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-1020/ieu-a-1020.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-1020/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 09:02:26 2020
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-1020/ieu-a-1020.vcf.gz ...
Read summary statistics for 2578062 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, 1138869 SNPs remain.
After merging with regression SNP LD, 1138869 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0721 (0.1555)
Lambda GC: 1.0265
Mean Chi^2: 1.0286
Intercept: 1.025 (0.0073)
Ratio: 0.8734 (0.2533)
Analysis finished at Wed Feb  5 09:02:57 2020
Total time elapsed: 31.08s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.979,
    "inflation_factor": 1.0367,
    "mean_EFFECT": -0.0001,
    "n": 2469,
    "n_snps": 2578062,
    "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": 19411,
    "n_est": 2448.9646,
    "ratio_se_n": 0.9959,
    "mean_diff": -0.0001,
    "ratio_diff": 7.4652,
    "sd_y_est1": 0.6613,
    "sd_y_est2": 0.6586,
    "r2_sum1": 0,
    "r2_sum2": 0,
    "r2_sum3": 0,
    "r2_sum4": 0,
    "ldsc_nsnp_merge_refpanel_ld": 1138869,
    "ldsc_nsnp_merge_regression_ld": 1138869,
    "ldsc_observed_scale_h2_beta": 0.0721,
    "ldsc_observed_scale_h2_se": 0.1555,
    "ldsc_intercept_beta": 1.025,
    "ldsc_intercept_se": 0.0073,
    "ldsc_lambda_gc": 1.0265,
    "ldsc_mean_chisq": 1.0286,
    "ldsc_ratio": 0.8741
}

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 2578062 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 8.516211e+00 5.637751e+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 7.932376e+07 5.562145e+07 6689.0000000 3.332626e+07 7.064748e+07 1.146547e+08 2.492086e+08 ▇▇▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA -1.225000e-04 3.620360e-02 -0.4527790 -1.815890e-02 -4.820000e-05 1.801890e-02 3.852080e-01 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 3.083730e-02 1.662360e-02 0.0163228 1.989900e-02 2.359050e-02 3.444720e-02 1.116980e-01 ▇▂▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.943346e-01 2.901662e-01 0.0000005 2.418332e-01 4.922435e-01 7.457444e-01 9.999999e-01 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.943346e-01 2.901662e-01 0.0000005 2.418331e-01 4.922437e-01 7.457452e-01 9.999999e-01 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA 3.416883e-01 2.773394e-01 0.0100002 1.017280e-01 2.683965e-01 5.375318e-01 9.900000e-01 ▇▅▃▂▂
numeric AF_reference 19411 0.9924707 NA NA NA NA NA 3.430599e-01 2.689383e-01 0.0001997 1.134190e-01 2.691690e-01 5.317490e-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 0.0732684 0.0559883 0.1906567 0.1906571 0.0276029 0.0371406 2469
1 740857 rs12082473 G A -0.0498580 0.0580071 0.3900560 0.3900562 0.0274006 0.0585064 2469
1 752566 rs3094315 G A 0.0462189 0.0210270 0.0279434 0.0279438 0.7432170 0.7182510 2469
1 754192 rs3131968 A G 0.0595149 0.0216890 0.0060693 0.0060693 0.6967960 0.6785140 2469
1 761732 rs2286139 C T 0.0524992 0.0203066 0.0097286 0.0097287 0.6902330 0.6257990 2469
1 777122 rs2980319 A T 0.0644756 0.0222471 0.0037536 0.0037536 0.7769980 0.7472040 2469
1 779322 rs4040617 A G -0.0696964 0.0232695 0.0027428 0.0027428 0.2087660 0.2264380 2469
1 785050 rs2905062 G A 0.0530424 0.0205935 0.0100039 0.0100041 0.6714540 0.6269970 2469
1 785989 rs2980300 T C 0.0512512 0.0201837 0.0111094 0.0111095 0.6629380 0.6269970 2469
1 792480 rs2905036 C T 0.0542852 0.0686264 0.4289296 0.4289294 0.9813380 0.9768370 2469
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51212875 rs2238837 A C 0.0149721 0.0187196 0.4238205 0.4238216 0.3673970 0.3724040 2469
22 51213613 rs34726907 C T -0.0153625 0.0281342 0.5850352 0.5850360 0.1313430 0.1727240 2469
22 51217134 rs117417021 A G 0.0165072 0.0201206 0.4119808 0.4119808 0.3994350 0.2671730 2469
22 51219006 rs28729663 G A -0.0324486 0.0227810 0.1543402 0.1543391 0.2110250 0.2052720 2469
23 35921591 rs2204667 C G -0.0392157 0.0292832 0.1805095 0.1805096 0.1200600 NA 2469
23 51115886 rs17864968 C G -0.0161856 0.0668038 0.8085586 0.8085589 0.0205441 NA 2469
23 51666786 rs14115 A G -0.0174998 0.0267761 0.5133942 0.5133950 0.1366080 NA 2469
23 70163799 rs1626496 A C -0.0503931 0.0372241 0.1758081 0.1758078 0.0722227 NA 2469
23 91415872 rs6562597 G A -0.0748643 0.0554515 0.1769889 0.1769884 0.0338732 0.0021192 2469
23 118495837 rs12882977 G A -0.0098779 0.0190305 0.6037220 0.6037222 0.3894150 0.2307280 2469

bcf preview

1   721290  rs12565286  G   C   .   PASS    AF=0.0276029    ES:SE:LP:AF:SS:ID   0.0732684:0.0559883:0.719748:0.0276029:2469:rs12565286
1   740857  rs12082473  G   A   .   PASS    AF=0.0274006    ES:SE:LP:AF:SS:ID   -0.049858:0.0580071:0.408873:0.0274006:2469:rs12082473
1   752566  rs3094315   G   A   .   PASS    AF=0.743217 ES:SE:LP:AF:SS:ID   0.0462189:0.021027:1.55372:0.743217:2469:rs3094315
1   754192  rs3131968   A   G   .   PASS    AF=0.696796 ES:SE:LP:AF:SS:ID   0.0595149:0.021689:2.21686:0.696796:2469:rs3131968
1   761732  rs2286139   C   T   .   PASS    AF=0.690233 ES:SE:LP:AF:SS:ID   0.0524992:0.0203066:2.01195:0.690233:2469:rs2286139
1   777122  rs2980319   A   T   .   PASS    AF=0.776998 ES:SE:LP:AF:SS:ID   0.0644756:0.0222471:2.42555:0.776998:2469:rs2980319
1   779322  rs4040617   A   G   .   PASS    AF=0.208766 ES:SE:LP:AF:SS:ID   -0.0696964:0.0232695:2.56181:0.208766:2469:rs4040617
1   785050  rs2905062   G   A   .   PASS    AF=0.671454 ES:SE:LP:AF:SS:ID   0.0530424:0.0205935:1.99983:0.671454:2469:rs2905062
1   785989  rs2980300   T   C   .   PASS    AF=0.662938 ES:SE:LP:AF:SS:ID   0.0512512:0.0201837:1.95431:0.662938:2469:rs2980300
1   792480  rs2905036   C   T   .   PASS    AF=0.981338 ES:SE:LP:AF:SS:ID   0.0542852:0.0686264:0.367614:0.981338:2469:rs2905036
1   798959  rs11240777  G   A   .   PASS    AF=0.347216 ES:SE:LP:AF:SS:ID   -0.022709:0.0197445:0.601912:0.347216:2469:rs11240777
1   799463  rs4245756   T   C   .   PASS    AF=0.984746 ES:SE:LP:AF:SS:ID   0.00400161:0.0762017:0.0185803:0.984746:2469:rs4245756
1   888659  rs3748597   T   C   .   PASS    AF=0.9375   ES:SE:LP:AF:SS:ID   0.0537815:0.0380377:0.80302:0.9375:2469:rs3748597
1   918573  rs2341354   A   G   .   PASS    AF=0.617305 ES:SE:LP:AF:SS:ID   0.00186307:0.0191522:0.0350306:0.617305:2469:rs2341354
1   926431  rs4970403   A   T   .   PASS    AF=0.914486 ES:SE:LP:AF:SS:ID   -0.0342603:0.0338608:0.506355:0.914486:2469:rs4970403
1   947034  rs2465126   G   A   .   PASS    AF=0.880941 ES:SE:LP:AF:SS:ID   -0.0142974:0.0296026:0.201273:0.880941:2469:rs2465126
1   949608  rs1921  G   A   .   PASS    AF=0.280156 ES:SE:LP:AF:SS:ID   -0.0223489:0.0202593:0.568692:0.280156:2469:rs1921
1   990417  rs2465136   T   C   .   PASS    AF=0.300631 ES:SE:LP:AF:SS:ID   -0.0168132:0.0201171:0.394387:0.300631:2469:rs2465136
1   990839  rs13129 C   T   .   PASS    AF=0.0213592    ES:SE:LP:AF:SS:ID   -0.0188582:0.0631181:0.116276:0.0213592:2469:rs13129
1   1003629 rs4075116   C   T   .   PASS    AF=0.750495 ES:SE:LP:AF:SS:ID   0.0243894:0.0213149:0.597699:0.750495:2469:rs4075116
1   1017170 rs3766193   C   G   .   PASS    AF=0.636104 ES:SE:LP:AF:SS:ID   0.0301396:0.0207541:0.834342:0.636104:2469:rs3766193
1   1017197 rs3766192   C   T   .   PASS    AF=0.612437 ES:SE:LP:AF:SS:ID   0.0183247:0.0201632:0.439561:0.612437:2469:rs3766192
1   1017216 rs6667248   A   G   .   PASS    AF=0.0359606    ES:SE:LP:AF:SS:ID   0.0428371:0.0508914:0.39801:0.0359606:2469:rs6667248
1   1017598 rs12096277  A   G   .   PASS    AF=0.0317325    ES:SE:LP:AF:SS:ID   0.0669975:0.0607504:0.568476:0.0317325:2469:rs12096277
1   1018562 rs9442371   C   T   .   PASS    AF=0.614501 ES:SE:LP:AF:SS:ID   0.0187536:0.0201105:0.454615:0.614501:2469:rs9442371
1   1018704 rs9442372   A   G   .   PASS    AF=0.671797 ES:SE:LP:AF:SS:ID   0.0254117:0.0197144:0.70465:0.671797:2469:rs9442372
1   1022037 rs6701114   C   T   .   PASS    AF=0.643505 ES:SE:LP:AF:SS:ID   0.0344314:0.0212937:0.975168:0.643505:2469:rs6701114
1   1036959 rs11579015  T   C   .   PASS    AF=0.153819 ES:SE:LP:AF:SS:ID   -0.0517621:0.0285784:1.15425:0.153819:2469:rs11579015
1   1039098 rs11260595  C   A   .   PASS    AF=0.0274139    ES:SE:LP:AF:SS:ID   0.127497:0.0569527:1.59897:0.0274139:2469:rs11260595
1   1041700 rs6604968   A   G   .   PASS    AF=0.235593 ES:SE:LP:AF:SS:ID   -0.0173649:0.0214516:0.378582:0.235593:2469:rs6604968
1   1048955 rs4970405   A   G   .   PASS    AF=0.121792 ES:SE:LP:AF:SS:ID   -0.0399158:0.0282925:0.800531:0.121792:2469:rs4970405
1   1060608 rs17160824  G   A   .   PASS    AF=0.141981 ES:SE:LP:AF:SS:ID   -0.0413623:0.0297699:0.783278:0.141981:2469:rs17160824
1   1089699 rs6686003   G   A   .   PASS    AF=0.0566586    ES:SE:LP:AF:SS:ID   -0.0107116:0.041652:0.0985158:0.0566586:2469:rs6686003
1   1089830 rs6700376   A   G   .   PASS    AF=0.0563009    ES:SE:LP:AF:SS:ID   -0.0103357:0.0419608:0.0939693:0.0563009:2469:rs6700376
1   1090557 rs7553429   A   C   .   PASS    AF=0.0685374    ES:SE:LP:AF:SS:ID   -0.018616:0.0421837:0.181121:0.0685374:2469:rs7553429
1   1097335 rs9442385   T   G   .   PASS    AF=0.875986 ES:SE:LP:AF:SS:ID   -0.0095882:0.0278476:0.136312:0.875986:2469:rs9442385
1   1099342 rs9660710   A   C   .   PASS    AF=0.862655 ES:SE:LP:AF:SS:ID   -0.012022:0.0290608:0.168062:0.862655:2469:rs9660710
1   1121014 rs3813204   G   A   .   PASS    AF=0.261842 ES:SE:LP:AF:SS:ID   0.0548446:0.0239189:1.66052:0.261842:2469:rs3813204
1   1121794 rs11260549  G   A   .   PASS    AF=0.28326  ES:SE:LP:AF:SS:ID   0.0515738:0.0220776:1.71019:0.28326:2469:rs11260549
1   1125553 rs10907174  A   T   .   PASS    AF=0.358099 ES:SE:LP:AF:SS:ID   0.0497048:0.0202522:1.85028:0.358099:2469:rs10907174
1   1129672 rs11260554  G   T   .   PASS    AF=0.286718 ES:SE:LP:AF:SS:ID   0.0483152:0.021124:1.65398:0.286718:2469:rs11260554
1   1130727 rs10907175  A   C   .   PASS    AF=0.0677966    ES:SE:LP:AF:SS:ID   0.0200911:0.0363803:0.235992:0.0677966:2469:rs10907175
1   1156131 rs2887286   T   C   .   PASS    AF=0.456416 ES:SE:LP:AF:SS:ID   0.0308139:0.0187423:0.999313:0.456416:2469:rs2887286
1   1158277 rs3813199   G   A   .   PASS    AF=0.0716707    ES:SE:LP:AF:SS:ID   -0.0109804:0.0363485:0.117711:0.0716707:2469:rs3813199
1   1158631 rs6603781   A   G   .   PASS    AF=0.925279 ES:SE:LP:AF:SS:ID   0.00773458:0.0354237:0.0824101:0.925279:2469:rs6603781
1   1162435 rs3766186   C   A   .   PASS    AF=0.0706432    ES:SE:LP:AF:SS:ID   -0.00843364:0.0375203:0.0850467:0.0706432:2469:rs3766186
1   1163804 rs7515488   C   T   .   PASS    AF=0.144801 ES:SE:LP:AF:SS:ID   -0.0214224:0.0270566:0.368051:0.144801:2469:rs7515488
1   1165310 rs11260562  G   A   .   PASS    AF=0.100922 ES:SE:LP:AF:SS:ID   -0.0246181:0.0302628:0.380964:0.100922:2469:rs11260562
1   1194804 rs11804831  T   C   .   PASS    AF=0.599022 ES:SE:LP:AF:SS:ID   0.00735282:0.021768:0.133401:0.599022:2469:rs11804831
1   1195690 rs11260568  G   C   .   PASS    AF=0.032219 ES:SE:LP:AF:SS:ID   0.0136589:0.0519928:0.10085:0.032219:2469:rs11260568