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-1005/ieu-a-1005.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-1005/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 08:50:12 2020
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-1005/ieu-a-1005.vcf.gz ...
Read summary statistics for 2958886 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, 1189306 SNPs remain.
After merging with regression SNP LD, 1189306 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0261 (0.0506)
Lambda GC: 1.0188
Mean Chi^2: 1.0199
Intercept: 1.0159 (0.0062)
Ratio: 0.7953 (0.3108)
Analysis finished at Wed Feb  5 08:50:46 2020
Total time elapsed: 33.95s

QC metrics

Metrics

Metrics

{
    "af_correlation": -0.9818,
    "inflation_factor": 1.0188,
    "mean_EFFECT": 0,
    "n": 7667,
    "n_snps": 2958886,
    "n_clumped_hits": 2,
    "n_p_sig": 2,
    "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": 23824,
    "n_est": 6825.8207,
    "ratio_se_n": 0.9435,
    "mean_diff": 0,
    "ratio_diff": 4.182,
    "sd_y_est1": 0.7084,
    "sd_y_est2": 0.6684,
    "r2_sum1": 0.0066,
    "r2_sum2": 0.0131,
    "r2_sum3": 0.0147,
    "r2_sum4": 0.0081,
    "ldsc_nsnp_merge_refpanel_ld": 1189306,
    "ldsc_nsnp_merge_regression_ld": 1189306,
    "ldsc_observed_scale_h2_beta": 0.0261,
    "ldsc_observed_scale_h2_se": 0.0506,
    "ldsc_intercept_beta": 1.0159,
    "ldsc_intercept_se": 0.0062,
    "ldsc_lambda_gc": 1.0188,
    "ldsc_mean_chisq": 1.0199,
    "ldsc_ratio": 0.799
}

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 2958886 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 8.529888e+00 5.645490e+00 1.000e+00 4.000000e+00 8.000000e+00 1.200000e+01 2.300000e+01 ▇▅▅▂▂
numeric POS 0 1.0000000 NA NA NA NA NA 7.917032e+07 5.563310e+07 6.689e+03 3.313840e+07 7.045021e+07 1.145119e+08 2.492107e+08 ▇▇▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA 2.330000e-05 2.215150e-02 -4.506e-01 -1.020000e-02 0.000000e+00 1.030000e-02 4.027000e-01 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 1.836370e-02 1.204290e-02 9.400e-03 1.100000e-02 1.370000e-02 2.050000e-02 1.813000e-01 ▇▁▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.970743e-01 2.895274e-01 0.000e+00 2.456999e-01 4.960004e-01 7.481006e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.970745e-01 2.895328e-01 0.000e+00 2.457356e-01 4.960789e-01 7.481339e-01 1.000000e+00 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA 6.527538e-01 2.534247e-01 1.000e-02 4.795000e-01 7.182000e-01 8.644000e-01 9.900000e-01 ▂▂▃▆▇
numeric AF_reference 23824 0.9919483 NA NA NA NA NA 3.327224e-01 2.763563e-01 1.997e-04 9.664540e-02 2.539940e-01 5.239620e-01 1.000000e+00 ▇▅▃▂▂
numeric N 0 1.0000000 NA NA NA NA NA 7.667000e+03 0.000000e+00 7.667e+03 7.667000e+03 7.667000e+03 7.667000e+03 7.667000e+03 ▁▁▇▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 721290 rs12565286 G C -0.0531 0.0260 0.0407596 0.0411210 0.9583 0.0371406 7667
1 723819 rs11804171 T A -0.0556 0.0385 0.1493001 0.1486951 0.9411 0.1345850 7667
1 723891 rs2977670 G C 0.0556 0.0385 0.1494999 0.1486951 0.0589 0.7799520 7667
1 740857 rs12082473 G A 0.0044 0.0210 0.8352000 0.8340394 0.8443 0.0585064 7667
1 752566 rs3094315 G A -0.0347 0.0133 0.0093910 0.0090801 0.4004 0.7182510 7667
1 753541 rs2073813 G A -0.0124 0.0247 0.6164999 0.6156504 0.8560 0.3019170 7667
1 754192 rs3131968 A G -0.0173 0.0129 0.1821998 0.1798928 0.3831 0.6785140 7667
1 761732 rs2286139 C T -0.0138 0.0119 0.2454997 0.2461857 0.4009 0.6257990 7667
1 765269 rs11240776 A G 0.0011 0.0613 0.9859000 0.9856831 0.9781 0.0065895 7667
1 775659 rs2905035 A G 0.0145 0.0248 0.5593002 0.5587646 0.1424 0.7450080 7667
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51223637 rs375798137 G A -0.0286 0.0406 0.4810996 0.4811629 0.9464 0.0788738 7667
22 51229805 rs9616985 T C 0.0251 0.0368 0.4939000 0.4951977 0.9311 0.0730831 7667
23 35921591 rs2204667 C G 0.0098 0.0148 0.5070000 0.5078673 0.8452 NA 7667
23 51115886 rs17864968 C G -0.0291 0.0274 0.2889003 0.2882158 0.9149 NA 7667
23 51666786 rs14115 A G 0.0092 0.0142 0.5169006 0.5170578 0.8074 NA 7667
23 57663373 rs28962478 A G -0.0345 0.0381 0.3653003 0.3651943 0.9415 NA 7667
23 70163799 rs1626496 A C 0.0062 0.0180 0.7300002 0.7305121 0.8857 NA 7667
23 91415872 rs6562597 G A 0.0038 0.0262 0.8843999 0.8846807 0.9322 0.0021192 7667
23 118495837 rs12882977 G A 0.0052 0.0107 0.6231004 0.6269804 0.6046 0.2307280 7667
23 147220746 rs2944613 T A 0.0736 0.0764 0.3355004 0.3353715 0.9857 NA 7667

bcf preview

1   721290  rs12565286  G   C   .   PASS    AF=0.9583   ES:SE:LP:AF:SS:ID   -0.0531:0.026:1.38977:0.9583:7667:rs12565286
1   723819  rs11804171  T   A   .   PASS    AF=0.9411   ES:SE:LP:AF:SS:ID   -0.0556:0.0385:0.82594:0.9411:7667:rs11804171
1   723891  rs2977670   G   C   .   PASS    AF=0.0589   ES:SE:LP:AF:SS:ID   0.0556:0.0385:0.825359:0.0589:7667:rs2977670
1   740857  rs12082473  G   A   .   PASS    AF=0.8443   ES:SE:LP:AF:SS:ID   0.0044:0.021:0.0782095:0.8443:7667:rs12082473
1   752566  rs3094315   G   A   .   PASS    AF=0.4004   ES:SE:LP:AF:SS:ID   -0.0347:0.0133:2.02729:0.4004:7667:rs3094315
1   753541  rs2073813   G   A   .   PASS    AF=0.856    ES:SE:LP:AF:SS:ID   -0.0124:0.0247:0.210067:0.856:7667:rs2073813
1   754192  rs3131968   A   G   .   PASS    AF=0.3831   ES:SE:LP:AF:SS:ID   -0.0173:0.0129:0.739452:0.3831:7667:rs3131968
1   761732  rs2286139   C   T   .   PASS    AF=0.4009   ES:SE:LP:AF:SS:ID   -0.0138:0.0119:0.609949:0.4009:7667:rs2286139
1   765269  rs11240776  A   G   .   PASS    AF=0.9781   ES:SE:LP:AF:SS:ID   0.0011:0.0613:0.00616713:0.9781:7667:rs11240776
1   775659  rs2905035   A   G   .   PASS    AF=0.1424   ES:SE:LP:AF:SS:ID   0.0145:0.0248:0.252355:0.1424:7667:rs2905035
1   777122  rs2980319   A   T   .   PASS    AF=0.3222   ES:SE:LP:AF:SS:ID   -0.0209:0.0119:1.10397:0.3222:7667:rs2980319
1   779322  rs4040617   A   G   .   PASS    AF=0.7171   ES:SE:LP:AF:SS:ID   0.0188:0.0123:0.904134:0.7171:7667:rs4040617
1   780785  rs2977612   T   A   .   PASS    AF=0.1459   ES:SE:LP:AF:SS:ID   0.0173:0.0248:0.312382:0.1459:7667:rs2977612
1   785050  rs2905062   G   A   .   PASS    AF=0.4092   ES:SE:LP:AF:SS:ID   -0.0126:0.0119:0.538051:0.4092:7667:rs2905062
1   785989  rs2980300   T   C   .   PASS    AF=0.41 ES:SE:LP:AF:SS:ID   -0.0096:0.0116:0.388808:0.41:7667:rs2980300
1   792480  rs2905036   C   T   .   PASS    AF=0.0726   ES:SE:LP:AF:SS:ID   -0.0222:0.029:0.352226:0.0726:7667:rs2905036
1   798959  rs11240777  G   A   .   PASS    AF=0.5877   ES:SE:LP:AF:SS:ID   0.005:0.0109:0.189029:0.5877:7667:rs11240777
1   799463  rs4245756   T   C   .   PASS    AF=0.0638   ES:SE:LP:AF:SS:ID   0.008:0.0309:0.099469:0.0638:7667:rs4245756
1   888659  rs3748597   T   C   .   PASS    AF=0.0709   ES:SE:LP:AF:SS:ID   -0.0031:0.0193:0.0591848:0.0709:7667:rs3748597
1   918573  rs2341354   A   G   .   PASS    AF=0.4716   ES:SE:LP:AF:SS:ID   0.0009:0.0103:0.0301184:0.4716:7667:rs2341354
1   926431  rs4970403   A   T   .   PASS    AF=0.185    ES:SE:LP:AF:SS:ID   -0.0168:0.0157:0.544698:0.185:7667:rs4970403
1   947034  rs2465126   G   A   .   PASS    AF=0.3046   ES:SE:LP:AF:SS:ID   0.0047:0.0139:0.131767:0.3046:7667:rs2465126
1   949608  rs1921  G   A   .   PASS    AF=0.6478   ES:SE:LP:AF:SS:ID   0.0028:0.0104:0.105684:0.6478:7667:rs1921
1   990380  rs3121561   C   T   .   PASS    AF=0.6994   ES:SE:LP:AF:SS:ID   0.016:0.0195:0.386898:0.6994:7667:rs3121561
1   990417  rs2465136   T   C   .   PASS    AF=0.6062   ES:SE:LP:AF:SS:ID   0.0037:0.0107:0.136796:0.6062:7667:rs2465136
1   990517  rs2710872   C   T   .   PASS    AF=0.1463   ES:SE:LP:AF:SS:ID   0.0307:0.0268:0.598944:0.1463:7667:rs2710872
1   990839  rs13129 C   T   .   PASS    AF=0.926    ES:SE:LP:AF:SS:ID   0.0329:0.0266:0.666956:0.926:7667:rs13129
1   1003629 rs4075116   C   T   .   PASS    AF=0.3677   ES:SE:LP:AF:SS:ID   -0.0041:0.0111:0.146545:0.3677:7667:rs4075116
1   1017170 rs3766193   C   G   .   PASS    AF=0.3936   ES:SE:LP:AF:SS:ID   -0.0063:0.0131:0.200728:0.3936:7667:rs3766193
1   1017197 rs3766192   C   T   .   PASS    AF=0.4027   ES:SE:LP:AF:SS:ID   -0.0014:0.0129:0.0398623:0.4027:7667:rs3766192
1   1017216 rs6667248   A   G   .   PASS    AF=0.8348   ES:SE:LP:AF:SS:ID   -0.0162:0.0207:0.36181:0.8348:7667:rs6667248
1   1017598 rs12096277  A   G   .   PASS    AF=0.838    ES:SE:LP:AF:SS:ID   -0.0147:0.0236:0.273191:0.838:7667:rs12096277
1   1018562 rs9442371   C   T   .   PASS    AF=0.3973   ES:SE:LP:AF:SS:ID   -0.0013:0.0127:0.0355518:0.3973:7667:rs9442371
1   1018704 rs9442372   A   G   .   PASS    AF=0.3877   ES:SE:LP:AF:SS:ID   -0.0076:0.0104:0.333482:0.3877:7667:rs9442372
1   1022037 rs6701114   C   T   .   PASS    AF=0.3265   ES:SE:LP:AF:SS:ID   -0.0204:0.0189:0.551139:0.3265:7667:rs6701114
1   1030565 rs6687776   C   T   .   PASS    AF=0.8507   ES:SE:LP:AF:SS:ID   0.0339:0.0268:0.68424:0.8507:7667:rs6687776
1   1030633 rs6678318   G   A   .   PASS    AF=0.8506   ES:SE:LP:AF:SS:ID   0.0339:0.0268:0.68466:0.8506:7667:rs6678318
1   1036959 rs11579015  T   C   .   PASS    AF=0.857    ES:SE:LP:AF:SS:ID   0.0304:0.0181:1.03433:0.857:7667:rs11579015
1   1039098 rs11260595  C   A   .   PASS    AF=0.9434   ES:SE:LP:AF:SS:ID   -0.024:0.0259:0.450016:0.9434:7667:rs11260595
1   1040026 rs6671356   T   C   .   PASS    AF=0.8531   ES:SE:LP:AF:SS:ID   0.0324:0.0261:0.668168:0.8531:7667:rs6671356
1   1041700 rs6604968   A   G   .   PASS    AF=0.6999   ES:SE:LP:AF:SS:ID   0.013:0.0115:0.590405:0.6999:7667:rs6604968
1   1046164 rs6666280   C   T   .   PASS    AF=0.8618   ES:SE:LP:AF:SS:ID   0.0309:0.026:0.630042:0.8618:7667:rs6666280
1   1048955 rs4970405   A   G   .   PASS    AF=0.8849   ES:SE:LP:AF:SS:ID   0.0181:0.017:0.541362:0.8849:7667:rs4970405
1   1049950 rs12726255  A   G   .   PASS    AF=0.8632   ES:SE:LP:AF:SS:ID   0.0296:0.026:0.592779:0.8632:7667:rs12726255
1   1053452 rs4970409   G   A   .   PASS    AF=0.8838   ES:SE:LP:AF:SS:ID   0.0231:0.0276:0.394156:0.8838:7667:rs4970409
1   1060608 rs17160824  G   A   .   PASS    AF=0.868    ES:SE:LP:AF:SS:ID   0.0324:0.0205:0.943476:0.868:7667:rs17160824
1   1061115 rs17160826  T   C   .   PASS    AF=0.8856   ES:SE:LP:AF:SS:ID   0.0239:0.0282:0.401647:0.8856:7667:rs17160826
1   1061152 rs12748370  T   C   .   PASS    AF=0.8856   ES:SE:LP:AF:SS:ID   0.024:0.0282:0.402195:0.8856:7667:rs12748370
1   1089699 rs6686003   G   A   .   PASS    AF=0.7737   ES:SE:LP:AF:SS:ID   -0.0148:0.0181:0.380907:0.7737:7667:rs6686003
1   1089830 rs6700376   A   G   .   PASS    AF=0.7743   ES:SE:LP:AF:SS:ID   -0.0147:0.0182:0.376544:0.7743:7667:rs6700376