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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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/dev/ieu-a-import/processed/ieu-a-836/ieu-a-836.vcf.gz \
--ref-ld-chr /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-836/ldsc.txt \
--w-ld-chr /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/reference/eur_w_ld_chr/ 

Beginning analysis at Tue Feb  4 18:56:58 2020
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-836/ieu-a-836.vcf.gz ...
Read summary statistics for 2318883 SNPs.
Reading reference panel LD Score from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/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 /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/reference/eur_w_ld_chr/[1-22] ...
Read regression weight LD Scores for 1290028 SNPs.
After merging with reference panel LD, 1112134 SNPs remain.
After merging with regression SNP LD, 1112134 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0785 (0.0057)
Lambda GC: 1.1623
Mean Chi^2: 1.2237
Intercept: 1.0235 (0.0084)
Ratio: 0.1053 (0.0376)
Analysis finished at Tue Feb  4 18:57:26 2020
Total time elapsed: 27.78s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9101,
    "inflation_factor": 1.2058,
    "mean_EFFECT": 0.0001,
    "n": 126559,
    "n_snps": 2318883,
    "n_clumped_hits": 3,
    "n_p_sig": 61,
    "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": 18238,
    "n_est": 142077.7598,
    "ratio_se_n": 1.0595,
    "mean_diff": -0,
    "ratio_diff": 13.7368,
    "sd_y_est1": 2.2925,
    "sd_y_est2": 2.429,
    "r2_sum1": 0.0056,
    "r2_sum2": 0.0011,
    "r2_sum3": 0.001,
    "r2_sum4": 0.0011,
    "ldsc_nsnp_merge_refpanel_ld": 1112134,
    "ldsc_nsnp_merge_regression_ld": 1112134,
    "ldsc_observed_scale_h2_beta": 0.0785,
    "ldsc_observed_scale_h2_se": 0.0057,
    "ldsc_intercept_beta": 1.0235,
    "ldsc_intercept_se": 0.0084,
    "ldsc_lambda_gc": 1.1623,
    "ldsc_mean_chisq": 1.2237,
    "ldsc_ratio": 0.1051
}

Flags

name value
af_correlation FALSE
inflation_factor TRUE
n FALSE
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 numeric.mean numeric.sd numeric.p0 numeric.p25 numeric.p50 numeric.p75 numeric.p100 numeric.hist
character ID 0 1.000000 3 42 0 2318883 0 NA NA NA NA NA NA NA NA
character REF 0 1.000000 1 1 0 4 0 NA NA NA NA NA NA NA NA
character ALT 0 1.000000 1 1 0 4 0 NA NA NA NA NA NA NA NA
numeric CHROM 0 1.000000 NA NA NA NA NA 8.566181e+00 5.646292e+00 1.00000e+00 4.000000e+00 8.000000e+00 1.200000e+01 2.300000e+01 ▇▅▅▂▂
numeric POS 0 1.000000 NA NA NA NA NA 7.887149e+07 5.557276e+07 1.61110e+04 3.279890e+07 7.032197e+07 1.142716e+08 2.492107e+08 ▇▇▅▂▁
numeric EFFECT 0 1.000000 NA NA NA NA NA 5.650000e-05 1.566520e-02 -1.38021e-01 -9.040700e-03 0.000000e+00 9.040700e-03 1.388920e-01 ▁▁▇▁▁
numeric SE 0 1.000000 NA NA NA NA NA 1.358060e-02 5.100600e-03 9.00000e-03 1.000000e-02 1.100000e-02 1.500000e-02 4.700000e-02 ▇▂▁▁▁
numeric PVAL 0 1.000000 NA NA NA NA NA 4.701528e-01 2.967237e-01 0.00000e+00 2.057998e-01 4.588999e-01 7.276994e-01 1.000000e+00 ▇▆▆▆▆
numeric PVAL_ztest 0 1.000000 NA NA NA NA NA 4.713971e-01 2.975433e-01 0.00000e+00 2.062659e-01 4.652696e-01 7.254151e-01 1.000000e+00 ▇▆▆▆▆
numeric AF 0 1.000000 NA NA NA NA NA 3.672074e-01 2.691351e-01 1.00000e-02 1.300000e-01 3.100000e-01 5.700000e-01 9.900000e-01 ▇▅▃▃▂
numeric AF_reference 18238 0.992135 NA NA NA NA NA 3.696519e-01 2.504941e-01 1.99700e-04 1.591450e-01 3.121010e-01 5.519170e-01 1.000000e+00 ▇▇▅▃▂
numeric N 0 1.000000 NA NA NA NA NA 1.265590e+05 0.000000e+00 1.26559e+05 1.265590e+05 1.265590e+05 1.265590e+05 1.265590e+05 ▁▁▇▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 998501 rs3813193 G C -0.0151136 0.014 0.2823001 0.2803458 0.16 0.206669 126559
1 1003629 rs4075116 C T 0.0178399 0.012 0.1198999 0.1371051 0.78 0.720647 126559
1 1005806 rs3934834 C T -0.0202027 0.014 0.1484998 0.1490064 0.13 0.223442 126559
1 1017170 rs3766193 C G 0.0242927 0.009 0.0129101 0.0069509 0.60 0.575479 126559
1 1017197 rs3766192 C T 0.0256677 0.010 0.0087339 0.0102651 0.61 0.511182 126559
1 1017587 rs3766191 C T -0.0232686 0.014 0.0964495 0.0965042 0.11 0.171126 126559
1 1018562 rs9442371 C T 0.0246926 0.010 0.0116600 0.0135393 0.62 0.530152 126559
1 1018704 rs9442372 A G 0.0232686 0.009 0.0177301 0.0097266 0.63 0.611022 126559
1 1021346 rs10907177 A G -0.0266419 0.014 0.0541801 0.0570415 0.13 0.178914 126559
1 1021415 rs3737728 A G 0.0181640 0.011 0.0920407 0.0986829 0.74 0.812700 126559
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51163138 rs715586 C T 0.0178399 0.014 0.2006000 0.2025647 0.16 0.0902556 126559
22 51165664 rs8137951 G A -0.0130852 0.010 0.2256000 0.1906970 0.26 0.4063500 126559
22 51171497 rs2301584 G A -0.0120726 0.013 0.3904002 0.3530645 0.14 0.2533950 126559
22 51175626 rs3810648 A G -0.0544882 0.022 0.0094161 0.0132590 0.07 0.1084270 126559
22 51178090 rs2285395 G A -0.0534008 0.020 0.0103999 0.0075842 0.07 0.0666933 126559
22 51196164 rs8136603 A T -0.0525924 0.023 0.0152999 0.0222177 0.07 0.1427720 126559
23 35921591 rs2204667 C G -0.0049875 0.013 0.7195997 0.7012327 0.16 NA 126559
23 51666786 rs14115 A G -0.0305292 0.022 0.1458999 0.1652312 0.03 NA 126559
23 70163799 rs1626496 A C -0.0314987 0.019 0.0861807 0.0973525 0.07 NA 126559
23 118495837 rs12882977 G A -0.0040080 0.010 0.6519000 0.6885659 0.49 0.2307280 126559

bcf preview

1   998501  rs3813193   G   C   .   PASS    AF=0.16 ES:SE:LP:AF:SS:ID   -0.0151136:0.014:0.549289:0.16:126559:rs3813193
1   1003629 rs4075116   C   T   .   PASS    AF=0.78 ES:SE:LP:AF:SS:ID   0.0178399:0.012:0.921181:0.78:126559:rs4075116
1   1005806 rs3934834   C   T   .   PASS    AF=0.13 ES:SE:LP:AF:SS:ID   -0.0202027:0.014:0.828274:0.13:126559:rs3934834
1   1017170 rs3766193   C   G   .   PASS    AF=0.6  ES:SE:LP:AF:SS:ID   0.0242927:0.009:1.88907:0.6:126559:rs3766193
1   1017197 rs3766192   C   T   .   PASS    AF=0.61 ES:SE:LP:AF:SS:ID   0.0256677:0.01:2.05879:0.61:126559:rs3766192
1   1017587 rs3766191   C   T   .   PASS    AF=0.11 ES:SE:LP:AF:SS:ID   -0.0232686:0.014:1.0157:0.11:126559:rs3766191
1   1018562 rs9442371   C   T   .   PASS    AF=0.62 ES:SE:LP:AF:SS:ID   0.0246926:0.01:1.9333:0.62:126559:rs9442371
1   1018704 rs9442372   A   G   .   PASS    AF=0.63 ES:SE:LP:AF:SS:ID   0.0232686:0.009:1.75129:0.63:126559:rs9442372
1   1021346 rs10907177  A   G   .   PASS    AF=0.13 ES:SE:LP:AF:SS:ID   -0.0266419:0.014:1.26616:0.13:126559:rs10907177
1   1021415 rs3737728   A   G   .   PASS    AF=0.74 ES:SE:LP:AF:SS:ID   0.018164:0.011:1.03602:0.74:126559:rs3737728
1   1021583 rs10907178  A   C   .   PASS    AF=0.11 ES:SE:LP:AF:SS:ID   -0.0237165:0.014:1.04101:0.11:126559:rs10907178
1   1021695 rs9442398   A   G   .   PASS    AF=0.76 ES:SE:LP:AF:SS:ID   0.0161294:0.011:0.865186:0.76:126559:rs9442398
1   1022037 rs6701114   C   T   .   PASS    AF=0.59 ES:SE:LP:AF:SS:ID   0.0266419:0.01:2.13811:0.59:126559:rs6701114
1   1030565 rs6687776   C   T   .   PASS    AF=0.09 ES:SE:LP:AF:SS:ID   -0.0283995:0.013:1.41976:0.09:126559:rs6687776
1   1030633 rs6678318   G   A   .   PASS    AF=0.09 ES:SE:LP:AF:SS:ID   -0.0242927:0.014:1.07526:0.09:126559:rs6678318
1   1031540 rs9651273   A   G   .   PASS    AF=0.68 ES:SE:LP:AF:SS:ID   0.00601807:0.012:0.204328:0.68:126559:rs9651273
1   1036959 rs11579015  T   C   .   PASS    AF=0.06 ES:SE:LP:AF:SS:ID   -0.0285875:0.017:1.09055:0.06:126559:rs11579015
1   1040026 rs6671356   T   C   .   PASS    AF=0.08 ES:SE:LP:AF:SS:ID   -0.0207825:0.015:0.83654:0.08:126559:rs6671356
1   1046164 rs6666280   C   T   .   PASS    AF=0.07 ES:SE:LP:AF:SS:ID   -0.0202027:0.015:0.769551:0.07:126559:rs6666280
1   1048955 rs4970405   A   G   .   PASS    AF=0.06 ES:SE:LP:AF:SS:ID   -0.0276152:0.017:0.993106:0.06:126559:rs4970405
1   1049950 rs12726255  A   G   .   PASS    AF=0.07 ES:SE:LP:AF:SS:ID   -0.0158733:0.015:0.526075:0.07:126559:rs12726255
1   1053452 rs4970409   G   A   .   PASS    AF=0.06 ES:SE:LP:AF:SS:ID   -0.0191828:0.017:0.592099:0.06:126559:rs4970409
1   1060608 rs17160824  G   A   .   PASS    AF=0.06 ES:SE:LP:AF:SS:ID   -0.0161294:0.016:0.497573:0.06:126559:rs17160824
1   1061115 rs17160826  T   C   .   PASS    AF=0.06 ES:SE:LP:AF:SS:ID   -0.0207825:0.017:0.681311:0.06:126559:rs17160826
1   1061152 rs12748370  T   C   .   PASS    AF=0.06 ES:SE:LP:AF:SS:ID   -0.0158733:0.017:0.472112:0.06:126559:rs12748370
1   1062638 rs9442373   C   A   .   PASS    AF=0.57 ES:SE:LP:AF:SS:ID   0.00995033:0.011:0.468393:0.57:126559:rs9442373
1   1064979 rs2298217   C   T   .   PASS    AF=0.09 ES:SE:LP:AF:SS:ID   -0.0222456:0.014:0.895513:0.09:126559:rs2298217
1   1066403 rs10907182  T   C   .   PASS    AF=0.7  ES:SE:LP:AF:SS:ID   0.0140989:0.011:0.741842:0.7:126559:rs10907182
1   1077064 rs4970357   C   A   .   PASS    AF=0.93 ES:SE:LP:AF:SS:ID   0.00498754:0.018:0.10585:0.93:126559:rs4970357
1   1087683 rs9442380   T   C   .   PASS    AF=0.91 ES:SE:LP:AF:SS:ID   0.00400802:0.017:0.0830199:0.91:126559:rs9442380
1   1089262 rs4970358   A   G   .   PASS    AF=0.97 ES:SE:LP:AF:SS:ID   0.0100503:0.022:0.186753:0.97:126559:rs4970358
1   1097335 rs9442385   T   G   .   PASS    AF=0.94 ES:SE:LP:AF:SS:ID   0:0.019:0.00484762:0.94:126559:rs9442385
1   1099342 rs9660710   A   C   .   PASS    AF=0.94 ES:SE:LP:AF:SS:ID   0.002002:0.018:0.0303046:0.94:126559:rs9660710
1   1100217 rs1891905   C   T   .   PASS    AF=0.96 ES:SE:LP:AF:SS:ID   0.00796817:0.023:0.146971:0.96:126559:rs1891905
1   1121014 rs3813204   G   A   .   PASS    AF=0.13 ES:SE:LP:AF:SS:ID   -0.00803217:0.016:0.215026:0.13:126559:rs3813204
1   1121794 rs11260549  G   A   .   PASS    AF=0.13 ES:SE:LP:AF:SS:ID   -0.00904074:0.015:0.260428:0.13:126559:rs11260549
1   1124663 rs6684820   G   A   .   PASS    AF=0.28 ES:SE:LP:AF:SS:ID   0.00697561:0.011:0.276052:0.28:126559:rs6684820
1   1125553 rs10907174  A   T   .   PASS    AF=0.24 ES:SE:LP:AF:SS:ID   0.00501254:0.012:0.158515:0.24:126559:rs10907174
1   1129672 rs11260554  G   T   .   PASS    AF=0.13 ES:SE:LP:AF:SS:ID   -0.00300451:0.015:0.0827571:0.13:126559:rs11260554
1   1130727 rs10907175  A   C   .   PASS    AF=0.11 ES:SE:LP:AF:SS:ID   0.0140989:0.017:0.379552:0.11:126559:rs10907175
1   1135242 rs9729550   A   C   .   PASS    AF=0.29 ES:SE:LP:AF:SS:ID   0.00803217:0.011:0.329847:0.29:126559:rs9729550
1   1138913 rs3819001   T   C   .   PASS    AF=0.05 ES:SE:LP:AF:SS:ID   -0.0009995:0.022:0.013497:0.05:126559:rs3819001
1   1140435 rs1815606   G   T   .   PASS    AF=0.33 ES:SE:LP:AF:SS:ID   0.00796817:0.011:0.33395:0.33:126559:rs1815606
1   1143657 rs3753348   C   G   .   PASS    AF=0.03 ES:SE:LP:AF:SS:ID   -0.00498754:0.025:0.075514:0.03:126559:rs3753348
1   1151300 rs3813200   C   T   .   PASS    AF=0.02 ES:SE:LP:AF:SS:ID   0.0411419:0.036:0.633577:0.02:126559:rs3813200
1   1152631 rs11721 C   A   .   PASS    AF=0.09 ES:SE:LP:AF:SS:ID   -0.00601807:0.017:0.14436:0.09:126559:rs11721
1   1156131 rs2887286   T   C   .   PASS    AF=0.19 ES:SE:LP:AF:SS:ID   0.0253178:0.014:1.19159:0.19:126559:rs2887286
1   1158277 rs3813199   G   A   .   PASS    AF=0.11 ES:SE:LP:AF:SS:ID   0.00598207:0.016:0.152859:0.11:126559:rs3813199
1   1162435 rs3766186   C   A   .   PASS    AF=0.11 ES:SE:LP:AF:SS:ID   0.00697561:0.016:0.176004:0.11:126559:rs3766186
1   1163804 rs7515488   C   T   .   PASS    AF=0.15 ES:SE:LP:AF:SS:ID   -0.00702462:0.013:0.217527:0.15:126559:rs7515488