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-1102/ieu-a-1102.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-1102/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 20:45:13 2020
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-1102/ieu-a-1102.vcf.gz ...
Read summary statistics for 2189545 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, 1067596 SNPs remain.
After merging with regression SNP LD, 1067596 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0197 (0.0055)
Lambda GC: 1.039
Mean Chi^2: 1.0642
Intercept: 1.0152 (0.0082)
Ratio: 0.2374 (0.127)
Analysis finished at Tue Feb  4 20:45:42 2020
Total time elapsed: 28.94s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9011,
    "inflation_factor": 1.0475,
    "mean_EFFECT": 0.0018,
    "n": 118147,
    "n_snps": 2189545,
    "n_clumped_hits": 4,
    "n_p_sig": 119,
    "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": 658,
    "n_miss_AF_reference": 18468,
    "n_est": 112860.2698,
    "ratio_se_n": 0.9774,
    "mean_diff": -0.0013,
    "ratio_diff": 116.3032,
    "sd_y_est1": 3.7475,
    "sd_y_est2": 3.6627,
    "r2_sum1": 0.0307,
    "r2_sum2": 0.0022,
    "r2_sum3": 0.0023,
    "r2_sum4": 0.0021,
    "ldsc_nsnp_merge_refpanel_ld": 1067596,
    "ldsc_nsnp_merge_regression_ld": 1067596,
    "ldsc_observed_scale_h2_beta": 0.0197,
    "ldsc_observed_scale_h2_se": 0.0055,
    "ldsc_intercept_beta": 1.0152,
    "ldsc_intercept_se": 0.0082,
    "ldsc_lambda_gc": 1.039,
    "ldsc_mean_chisq": 1.0642,
    "ldsc_ratio": 0.2368
}

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 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 2189545 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 8.602095e+00 5.664015e+00 1.0000e+00 4.000000e+00 8.000000e+00 1.200000e+01 2.300000e+01 ▇▅▅▂▂
numeric POS 0 1.0000000 NA NA NA NA NA 7.871917e+07 5.573840e+07 1.1523e+04 3.243192e+07 7.007253e+07 1.143565e+08 2.491752e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA 1.826200e-03 2.177280e-02 -7.6000e-01 -1.200000e-02 1.400000e-03 1.500000e-02 5.000000e-01 ▁▁▅▇▁
numeric SE 0 1.0000000 NA NA NA NA NA 2.022220e-02 6.331200e-03 1.5000e-02 1.600000e-02 1.800000e-02 2.300000e-02 4.400000e-01 ▇▁▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.922846e-01 2.907589e-01 0.0000e+00 2.399999e-01 4.899999e-01 7.400005e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.919755e-01 2.908966e-01 0.0000e+00 2.350305e-01 4.917677e-01 7.439200e-01 1.000000e+00 ▇▇▇▇▇
numeric AF 658 0.9996995 NA NA NA NA NA 3.810087e-01 2.564856e-01 4.0000e-03 1.590000e-01 3.250000e-01 5.750000e-01 9.960000e-01 ▇▆▅▃▂
numeric AF_reference 18468 0.9915654 NA NA NA NA NA 3.807157e-01 2.427759e-01 1.9970e-04 1.773160e-01 3.294730e-01 5.595050e-01 1.000000e+00 ▇▇▅▃▂
numeric N 0 1.0000000 NA NA NA NA NA 1.172665e+05 2.630388e+03 4.1803e+04 1.180750e+05 1.181360e+05 1.181400e+05 1.181470e+05 ▁▁▁▁▇

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 721290 rs12565286 G C 0.0590 0.064 0.3500000 0.3565938 0.032 0.0371406 103180
1 723819 rs11804171 T A 0.0750 0.066 0.2500000 0.2558044 0.034 0.1345850 100893
1 723891 rs2977670 G C -0.0670 0.068 0.3200000 0.3244796 0.934 0.7799520 97600
1 750235 rs12138618 G A -0.1100 0.083 0.1900002 0.1850713 0.062 NA 92771
1 752566 rs3094315 G A -0.0200 0.028 0.4700002 0.4750505 0.835 0.7182510 111704
1 754192 rs3131968 A G 0.0081 0.036 0.8200001 0.8219793 0.885 0.6785140 99594
1 768448 rs12562034 G A -0.0100 0.038 0.7899998 0.7924289 0.102 0.1918930 107322
1 775659 rs2905035 A G -0.0092 0.036 0.8000000 0.7982940 0.885 0.7450080 101946
1 776546 rs12124819 A G -0.0046 0.032 0.8900000 0.8856979 0.288 0.0756789 108269
1 777122 rs2980319 A T -0.0250 0.031 0.4100001 0.4199825 0.866 0.7472040 113953
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51212875 rs2238837 A C 0.0010 0.025 0.9699999 0.9680931 0.385 0.3724040 100331
22 51216564 rs9616970 T C -0.0380 0.034 0.2700001 0.2637178 0.146 0.1563500 108372
22 51217134 rs117417021 A G -0.0044 0.027 0.8700001 0.8705476 0.415 0.2671730 102775
22 51222100 rs114553188 G T -0.0066 0.048 0.8900000 0.8906356 0.062 0.0880591 98167
22 51223637 rs375798137 G A -0.0110 0.048 0.8300000 0.8187394 0.062 0.0788738 97004
22 51229805 rs9616985 T C -0.0630 0.051 0.2200002 0.2167211 0.092 0.0730831 88676
23 35921591 rs2204667 C G 0.0170 0.021 0.4299995 0.4182139 0.162 NA 113634
23 51666786 rs14115 A G 0.0590 0.033 0.0739997 0.0737956 0.027 NA 117304
23 70163799 rs1626496 A C -0.0220 0.029 0.4500005 0.4480795 0.069 NA 117302
23 118495837 rs12882977 G A 0.0092 0.016 0.5700002 0.5652913 0.508 0.2307280 106243

bcf preview

1   721290  rs12565286  G   C   .   PASS    AF=0.032    ES:SE:LP:AF:SS:ID   0.059:0.064:0.455932:0.032:103180:rs12565286
1   723819  rs11804171  T   A   .   PASS    AF=0.034    ES:SE:LP:AF:SS:ID   0.075:0.066:0.60206:0.034:100893:rs11804171
1   723891  rs2977670   G   C   .   PASS    AF=0.934    ES:SE:LP:AF:SS:ID   -0.067:0.068:0.49485:0.934:97600:rs2977670
1   750235  rs12138618  G   A   .   PASS    AF=0.062    ES:SE:LP:AF:SS:ID   -0.11:0.083:0.721246:0.062:92771:rs12138618
1   752566  rs3094315   G   A   .   PASS    AF=0.835    ES:SE:LP:AF:SS:ID   -0.02:0.028:0.327902:0.835:111704:rs3094315
1   754192  rs3131968   A   G   .   PASS    AF=0.885    ES:SE:LP:AF:SS:ID   0.0081:0.036:0.0861861:0.885:99594:rs3131968
1   768448  rs12562034  G   A   .   PASS    AF=0.102    ES:SE:LP:AF:SS:ID   -0.01:0.038:0.102373:0.102:107322:rs12562034
1   775659  rs2905035   A   G   .   PASS    AF=0.885    ES:SE:LP:AF:SS:ID   -0.0092:0.036:0.09691:0.885:101946:rs2905035
1   776546  rs12124819  A   G   .   PASS    AF=0.288    ES:SE:LP:AF:SS:ID   -0.0046:0.032:0.05061:0.288:108269:rs12124819
1   777122  rs2980319   A   T   .   PASS    AF=0.866    ES:SE:LP:AF:SS:ID   -0.025:0.031:0.387216:0.866:113953:rs2980319
1   779322  rs4040617   A   G   .   PASS    AF=0.133    ES:SE:LP:AF:SS:ID   0.012:0.035:0.136677:0.133:96454:rs4040617
1   780785  rs2977612   T   A   .   PASS    AF=0.877    ES:SE:LP:AF:SS:ID   -0.02:0.032:0.275724:0.877:110725:rs2977612
1   785050  rs2905062   G   A   .   PASS    AF=0.868    ES:SE:LP:AF:SS:ID   -0.024:0.032:0.337242:0.868:111664:rs2905062
1   785989  rs2980300   T   C   .   PASS    AF=0.868    ES:SE:LP:AF:SS:ID   -0.027:0.031:0.420216:0.868:113951:rs2980300
1   798026  rs4951864   C   T   .   PASS    AF=0.9  ES:SE:LP:AF:SS:ID   0.065:0.056:0.619789:0.9:98757:rs4951864
1   798801  rs12132517  G   A   .   PASS    AF=0.108    ES:SE:LP:AF:SS:ID   -0.062:0.056:0.585027:0.108:97809:rs12132517
1   798959  rs11240777  G   A   .   PASS    AF=0.219    ES:SE:LP:AF:SS:ID   -0.018:0.03:0.267606:0.219:113129:rs11240777
1   846864  rs950122    G   C   .   PASS    AF=0.138    ES:SE:LP:AF:SS:ID   -0.036:0.039:0.443698:0.138:95297:rs950122
1   882033  rs2272756   G   A   .   PASS    AF=0.23 ES:SE:LP:AF:SS:ID   0.044:0.034:0.721246:0.23:107696:rs2272756
1   962210  rs3128126   A   G   .   PASS    AF=0.415    ES:SE:LP:AF:SS:ID   0.02:0.026:0.346787:0.415:110947:rs3128126
1   990380  rs3121561   C   T   .   PASS    AF=0.254    ES:SE:LP:AF:SS:ID   0.022:0.025:0.420216:0.254:113871:rs3121561
1   998501  rs3813193   G   C   .   PASS    AF=0.146    ES:SE:LP:AF:SS:ID   0.018:0.027:0.30103:0.146:114971:rs3813193
1   1003629 rs4075116   C   T   .   PASS    AF=0.734    ES:SE:LP:AF:SS:ID   -0.0091:0.02:0.187087:0.734:118106:rs4075116
1   1005806 rs3934834   C   T   .   PASS    AF=0.124    ES:SE:LP:AF:SS:ID   0.019:0.025:0.356547:0.124:117279:rs3934834
1   1017170 rs3766193   C   G   .   PASS    AF=0.587    ES:SE:LP:AF:SS:ID   -0.0098:0.018:0.229148:0.587:113908:rs3766193
1   1017197 rs3766192   C   T   .   PASS    AF=0.571    ES:SE:LP:AF:SS:ID   -0.0048:0.017:0.107905:0.571:113959:rs3766192
1   1017587 rs3766191   C   T   .   PASS    AF=0.124    ES:SE:LP:AF:SS:ID   0.019:0.025:0.356547:0.124:117279:rs3766191
1   1018562 rs9442371   C   T   .   PASS    AF=0.608    ES:SE:LP:AF:SS:ID   -0.0064:0.017:0.154902:0.608:117280:rs9442371
1   1018704 rs9442372   A   G   .   PASS    AF=0.588    ES:SE:LP:AF:SS:ID   -0.0062:0.017:0.148742:0.588:117277:rs9442372
1   1021346 rs10907177  A   G   .   PASS    AF=0.137    ES:SE:LP:AF:SS:ID   0.015:0.025:0.267606:0.137:117280:rs10907177
1   1021415 rs3737728   A   G   .   PASS    AF=0.735    ES:SE:LP:AF:SS:ID   -0.0063:0.018:0.136677:0.735:118143:rs3737728
1   1021583 rs10907178  A   C   .   PASS    AF=0.112    ES:SE:LP:AF:SS:ID   0.013:0.025:0.221849:0.112:114163:rs10907178
1   1021695 rs9442398   A   G   .   PASS    AF=0.726    ES:SE:LP:AF:SS:ID   -0.0029:0.019:0.0555173:0.726:118141:rs9442398
1   1022037 rs6701114   C   T   .   PASS    AF=0.585    ES:SE:LP:AF:SS:ID   -0.012:0.018:0.29243:0.585:117227:rs6701114
1   1025301 rs9442400   T   C   .   PASS    AF=0.952    ES:SE:LP:AF:SS:ID   0.03:0.065:0.187087:0.952:98552:rs9442400
1   1026707 rs4074137   C   A   .   PASS    AF=0.623    ES:SE:LP:AF:SS:ID   -0.0045:0.018:0.09691:0.623:114993:rs4074137
1   1030565 rs6687776   C   T   .   PASS    AF=0.133    ES:SE:LP:AF:SS:ID   -0.0025:0.022:0.0409586:0.133:117285:rs6687776
1   1030633 rs6678318   G   A   .   PASS    AF=0.134    ES:SE:LP:AF:SS:ID   -0.0022:0.022:0.0362122:0.134:113975:rs6678318
1   1031540 rs9651273   A   G   .   PASS    AF=0.717    ES:SE:LP:AF:SS:ID   -0.016:0.018:0.431798:0.717:117242:rs9651273
1   1036959 rs11579015  T   C   .   PASS    AF=0.046    ES:SE:LP:AF:SS:ID   0:0.026:-0:0.046:117280:rs11579015
1   1040026 rs6671356   T   C   .   PASS    AF=0.115    ES:SE:LP:AF:SS:ID   0.017:0.023:0.327902:0.115:117279:rs6671356
1   1046164 rs6666280   C   T   .   PASS    AF=0.062    ES:SE:LP:AF:SS:ID   0.018:0.023:0.366532:0.062:117274:rs6666280
1   1048955 rs4970405   A   G   .   PASS    AF=0.088    ES:SE:LP:AF:SS:ID   0.012:0.025:0.200659:0.088:117273:rs4970405
1   1049950 rs12726255  A   G   .   PASS    AF=0.115    ES:SE:LP:AF:SS:ID   0.021:0.024:0.431798:0.115:117261:rs12726255
1   1053452 rs4970409   G   A   .   PASS    AF=0.093    ES:SE:LP:AF:SS:ID   0.0021:0.025:0.0315171:0.093:115502:rs4970409
1   1060174 rs7548798   C   T   .   PASS    AF=0.314    ES:SE:LP:AF:SS:ID   0.016:0.022:0.318759:0.314:105268:rs7548798
1   1060608 rs17160824  G   A   .   PASS    AF=0.097    ES:SE:LP:AF:SS:ID   0.0043:0.025:0.0655015:0.097:117263:rs17160824
1   1061115 rs17160826  T   C   .   PASS    AF=0.051    ES:SE:LP:AF:SS:ID   0.0063:0.026:0.09691:0.051:117259:rs17160826
1   1061152 rs12748370  T   C   .   PASS    AF=0.055    ES:SE:LP:AF:SS:ID   0.0028:0.026:0.0409586:0.055:115488:rs12748370
1   1061166 rs11807848  T   C   .   PASS    AF=0.389    ES:SE:LP:AF:SS:ID   0.014:0.018:0.356547:0.389:117252:rs11807848