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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    "gwas_harmonisation_command": "--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/vcf_09_19b/bgzip_vcf/data.batch_41203_6262.vcf.gz --id UKB-b:471 --data /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/raw-output/data.batch_41203_6262.txt.gz --cohort_cases 1374 --cohort_controls 461636 --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-471/UKB-b-471_data.vcf.gz \
--ref-ld-chr ../reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-471/ldsc.txt \
--w-ld-chr ../reference/eur_w_ld_chr/ 

Beginning analysis at Thu Oct 17 14:44:38 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-471/UKB-b-471_data.vcf.gz ...
Read summary statistics for 2269961 SNPs.
Dropped 247 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, 577994 SNPs remain.
After merging with regression SNP LD, 577994 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0025 (0.0016)
Lambda GC: 1.1283
Mean Chi^2: 1.1323
Intercept: 1.1055 (0.0125)
Ratio: 0.7975 (0.0945)
Analysis finished at Thu Oct 17 14:45:11 2019
Total time elapsed: 32.94s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.7382,
    "inflation_factor": 1.1474,
    "mean_EFFECT": 7.8291e-07,
    "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": 17959,
    "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": 577994,
    "ldsc_nsnp_merge_regression_ld": 577994,
    "ldsc_observed_scale_h2_beta": 0.0025,
    "ldsc_observed_scale_h2_se": 0.0016,
    "ldsc_intercept_beta": 1.1055,
    "ldsc_intercept_se": 0.0125,
    "ldsc_lambda_gc": 1.1283,
    "ldsc_mean_chisq": 1.1323,
    "ldsc_ratio": 0.7974
}
 

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 4 58 0 2269716 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 2269961 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 8.649782e+00 5.767584e+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 7.862317e+07 5.665141e+07 5687.0000000 3.174045e+07 6.908611e+07 1.147501e+08 2.491722e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA NA NA 8.000000e-07 1.264000e-04 -0.0006445 -8.410000e-05 6.000000e-07 8.570000e-05 6.381000e-04 ▁▂▇▂▁
numeric SE 0 1.0000000 NA NA NA NA NA NA NA 1.186000e-04 5.400000e-06 0.0001087 1.140000e-04 1.170000e-04 1.222000e-04 2.347000e-04 ▇▁▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA NA NA 4.800860e-01 2.940112e-01 0.0000002 2.200002e-01 4.700002e-01 7.300002e-01 1.000000e+00 ▇▇▆▆▆
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA NA NA 4.800899e-01 2.939845e-01 0.0000002 2.193670e-01 4.732861e-01 7.349008e-01 9.999990e-01 ▇▇▇▆▆
numeric AF 0 1.0000000 NA NA NA NA NA NA NA 4.609558e-01 1.398114e-01 0.2547310 3.380320e-01 4.421390e-01 5.742500e-01 7.452690e-01 ▇▆▅▅▃
numeric AF_reference 17959 0.9920884 NA NA NA NA NA NA NA 4.417252e-01 1.691382e-01 0.0001997 3.097040e-01 4.291130e-01 5.648960e-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 0.0002409 0.0002000 0.2300001 0.2284749 0.623765 0.7821490 NA
1 54676 rs2462492 C T 0.0001665 0.0001981 0.4000000 0.4007060 0.400401 NA NA
1 91536 rs6702460 G T 0.0004890 0.0001951 0.0120000 0.0122040 0.456846 0.4207270 NA
1 706368 rs55727773 A G -0.0002586 0.0001383 0.0619998 0.0615594 0.515645 0.2751600 NA
1 763394 rs369924889 G A -0.0002188 0.0001622 0.1800002 0.1773925 0.706753 0.6176120 NA
1 776546 rs12124819 A G -0.0001076 0.0001479 0.4700002 0.4668228 0.265385 0.0756789 NA
1 814495 rs74461805 C A 0.0000114 0.0001897 0.9500000 0.9520846 0.340396 NA NA
1 830181 rs28444699 A G -0.0000437 0.0001269 0.7300002 0.7307720 0.697255 0.6912940 NA
1 831489 rs4970385 C T -0.0000636 0.0001246 0.6100002 0.6095247 0.705397 0.6491610 NA
1 831909 rs9697642 C T -0.0000689 0.0001246 0.5800000 0.5803713 0.705442 0.6485620 NA
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51174662 rs1858748 T C 0.0001429 0.0001338 0.2900000 0.2855802 0.737429 0.732827 NA
22 51180501 rs5770999 T C 0.0001296 0.0001302 0.3200000 0.3195489 0.713656 0.636981 NA
22 51181919 rs9616825 G C 0.0000943 0.0001296 0.4700002 0.4665404 0.695470 0.619409 NA
22 51182485 rs6009961 A G 0.0001251 0.0001306 0.3400001 0.3381317 0.715502 0.638379 NA
22 51186143 rs2879914 T C 0.0002114 0.0001211 0.0810009 0.0810277 0.381825 0.273363 NA
22 51186228 rs3865766 C T 0.0000501 0.0001181 0.6700003 0.6713521 0.451061 0.453275 NA
22 51197266 rs61290853 A G 0.0000601 0.0001219 0.6200004 0.6219613 0.386333 0.422923 NA
22 51211106 rs9628250 T C 0.0000768 0.0001368 0.5700002 0.5747179 0.271547 0.167133 NA
22 51212875 rs2238837 A C 0.0001313 0.0001300 0.3100002 0.3124402 0.331457 0.372404 NA
22 51237063 rs3896457 T C 0.0002942 0.0001331 0.0269998 0.0270614 0.297974 0.205072 NA

bcf preview

1   49298   rs10399793  T   C   .   PASS    AF=0.623765 ES:SE:LP:AF:ID  0.000240869:0.000200008:0.638272:0.623765:rs10399793
1   54676   rs2462492   C   T   .   PASS    AF=0.400401 ES:SE:LP:AF:ID  0.000166515:0.000198147:0.39794:0.400401:rs2462492
1   91536   rs6702460   G   T   .   PASS    AF=0.456846 ES:SE:LP:AF:ID  0.000488955:0.000195099:1.92082:0.456846:rs6702460
1   706368  rs12029736  A   G   .   PASS    AF=0.515645 ES:SE:LP:AF:ID  -0.000258628:0.000138344:1.20761:0.515645:rs12029736
1   763394  rs3115847   G   A   .   PASS    AF=0.706753 ES:SE:LP:AF:ID  -0.000218773:0.000162195:0.744727:0.706753:rs3115847
1   776546  rs12124819  A   G   .   PASS    AF=0.265385 ES:SE:LP:AF:ID  -0.000107601:0.000147873:0.327902:0.265385:rs12124819
1   814495  rs74461805  C   A   .   PASS    AF=0.340396 ES:SE:LP:AF:ID  1.13985e-05:0.000189693:0.0222764:0.340396:rs74461805
1   830181  rs28444699  A   G   .   PASS    AF=0.697255 ES:SE:LP:AF:ID  -4.36713e-05:0.000126915:0.136677:0.697255:rs28444699
1   831489  rs4970385   C   T   .   PASS    AF=0.705397 ES:SE:LP:AF:ID  -6.36489e-05:0.000124618:0.21467:0.705397:rs4970385
1   831909  rs9697642   C   T   .   PASS    AF=0.705442 ES:SE:LP:AF:ID  -6.88919e-05:0.000124614:0.236572:0.705442:rs9697642
1   832066  rs9697380   G   C   .   PASS    AF=0.705627 ES:SE:LP:AF:ID  -6.25627e-05:0.000124619:0.207608:0.705627:rs9697380
1   832318  rs4500250   C   A   .   PASS    AF=0.705655 ES:SE:LP:AF:ID  -6.19063e-05:0.000124633:0.207608:0.705655:rs4500250
1   832398  rs4553118   T   C   .   PASS    AF=0.730129 ES:SE:LP:AF:ID  -5.51668e-05:0.000128028:0.173925:0.730129:rs4553118
1   832918  rs28765502  T   C   .   PASS    AF=0.294377 ES:SE:LP:AF:ID  6.13375e-05:0.000124627:0.207608:0.294377:rs28765502
1   836896  rs28705752  T   C   .   PASS    AF=0.269511 ES:SE:LP:AF:ID  0.000166343:0.000127039:0.721246:0.269511:rs28705752
1   839103  rs28562941  A   G   .   PASS    AF=0.270019 ES:SE:LP:AF:ID  0.000167612:0.000127129:0.721246:0.270019:rs28562941
1   840753  rs4970382   T   C   .   PASS    AF=0.400124 ES:SE:LP:AF:ID  8.29865e-05:0.000114949:0.327902:0.400124:rs4970382
1   843405  rs11516185  A   G   .   PASS    AF=0.362606 ES:SE:LP:AF:ID  0.000151943:0.000142693:0.537602:0.362606:rs11516185
1   850218  rs6664536   T   A   .   PASS    AF=0.590331 ES:SE:LP:AF:ID  -0.00010491:0.000114614:0.443698:0.590331:rs6664536
1   850371  rs6679046   G   T   .   PASS    AF=0.603723 ES:SE:LP:AF:ID  -0.000107854:0.000115257:0.455932:0.603723:rs6679046
1   850780  rs6657440   C   T   .   PASS    AF=0.603942 ES:SE:LP:AF:ID  -0.000126237:0.000115241:0.568636:0.603942:rs6657440
1   852037  rs4970463   G   A   .   PASS    AF=0.589686 ES:SE:LP:AF:ID  -0.000100955:0.0001148:0.420216:0.589686:rs4970463
1   852063  rs28436996  G   A   .   PASS    AF=0.589665 ES:SE:LP:AF:ID  -9.98458e-05:0.000114749:0.420216:0.589665:rs28436996
1   852875  rs13303369  C   T   .   PASS    AF=0.607671 ES:SE:LP:AF:ID  -0.000104814:0.000115499:0.443698:0.607671:rs13303369
1   853954  rs1806509   C   A   .   PASS    AF=0.607829 ES:SE:LP:AF:ID  -0.00010126:0.000115514:0.420216:0.607829:rs1806509
1   854777  rs13303019  A   G   .   PASS    AF=0.610316 ES:SE:LP:AF:ID  -0.00011721:0.000115628:0.508638:0.610316:rs13303019
1   854978  rs13303057  A   C   .   PASS    AF=0.603283 ES:SE:LP:AF:ID  -0.000104026:0.000115285:0.431798:0.603283:rs13303057
1   855075  rs6673914   C   G   .   PASS    AF=0.610337 ES:SE:LP:AF:ID  -0.000121898:0.00011563:0.537602:0.610337:rs6673914
1   856099  rs28534711  T   G   .   PASS    AF=0.389936 ES:SE:LP:AF:ID  0.000118754:0.000115652:0.522879:0.389936:rs28534711
1   856108  rs28742275  A   G   .   PASS    AF=0.38992  ES:SE:LP:AF:ID  0.000114462:0.000115658:0.49485:0.38992:rs28742275
1   856476  rs4040605   A   G   .   PASS    AF=0.350356 ES:SE:LP:AF:ID  6.81616e-05:0.000118813:0.244125:0.350356:rs4040605
1   866893  rs2880024   T   C   .   PASS    AF=0.610552 ES:SE:LP:AF:ID  -6.05038e-05:0.000116279:0.221849:0.610552:rs2880024
1   868418  rs28546443  C   T   .   PASS    AF=0.297867 ES:SE:LP:AF:ID  -5.89093e-05:0.000127757:0.19382:0.297867:rs28546443
1   870645  rs28576697  T   C   .   PASS    AF=0.291285 ES:SE:LP:AF:ID  -7.98711e-05:0.00012674:0.275724:0.291285:rs28576697
1   871334  rs4072383   G   T   .   PASS    AF=0.72062  ES:SE:LP:AF:ID  4.12093e-05:0.000125955:0.130768:0.72062:rs4072383
1   872352  rs1806780   G   C   .   PASS    AF=0.267527 ES:SE:LP:AF:ID  -1.68932e-05:0.000127662:0.05061:0.267527:rs1806780
1   873558  rs1110052   G   T   .   PASS    AF=0.715251 ES:SE:LP:AF:ID  5.38759e-05:0.000124954:0.173925:0.715251:rs1110052
1   875770  rs4970379   A   G   .   PASS    AF=0.600085 ES:SE:LP:AF:ID  -7.46516e-05:0.000117246:0.283997:0.600085:rs4970379
1   881627  rs2272757   G   A   .   PASS    AF=0.652393 ES:SE:LP:AF:ID  -8.64637e-05:0.000118438:0.327902:0.652393:rs2272757
1   891059  rs13303065  C   T   .   PASS    AF=0.652432 ES:SE:LP:AF:ID  -8.31428e-05:0.00011842:0.318759:0.652432:rs13303065
1   891945  rs13303106  A   G   .   PASS    AF=0.652494 ES:SE:LP:AF:ID  -7.85382e-05:0.000118558:0.29243:0.652494:rs13303106
1   900505  rs28705211  G   C   .   PASS    AF=0.271763 ES:SE:LP:AF:ID  2.28654e-05:0.00012817:0.0655015:0.271763:rs28705211
1   903245  rs28690976  A   G   .   PASS    AF=0.566938 ES:SE:LP:AF:ID  -0.000141178:0.000117754:0.638272:0.566938:rs28690976
1   909073  rs3892467   C   T   .   PASS    AF=0.386681 ES:SE:LP:AF:ID  -0.000111038:0.000117434:0.468521:0.386681:rs3892467
1   909238  rs3829740   G   C   .   PASS    AF=0.571408 ES:SE:LP:AF:ID  -0.000130106:0.000113731:0.60206:0.571408:rs3829740
1   910394  rs28477686  C   T   .   PASS    AF=0.324458 ES:SE:LP:AF:ID  8.22881e-05:0.000123272:0.30103:0.324458:rs28477686
1   912049  rs7367995   T   C   .   PASS    AF=0.585249 ES:SE:LP:AF:ID  -7.58002e-05:0.000114884:0.29243:0.585249:rs7367995
1   913889  rs2340596   G   A   .   PASS    AF=0.59921  ES:SE:LP:AF:ID  -8.67443e-05:0.000115071:0.346787:0.59921:rs2340596
1   914333  rs13302979  C   G   .   PASS    AF=0.602516 ES:SE:LP:AF:ID  -9.07897e-05:0.000115419:0.366532:0.602516:rs13302979
1   914852  rs13303368  G   C   .   PASS    AF=0.600074 ES:SE:LP:AF:ID  -9.0167e-05:0.000115198:0.366532:0.600074:rs13303368