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-1023/ieu-a-1023.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-1023/ldsc.txt \
--w-ld-chr /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/reference/eur_w_ld_chr/ 

Beginning analysis at Wed Feb  5 09:20:47 2020
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-1023/ieu-a-1023.vcf.gz ...
Read summary statistics for 2673086 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, 1120704 SNPs remain.
After merging with regression SNP LD, 1120704 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0465 (0.1498)
Lambda GC: 1.024
Mean Chi^2: 1.0279
Intercept: 1.0255 (0.0072)
Ratio: 0.9151 (0.2598)
Analysis finished at Wed Feb  5 09:21:19 2020
Total time elapsed: 32.23s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.918,
    "inflation_factor": 1.0214,
    "mean_EFFECT": -0.0001,
    "n": 2469,
    "n_snps": 2673086,
    "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": 20307,
    "n_est": 2440.1042,
    "ratio_se_n": 0.9941,
    "mean_diff": -0.0001,
    "ratio_diff": 23.3144,
    "sd_y_est1": 0.636,
    "sd_y_est2": 0.6323,
    "r2_sum1": 0,
    "r2_sum2": 0,
    "r2_sum3": 0,
    "r2_sum4": 0,
    "ldsc_nsnp_merge_refpanel_ld": 1120704,
    "ldsc_nsnp_merge_regression_ld": 1120704,
    "ldsc_observed_scale_h2_beta": 0.0465,
    "ldsc_observed_scale_h2_se": 0.1498,
    "ldsc_intercept_beta": 1.0255,
    "ldsc_intercept_se": 0.0072,
    "ldsc_lambda_gc": 1.024,
    "ldsc_mean_chisq": 1.0279,
    "ldsc_ratio": 0.914
}

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 numeric.mean numeric.sd numeric.p0 numeric.p25 numeric.p50 numeric.p75 numeric.p100 numeric.hist
character ID 0 1.0000000 3 42 0 2673086 0 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
character ALT 0 1.0000000 1 1 0 4 0 NA NA NA NA NA NA NA NA
numeric CHROM 0 1.0000000 NA NA NA NA NA 8.489561e+00 5.631586e+00 1.0000000 4.000000e+00 8.000000e+00 1.200000e+01 2.300000e+01 ▇▅▅▂▁
numeric POS 0 1.0000000 NA NA NA NA NA 7.937692e+07 5.551998e+07 6689.0000000 3.351035e+07 7.069825e+07 1.146020e+08 2.491987e+08 ▇▇▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA -9.420000e-05 3.057940e-02 -0.3270960 -1.696240e-02 -5.230000e-05 1.676280e-02 3.902800e-01 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 2.754620e-02 1.233070e-02 0.0167374 1.926560e-02 2.285060e-02 3.092290e-02 1.030880e-01 ▇▂▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.964789e-01 2.898211e-01 0.0000005 2.443713e-01 4.954490e-01 7.475358e-01 9.999997e-01 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.964789e-01 2.898211e-01 0.0000005 2.443716e-01 4.954496e-01 7.475357e-01 9.999997e-01 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA 3.426217e-01 2.733125e-01 0.0100005 1.117020e-01 2.580975e-01 5.369920e-01 9.899960e-01 ▇▅▂▂▂
numeric AF_reference 20307 0.9924032 NA NA NA NA NA 3.348151e-01 2.763268e-01 0.0001997 9.904150e-02 2.567890e-01 5.261580e-01 1.000000e+00 ▇▅▃▂▂
numeric N 0 1.0000000 NA NA NA NA NA 2.469000e+03 0.000000e+00 2469.0000000 2.469000e+03 2.469000e+03 2.469000e+03 2.469000e+03 ▁▁▇▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 721290 rs12565286 G C 0.0575874 0.0510987 0.2597497 0.2597494 0.0315041 0.0371406 2469
1 740857 rs12082473 G A 0.0045684 0.0231006 0.8432315 0.8432316 0.1826490 0.0585064 2469
1 752566 rs3094315 G A 0.0275463 0.0182732 0.1316910 0.1316902 0.4542140 0.7182510 2469
1 754192 rs3131968 A G -0.0015357 0.0213014 0.9425285 0.9425283 0.3619530 0.6785140 2469
1 761732 rs2286139 C T -0.0126810 0.0205675 0.5375291 0.5375281 0.2750100 0.6257990 2469
1 765269 rs11240776 A G -0.0010803 0.0612693 0.9859325 0.9859326 0.0219067 0.0065895 2469
1 777122 rs2980319 A T 0.0065806 0.0179709 0.7142282 0.7142289 0.4927070 0.7472040 2469
1 779322 rs4040617 A G -0.0024602 0.0186629 0.8951256 0.8951260 0.4300100 0.2264380 2469
1 785050 rs2905062 G A -0.0043983 0.0208090 0.8326015 0.8326011 0.2770300 0.6269970 2469
1 785989 rs2980300 T C -0.0047814 0.0206647 0.8170217 0.8170214 0.2735430 0.6269970 2469
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51217134 rs117417021 A G -0.0240230 0.0195531 0.2192194 0.2192206 0.5255870 0.2671730 2469
22 51219006 rs28729663 G A -0.0173475 0.0187089 0.3538058 0.3538058 0.3369210 0.2052720 2469
23 35921591 rs2204667 C G 0.0229185 0.0244281 0.3481401 0.3481404 0.1704600 NA 2469
23 51115886 rs17864968 C G 0.0382114 0.0300448 0.2034398 0.2034392 0.0981794 NA 2469
23 51666786 rs14115 A G 0.0037012 0.0197591 0.8514115 0.8514111 0.2739310 NA 2469
23 57663373 rs28962478 A G 0.0344613 0.0380681 0.3653306 0.3653308 0.0585409 NA 2469
23 70163799 rs1626496 A C 0.0134311 0.0255358 0.5989092 0.5989081 0.1551470 NA 2469
23 91415872 rs6562597 G A 0.0319407 0.0330358 0.3336199 0.3336185 0.0912619 0.0021192 2469
23 118495837 rs12882977 G A 0.0024646 0.0204652 0.9041429 0.9041431 0.2552720 0.2307280 2469
23 147220746 rs2944613 T A -0.0736313 0.0764468 0.3354617 0.3354620 0.0142719 NA 2469

bcf preview

1   721290  rs12565286  G   C   .   PASS    AF=0.0315041    ES:SE:LP:AF:SS:ID   0.0575874:0.0510987:0.585445:0.0315041:2469:rs12565286
1   740857  rs12082473  G   A   .   PASS    AF=0.182649 ES:SE:LP:AF:SS:ID   0.00456841:0.0231006:0.0740532:0.182649:2469:rs12082473
1   752566  rs3094315   G   A   .   PASS    AF=0.454214 ES:SE:LP:AF:SS:ID   0.0275463:0.0182732:0.880444:0.454214:2469:rs3094315
1   754192  rs3131968   A   G   .   PASS    AF=0.361953 ES:SE:LP:AF:SS:ID   -0.00153567:0.0213014:0.0257055:0.361953:2469:rs3131968
1   761732  rs2286139   C   T   .   PASS    AF=0.27501  ES:SE:LP:AF:SS:ID   -0.012681:0.0205675:0.269598:0.27501:2469:rs2286139
1   765269  rs11240776  A   G   .   PASS    AF=0.0219067    ES:SE:LP:AF:SS:ID   -0.00108029:0.0612693:0.00615281:0.0219067:2469:rs11240776
1   777122  rs2980319   A   T   .   PASS    AF=0.492707 ES:SE:LP:AF:SS:ID   0.00658063:0.0179709:0.146163:0.492707:2469:rs2980319
1   779322  rs4040617   A   G   .   PASS    AF=0.43001  ES:SE:LP:AF:SS:ID   -0.00246016:0.0186629:0.048116:0.43001:2469:rs4040617
1   785050  rs2905062   G   A   .   PASS    AF=0.27703  ES:SE:LP:AF:SS:ID   -0.00439833:0.020809:0.0795628:0.27703:2469:rs2905062
1   785989  rs2980300   T   C   .   PASS    AF=0.273543 ES:SE:LP:AF:SS:ID   -0.00478135:0.0206647:0.0877664:0.273543:2469:rs2980300
1   792480  rs2905036   C   T   .   PASS    AF=0.915755 ES:SE:LP:AF:SS:ID   0.0151938:0.0319691:0.197501:0.915755:2469:rs2905036
1   798959  rs11240777  G   A   .   PASS    AF=0.659781 ES:SE:LP:AF:SS:ID   -0.00182561:0.0190766:0.0344411:0.659781:2469:rs11240777
1   799463  rs4245756   T   C   .   PASS    AF=0.926661 ES:SE:LP:AF:SS:ID   -0.0103675:0.0337637:0.119874:0.926661:2469:rs4245756
1   888659  rs3748597   T   C   .   PASS    AF=0.916328 ES:SE:LP:AF:SS:ID   -0.0070966:0.0319648:0.0839127:0.916328:2469:rs3748597
1   918573  rs2341354   A   G   .   PASS    AF=0.322811 ES:SE:LP:AF:SS:ID   0.00246417:0.0190656:0.0471289:0.322811:2469:rs2341354
1   926431  rs4970403   A   T   .   PASS    AF=0.733793 ES:SE:LP:AF:SS:ID   0.0486438:0.0204516:1.75985:0.733793:2469:rs4970403
1   947034  rs2465126   G   A   .   PASS    AF=0.550731 ES:SE:LP:AF:SS:ID   0.012342:0.0180656:0.305836:0.550731:2469:rs2465126
1   949608  rs1921  G   A   .   PASS    AF=0.406352 ES:SE:LP:AF:SS:ID   0.0174629:0.0180721:0.476385:0.406352:2469:rs1921
1   990417  rs2465136   T   C   .   PASS    AF=0.599834 ES:SE:LP:AF:SS:ID   0.014697:0.0184642:0.370541:0.599834:2469:rs2465136
1   990839  rs13129 C   T   .   PASS    AF=0.0911669    ES:SE:LP:AF:SS:ID   -0.0361281:0.0307398:0.620007:0.0911669:2469:rs13129
1   1003629 rs4075116   C   T   .   PASS    AF=0.446217 ES:SE:LP:AF:SS:ID   -0.00529928:0.0180141:0.114285:0.446217:2469:rs4075116
1   1017216 rs6667248   A   G   .   PASS    AF=0.191002 ES:SE:LP:AF:SS:ID   0.0108988:0.0227185:0.199683:0.191002:2469:rs6667248
1   1017598 rs12096277  A   G   .   PASS    AF=0.185119 ES:SE:LP:AF:SS:ID   0.00541836:0.0255925:0.0797055:0.185119:2469:rs12096277
1   1018704 rs9442372   A   G   .   PASS    AF=0.582052 ES:SE:LP:AF:SS:ID   0.0143792:0.0182455:0.365884:0.582052:2469:rs9442372
1   1039098 rs11260595  C   A   .   PASS    AF=0.0777823    ES:SE:LP:AF:SS:ID   0.00761918:0.0335141:0.0861028:0.0777823:2469:rs11260595
1   1041700 rs6604968   A   G   .   PASS    AF=0.451397 ES:SE:LP:AF:SS:ID   -0.00388878:0.0179798:0.081569:0.451397:2469:rs6604968
1   1048955 rs4970405   A   G   .   PASS    AF=0.0245138    ES:SE:LP:AF:SS:ID   0.0581234:0.0574166:0.506696:0.0245138:2469:rs4970405
1   1089699 rs6686003   G   A   .   PASS    AF=0.266005 ES:SE:LP:AF:SS:ID   0.0207149:0.0201496:0.517233:0.266005:2469:rs6686003
1   1089830 rs6700376   A   G   .   PASS    AF=0.265013 ES:SE:LP:AF:SS:ID   0.0205012:0.0202276:0.507505:0.265013:2469:rs6700376
1   1090557 rs7553429   A   C   .   PASS    AF=0.287639 ES:SE:LP:AF:SS:ID   0.0162646:0.0207569:0.363223:0.287639:2469:rs7553429
1   1097335 rs9442385   T   G   .   PASS    AF=0.824561 ES:SE:LP:AF:SS:ID   -0.0178453:0.0234921:0.349232:0.824561:2469:rs9442385
1   1099342 rs9660710   A   C   .   PASS    AF=0.815605 ES:SE:LP:AF:SS:ID   -0.0187096:0.0243111:0.355029:0.815605:2469:rs9660710
1   1121794 rs11260549  G   A   .   PASS    AF=0.0471416    ES:SE:LP:AF:SS:ID   -0.0809565:0.0458485:1.11104:0.0471416:2469:rs11260549
1   1125553 rs10907174  A   T   .   PASS    AF=0.174785 ES:SE:LP:AF:SS:ID   -0.0337193:0.0253087:0.738133:0.174785:2469:rs10907174
1   1129672 rs11260554  G   T   .   PASS    AF=0.0444399    ES:SE:LP:AF:SS:ID   -0.0804887:0.0428889:1.2178:0.0444399:2469:rs11260554
1   1130727 rs10907175  A   C   .   PASS    AF=0.124747 ES:SE:LP:AF:SS:ID   -0.0214748:0.0274474:0.362531:0.124747:2469:rs10907175
1   1156131 rs2887286   T   C   .   PASS    AF=0.477724 ES:SE:LP:AF:SS:ID   0.0165591:0.0177453:0.455015:0.477724:2469:rs2887286
1   1158277 rs3813199   G   A   .   PASS    AF=0.162885 ES:SE:LP:AF:SS:ID   -0.0397701:0.0241472:1.00191:0.162885:2469:rs3813199
1   1158631 rs6603781   A   G   .   PASS    AF=0.979107 ES:SE:LP:AF:SS:ID   -0.0698453:0.0631785:0.570356:0.979107:2469:rs6603781
1   1162435 rs3766186   C   A   .   PASS    AF=0.161643 ES:SE:LP:AF:SS:ID   -0.0397869:0.0246167:0.974536:0.161643:2469:rs3766186
1   1163804 rs7515488   C   T   .   PASS    AF=0.204105 ES:SE:LP:AF:SS:ID   -0.0075916:0.0238577:0.124747:0.204105:2469:rs7515488
1   1165310 rs11260562  G   A   .   PASS    AF=0.162942 ES:SE:LP:AF:SS:ID   0.00919997:0.0241554:0.152858:0.162942:2469:rs11260562
1   1182031 rs7539412   C   T   .   PASS    AF=0.0421169    ES:SE:LP:AF:SS:ID   -0.0151272:0.0449876:0.132721:0.0421169:2469:rs7539412
1   1195690 rs11260568  G   C   .   PASS    AF=0.0791819    ES:SE:LP:AF:SS:ID   0.0248581:0.0320627:0.358363:0.0791819:2469:rs11260568
1   1196471 rs6673601   G   A   .   PASS    AF=0.0435399    ES:SE:LP:AF:SS:ID   -0.0117675:0.0432358:0.104859:0.0435399:2469:rs6673601
1   1198618 rs12563338  T   A   .   PASS    AF=0.244633 ES:SE:LP:AF:SS:ID   0.0297526:0.0210641:0.801866:0.244633:2469:rs12563338
1   1203938 rs4018608   T   C   .   PASS    AF=0.254566 ES:SE:LP:AF:SS:ID   0.0276196:0.0214065:0.705611:0.254566:2469:rs4018608
1   1206343 rs6667923   C   A   .   PASS    AF=0.226396 ES:SE:LP:AF:SS:ID   0.00600136:0.0230953:0.0996452:0.226396:2469:rs6667923
1   1211292 rs6685064   C   T   .   PASS    AF=0.510126 ES:SE:LP:AF:SS:ID   0.0166:0.0179436:0.449889:0.510126:2469:rs6685064
1   1217058 rs3753340   G   A   .   PASS    AF=0.0931652    ES:SE:LP:AF:SS:ID   0.0215259:0.0302967:0.321125:0.0931652:2469:rs3753340