  0.000492797:0.00516163:0.0362122:0.033677:rs149887893
1   715265  rs12184267  C   T   .   PASS    AF=0.037457 ES:SE:LP:AF:ID  -0.000383532:0.00468134:0.0315171:0.037457:rs12184267
1   715367  rs12184277  A   G   .   PASS    AF=0.037644 ES:SE:LP:AF:ID  -0.000650046:0.00465685:0.05061:0.037644:rs12184277
1   717485  rs12184279  C   A   .   PASS    AF=0.03722  ES:SE:LP:AF:ID  -0.000438897:0.0046994:0.0315171:0.03722:rs12184279
1   717587  rs144155419 G   A   .   PASS    AF=0.016282 ES:SE:LP:AF:ID  0.00249203:0.00737132:0.130768:0.016282:rs144155419
1   720381  rs116801199 G   T   .   PASS    AF=0.03786  ES:SE:LP:AF:ID  -0.000584847:0.00464093:0.0457575:0.03786:rs116801199
1   721290  rs12565286  G   C   .   PASS    AF=0.037955 ES:SE:LP:AF:ID  -0.000618307:0.00462621:0.05061:0.037955:rs12565286
1   722670  rs116030099 T   C   .   PASS    AF=0.102736 ES:SE:LP:AF:ID  -0.000275866:0.00337933:0.0315171:0.102736:rs116030099
1   723891  rs2977670   G   C   .   PASS    AF=0.95809  ES:SE:LP:AF:ID  -2.44837e-05:0.00446822:-0:0.95809:rs2977670
1   724849  rs12126395  C   A   .   PASS    AF=0.03169  ES:SE:LP:AF:ID  -0.00306157:0.00818204:0.148742:0.03169:rs12126395
1   725060  rs865924913 A   T   .   PASS    AF=0.052723 ES:SE:LP:AF:ID  -0.00293569:0.0065904:0.180456:0.052723:rs865924913
1   726794  rs28454925  C   G   .   PASS    AF=0.037449 ES:SE:LP:AF:ID  -0.000492852:0.00465659:0.0362122:0.037449:rs28454925
1   729632  rs116720794 C   T   .   PASS    AF=0.037717 ES:SE:LP:AF:ID  -0.000325928:0.00461801:0.0268721:0.037717:rs116720794
1   729679  rs4951859   C   G   .   PASS    AF=0.841441 ES:SE:LP:AF:ID  -0.000170429:0.00241271:0.0268721:0.841441:rs4951859
1   730087  rs148120343 T   C   .   PASS    AF=0.056334 ES:SE:LP:AF:ID  0.00261679:0.00391932:0.30103:0.056334:rs148120343
1   731718  rs58276399  T   C   .   PASS    AF=0.123078 ES:SE:LP:AF:ID  0.00180172:0.00265004:0.30103:0.123078:rs58276399
1   732989  rs369030935 C   T   .   PASS    AF=0.02513  ES:SE:LP:AF:ID  0.00302572:0.0065995:0.187087:0.02513:rs369030935
1   734349  rs141242758 T   C   .   PASS    AF=0.12233  ES:SE:LP:AF:ID  0.00188936:0.0026509:0.318759:0.12233:rs141242758
1   736289  rs79010578  T   A   .   PASS    AF=0.134139 ES:SE:LP:AF:ID  0.000181512:0.00260229:0.0268721:0.134139:rs79010578
1   736689  rs181876450 T   C   .   PASS    AF=0.011558 ES:SE:LP:AF:ID  -0.00218052:0.00927467:0.091515:0.011558:rs181876450
1   740284  rs61770167  C   T   .   PASS    AF=0.0061   ES:SE:LP:AF:ID  -0.0098785:0.0117777:0.39794:0.0061:rs61770167
1   752478  rs146277091 G   A   .   PASS    AF=0.0376   ES:SE:LP:AF:ID  -0.000219251:0.00457522:0.0177288:0.0376:rs146277091
1   752566  rs3094315   G   A   .   PASS    AF=0.837029 ES:SE:LP:AF:ID  0.000275366:0.00233401:0.0409586:0.837029:rs3094315
1   752721  rs3131972   A   G   .   PASS    AF=0.836733 ES:SE:LP:AF:ID  4.91557e-05:0.00233229:0.00877392:0.836733:rs3131972
1   753405  rs3115860   C   A   .   PASS    AF=0.868562 ES:SE:LP:AF:ID  -0.00128776:0.00250617:0.21467:0.868562:rs3115860
1   753541  rs2073813   G   A   .   PASS    AF=0.131004 ES:SE:LP:AF:ID  0.00162421:0.00251261:0.283997:0.131004:rs2073813
1   754063  rs12184312  G   T   .   PASS    AF=0.038045 ES:SE:LP:AF:ID  -0.00043735:0.00450345:0.0362122:0.038045:rs12184312
1   754105  rs12184325  C   T   .   PASS    AF=0.038292 ES:SE:LP:AF:ID  -0.000410661:0.00447554:0.0315171:0.038292:rs12184325
1   754182  rs3131969   A   G   .   PASS    AF=0.867976 ES:SE:LP:AF:ID  -0.00152543:0.00250214:0.267606:0.867976:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.86805  ES:SE:LP:AF:ID  -0.00154374:0.00250316:0.267606:0.86805:rs3131968
1   754211  rs12184313  G   A   .   PASS    AF=0.038199 ES:SE:LP:AF:ID  -0.000543241:0.00449621:0.0457575:0.038199:rs12184313
1   754334  rs3131967   T   C   .   PASS    AF=0.867987 ES:SE:LP:AF:ID  -0.00152259:0.00250208:0.267606:0.867987:rs3131967
1   754433  rs150578204 G   A   .   PASS    AF=0.005396 ES:SE:LP:AF:ID  0.000286016:0.0125403:0.00877392:0.005396:rs150578204
1   754503  rs3115859   G   A   .   PASS    AF=0.836159 ES:SE:LP:AF:ID  8.35329e-05:0.00232547:0.0132283:0.836159:rs3115859
1   754629  rs10454459  A   G   .   PASS    AF=0.038203 ES:SE:LP:AF:ID  -0.000499498:0.00450277:0.0409586:0.038203:rs10454459
1   754964  rs3131966   C   T   .   PASS    AF=0.836793 ES:SE:LP:AF:ID  0.000106327:0.00233184:0.0177288:0.836793:rs3131966
1   755240  rs181660517 T   G   .   PASS    AF=0.01303  ES:SE:LP:AF:ID  -0.00293686:0.00843635:0.136677:0.01303:rs181660517
1   755435  rs184270342 T   G   .   PASS    AF=0.005662 ES:SE:LP:AF:ID  -0.0025817:0.0125239:0.0757207:0.005662:rs184270342
1   755775  rs3131965   A   G   .   PASS    AF=0.838109 ES:SE:LP:AF:ID  9.22888e-05:0.00236467:0.0132283:0.838109:rs3131965
1   755890  rs3115858   A   T   .   PASS    AF=0.868228 ES:SE:LP:AF:ID  -0.00144227:0.00249886:0.251812:0.868228:rs3115858