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-961/ieu-a-961.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-961/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 16:09:14 2020
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-961/ieu-a-961.vcf.gz ...
Read summary statistics for 2458024 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, 1158613 SNPs remain.
After merging with regression SNP LD, 1158613 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0329 (0.0075)
Lambda GC: 1.0515
Mean Chi^2: 1.0488
Intercept: 1.0055 (0.0055)
Ratio: 0.1126 (0.1138)
Analysis finished at Tue Feb  4 16:09:44 2020
Total time elapsed: 29.59s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9263,
    "inflation_factor": 1.0557,
    "mean_EFFECT": -0.0057,
    "n": 68028,
    "n_snps": 2458024,
    "n_clumped_hits": 1,
    "n_p_sig": 129,
    "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": 20452,
    "n_est": 62722.6046,
    "ratio_se_n": 0.9602,
    "mean_diff": 0.0056,
    "ratio_diff": 30.3479,
    "sd_y_est1": 16.0076,
    "sd_y_est2": 15.3707,
    "r2_sum1": 0.5013,
    "r2_sum2": 0.002,
    "r2_sum3": 0.0021,
    "r2_sum4": 0.0022,
    "ldsc_nsnp_merge_refpanel_ld": 1158613,
    "ldsc_nsnp_merge_regression_ld": 1158613,
    "ldsc_observed_scale_h2_beta": 0.0329,
    "ldsc_observed_scale_h2_se": 0.0075,
    "ldsc_intercept_beta": 1.0055,
    "ldsc_intercept_se": 0.0055,
    "ldsc_lambda_gc": 1.0515,
    "ldsc_mean_chisq": 1.0488,
    "ldsc_ratio": 0.1127
}

Flags

name value
af_correlation FALSE
inflation_factor FALSE
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 TRUE
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 2458024 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 8.593707e+00 5.661230e+00 1.00000e+00 4.000000e+00 8.000000e+00 1.200000e+01 2.30000e+01 ▇▅▅▂▂
numeric POS 0 1.0000000 NA NA NA NA NA 7.882070e+07 5.567399e+07 1.15230e+04 3.265417e+07 7.023527e+07 1.143004e+08 2.49219e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA -5.749300e-03 3.150275e-01 -1.48912e+01 -8.470000e-02 -2.700000e-03 7.900000e-02 2.21979e+01 ▁▃▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 1.668909e-01 2.971751e-01 8.01000e-02 8.820000e-02 1.053000e-01 1.490000e-01 1.02155e+01 ▇▁▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.918981e-01 2.905215e-01 0.00000e+00 2.380000e-01 4.883003e-01 7.435993e-01 1.00000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.918981e-01 2.905214e-01 0.00000e+00 2.380294e-01 4.883397e-01 7.435365e-01 1.00000e+00 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA 3.586856e-01 2.709367e-01 1.00000e-02 1.247000e-01 2.942000e-01 5.557000e-01 9.90000e-01 ▇▅▃▂▂
numeric AF_reference 20452 0.9916795 NA NA NA NA NA 3.612169e-01 2.556133e-01 1.99700e-04 1.459660e-01 2.987220e-01 5.453270e-01 1.00000e+00 ▇▆▃▃▂
numeric N 0 1.0000000 NA NA NA NA NA 6.802800e+04 0.000000e+00 6.80280e+04 6.802800e+04 6.802800e+04 6.802800e+04 6.80280e+04 ▁▁▇▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 721290 rs12565286 G C -0.4029 0.5634 0.4744998 0.4745334 0.0434 0.0371406 68028
1 723819 rs11804171 T A -0.4092 0.5649 0.4688997 0.4688349 0.0434 0.1345850 68028
1 752566 rs3094315 G A -0.0350 0.1740 0.8407001 0.8405817 0.8240 0.7182510 68028
1 754192 rs3131968 A G -0.2606 0.3068 0.3955997 0.3956514 0.8652 0.6785140 68028
1 768448 rs12562034 G A 0.3748 0.3467 0.2795999 0.2796749 0.1130 0.1918930 68028
1 775659 rs2905035 A G -0.2014 0.2157 0.3506001 0.3504565 0.8597 0.7450080 68028
1 776546 rs12124819 A G -0.4173 0.4696 0.3742002 0.3742027 0.2418 0.0756789 68028
1 777122 rs2980319 A T -0.2014 0.2143 0.3472002 0.3473181 0.8598 0.7472040 68028
1 779322 rs4040617 A G 0.2041 0.2141 0.3406003 0.3404417 0.1399 0.2264380 68028
1 780785 rs2977612 T A -0.2029 0.2142 0.3435002 0.3435137 0.8599 0.6693290 68028
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51171693 rs756638 G A -0.0587 0.1148 0.6092998 0.6091242 0.2731 0.3049120 68028
22 51175626 rs3810648 A G 0.1275 0.1805 0.4799997 0.4799573 0.0600 0.1084270 68028
22 51178090 rs2285395 G A 0.1507 0.1840 0.4129001 0.4127740 0.0578 0.0666933 68028
22 51196164 rs8136603 A T -0.2191 0.3674 0.5510005 0.5509396 0.0571 0.1427720 68028
22 51212875 rs2238837 A C -0.1518 0.1977 0.4423999 0.4425882 0.3505 0.3724040 68028
23 35921591 rs2204667 C G -0.2475 0.1116 0.0265999 0.0265724 0.1615 NA 68028
23 51666786 rs14115 A G -0.2457 0.1769 0.1647999 0.1648570 0.0579 NA 68028
23 70163799 rs1626496 A C -0.0455 0.1603 0.7765993 0.7765309 0.0795 NA 68028
23 91415872 rs6562597 G A 0.3839 0.3088 0.2139001 0.2137943 0.0218 0.0021192 68028
23 118495837 rs12882977 G A 0.0634 0.0821 0.4400003 0.4399788 0.4891 0.2307280 68028

bcf preview

1   721290  rs12565286  G   C   .   PASS    AF=0.0434   ES:SE:LP:AF:SS:ID   -0.4029:0.5634:0.323764:0.0434:68028:rs12565286
1   723819  rs11804171  T   A   .   PASS    AF=0.0434   ES:SE:LP:AF:SS:ID   -0.4092:0.5649:0.32892:0.0434:68028:rs11804171
1   752566  rs3094315   G   A   .   PASS    AF=0.824    ES:SE:LP:AF:SS:ID   -0.035:0.174:0.0753589:0.824:68028:rs3094315
1   754192  rs3131968   A   G   .   PASS    AF=0.8652   ES:SE:LP:AF:SS:ID   -0.2606:0.3068:0.402744:0.8652:68028:rs3131968
1   768448  rs12562034  G   A   .   PASS    AF=0.113    ES:SE:LP:AF:SS:ID   0.3748:0.3467:0.553463:0.113:68028:rs12562034
1   775659  rs2905035   A   G   .   PASS    AF=0.8597   ES:SE:LP:AF:SS:ID   -0.2014:0.2157:0.455188:0.8597:68028:rs2905035
1   776546  rs12124819  A   G   .   PASS    AF=0.2418   ES:SE:LP:AF:SS:ID   -0.4173:0.4696:0.426896:0.2418:68028:rs12124819
1   777122  rs2980319   A   T   .   PASS    AF=0.8598   ES:SE:LP:AF:SS:ID   -0.2014:0.2143:0.45942:0.8598:68028:rs2980319
1   779322  rs4040617   A   G   .   PASS    AF=0.1399   ES:SE:LP:AF:SS:ID   0.2041:0.2141:0.467755:0.1399:68028:rs4040617
1   780785  rs2977612   T   A   .   PASS    AF=0.8599   ES:SE:LP:AF:SS:ID   -0.2029:0.2142:0.464073:0.8599:68028:rs2977612
1   785050  rs2905062   G   A   .   PASS    AF=0.8594   ES:SE:LP:AF:SS:ID   -0.1879:0.2173:0.412177:0.8594:68028:rs2905062
1   785989  rs2980300   T   C   .   PASS    AF=0.859    ES:SE:LP:AF:SS:ID   -0.1847:0.2173:0.403073:0.859:68028:rs2980300
1   798026  rs4951864   C   T   .   PASS    AF=0.9147   ES:SE:LP:AF:SS:ID   -0.8367:0.6148:0.760701:0.9147:68028:rs4951864
1   798801  rs12132517  G   A   .   PASS    AF=0.1103   ES:SE:LP:AF:SS:ID   0.7714:0.5614:0.771087:0.1103:68028:rs12132517
1   798959  rs11240777  G   A   .   PASS    AF=0.2179   ES:SE:LP:AF:SS:ID   0.2756:0.1995:0.776764:0.2179:68028:rs11240777
1   962210  rs3128126   A   G   .   PASS    AF=0.415    ES:SE:LP:AF:SS:ID   -0.8931:5.1089:0.064896:0.415:68028:rs3128126
1   990380  rs3121561   C   T   .   PASS    AF=0.275    ES:SE:LP:AF:SS:ID   -2.1978:5.2569:0.170118:0.275:68028:rs3121561
1   998501  rs3813193   G   C   .   PASS    AF=0.1742   ES:SE:LP:AF:SS:ID   -0.0964:0.2059:0.193956:0.1742:68028:rs3813193
1   1003629 rs4075116   C   T   .   PASS    AF=0.7286   ES:SE:LP:AF:SS:ID   0.3472:0.1843:1.22534:0.7286:68028:rs4075116
1   1005806 rs3934834   C   T   .   PASS    AF=0.1458   ES:SE:LP:AF:SS:ID   -0.0288:0.1619:0.0660068:0.1458:68028:rs3934834
1   1017170 rs3766193   C   G   .   PASS    AF=0.5383   ES:SE:LP:AF:SS:ID   -0.0041:0.1569:0.00926167:0.5383:68028:rs3766193
1   1017197 rs3766192   C   T   .   PASS    AF=0.5598   ES:SE:LP:AF:SS:ID   0.0161:0.1098:0.0538426:0.5598:68028:rs3766192
1   1017587 rs3766191   C   T   .   PASS    AF=0.1429   ES:SE:LP:AF:SS:ID   0.0136:0.1614:0.0301184:0.1429:68028:rs3766191
1   1018562 rs9442371   C   T   .   PASS    AF=0.5675   ES:SE:LP:AF:SS:ID   0.0112:0.1072:0.037678:0.5675:68028:rs9442371
1   1018704 rs9442372   A   G   .   PASS    AF=0.5673   ES:SE:LP:AF:SS:ID   0.0122:0.1066:0.0413883:0.5673:68028:rs9442372
1   1021346 rs10907177  A   G   .   PASS    AF=0.1494   ES:SE:LP:AF:SS:ID   -0.0173:0.1801:0.0347042:0.1494:68028:rs10907177
1   1021415 rs3737728   A   G   .   PASS    AF=0.7249   ES:SE:LP:AF:SS:ID   0.1057:0.1112:0.466355:0.7249:68028:rs3737728
1   1021583 rs10907178  A   C   .   PASS    AF=0.1472   ES:SE:LP:AF:SS:ID   -0.0145:0.1841:0.0281677:0.1472:68028:rs10907178
1   1021695 rs9442398   A   G   .   PASS    AF=0.7348   ES:SE:LP:AF:SS:ID   0.0732:0.1212:0.262807:0.7348:68028:rs9442398
1   1022037 rs6701114   C   T   .   PASS    AF=0.5631   ES:SE:LP:AF:SS:ID   -0.0453:0.1338:0.133713:0.5631:68028:rs6701114
1   1026707 rs4074137   C   A   .   PASS    AF=0.6115   ES:SE:LP:AF:SS:ID   0.0743:0.1119:0.295249:0.6115:68028:rs4074137
1   1030565 rs6687776   C   T   .   PASS    AF=0.1588   ES:SE:LP:AF:SS:ID   0.1413:0.1342:0.533726:0.1588:68028:rs6687776
1   1030633 rs6678318   G   A   .   PASS    AF=0.1611   ES:SE:LP:AF:SS:ID   0.1334:0.2075:0.283746:0.1611:68028:rs6678318
1   1031540 rs9651273   A   G   .   PASS    AF=0.7306   ES:SE:LP:AF:SS:ID   0.0894:0.1139:0.364215:0.7306:68028:rs9651273
1   1036959 rs11579015  T   C   .   PASS    AF=0.1064   ES:SE:LP:AF:SS:ID   0.102:0.165:0.27043:0.1064:68028:rs11579015
1   1040026 rs6671356   T   C   .   PASS    AF=0.1414   ES:SE:LP:AF:SS:ID   0.1605:0.1469:0.561141:0.1414:68028:rs6671356
1   1046164 rs6666280   C   T   .   PASS    AF=0.1355   ES:SE:LP:AF:SS:ID   0.1545:0.1447:0.54409:0.1355:68028:rs6666280
1   1048955 rs4970405   A   G   .   PASS    AF=0.1061   ES:SE:LP:AF:SS:ID   0.132:0.1621:0.381534:0.1061:68028:rs4970405
1   1049950 rs12726255  A   G   .   PASS    AF=0.1377   ES:SE:LP:AF:SS:ID   0.1725:0.1417:0.650722:0.1377:68028:rs12726255
1   1053452 rs4970409   G   A   .   PASS    AF=0.1079   ES:SE:LP:AF:SS:ID   0.0946:0.1628:0.250882:0.1079:68028:rs4970409
1   1060174 rs7548798   C   T   .   PASS    AF=0.3226   ES:SE:LP:AF:SS:ID   0.0639:0.3228:0.0741724:0.3226:68028:rs7548798
1   1060235 rs7540009   G   A   .   PASS    AF=0.0327   ES:SE:LP:AF:SS:ID   0.3135:0.3258:0.47379:0.0327:68028:rs7540009
1   1060608 rs17160824  G   A   .   PASS    AF=0.1154   ES:SE:LP:AF:SS:ID   0.0564:0.1694:0.131238:0.1154:68028:rs17160824
1   1061115 rs17160826  T   C   .   PASS    AF=0.1067   ES:SE:LP:AF:SS:ID   0.0978:0.1663:0.254691:0.1067:68028:rs17160826
1   1061152 rs12748370  T   C   .   PASS    AF=0.1065   ES:SE:LP:AF:SS:ID   0.0993:0.1669:0.25814:0.1065:68028:rs12748370
1   1061166 rs11807848  T   C   .   PASS    AF=0.4133   ES:SE:LP:AF:SS:ID   -0.0058:0.2136:0.00943917:0.4133:68028:rs11807848
1   1062015 rs9659914   C   T   .   PASS    AF=0.0304   ES:SE:LP:AF:SS:ID   0.3701:0.3551:0.526805:0.0304:68028:rs9659914
1   1062638 rs9442373   C   A   .   PASS    AF=0.548    ES:SE:LP:AF:SS:ID   -0.0902:0.2105:0.175029:0.548:68028:rs9442373
1   1064979 rs2298217   C   T   .   PASS    AF=0.1474   ES:SE:LP:AF:SS:ID   -0.1057:0.1486:0.321846:0.1474:68028:rs2298217
1   1066029 rs12145826  G   A   .   PASS    AF=0.0907   ES:SE:LP:AF:SS:ID   0.0347:0.3766:0.0330608:0.0907:68028:rs12145826