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-87/ieu-a-87.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-87/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 11:46:45 2020
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-87/ieu-a-87.vcf.gz ...
Read summary statistics for 1937597 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, 954520 SNPs remain.
After merging with regression SNP LD, 954520 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.3567 (0.055)
Lambda GC: 0.977
Mean Chi^2: 1.0194
Intercept: 0.957 (0.0063)
Ratio < 0 (usually indicates GC correction).
Analysis finished at Wed Feb  5 11:47:10 2020
Total time elapsed: 24.95s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.8803,
    "inflation_factor": 1,
    "mean_EFFECT": -0.0005,
    "n": 10255,
    "n_snps": 1937597,
    "n_clumped_hits": 2,
    "n_p_sig": 37,
    "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": 1980,
    "n_miss_AF_reference": 15677,
    "n_est": 10251.6418,
    "ratio_se_n": 0.9998,
    "mean_diff": 0.0003,
    "ratio_diff": 14.9788,
    "sd_y_est1": 2.2808,
    "sd_y_est2": 2.2805,
    "r2_sum1": 0.0375,
    "r2_sum2": 0.0072,
    "r2_sum3": 0.0072,
    "r2_sum4": 0.0079,
    "ldsc_nsnp_merge_refpanel_ld": 954520,
    "ldsc_nsnp_merge_regression_ld": 954520,
    "ldsc_observed_scale_h2_beta": 0.3567,
    "ldsc_observed_scale_h2_se": 0.055,
    "ldsc_intercept_beta": 0.957,
    "ldsc_intercept_se": 0.0063,
    "ldsc_lambda_gc": 0.977,
    "ldsc_mean_chisq": 1.0194,
    "ldsc_ratio": -2.2165
}

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 1937597 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 8.572565e+00 5.653004e+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 7.884408e+07 5.575817e+07 1.1543e+04 3.251192e+07 7.018599e+07 1.145490e+08 2.491722e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA -4.983000e-04 4.342010e-02 -2.9000e-01 -2.600000e-02 -3.000000e-04 2.500000e-02 3.600000e-01 ▁▂▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 4.069200e-02 1.327910e-02 1.0000e-04 3.200000e-02 3.600000e-02 4.800000e-02 1.200000e-01 ▁▇▂▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.999065e-01 2.900697e-01 0.0000e+00 2.500000e-01 5.000000e-01 7.499995e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.999291e-01 2.900567e-01 0.0000e+00 2.475789e-01 5.049851e-01 7.519046e-01 1.000000e+00 ▇▇▇▇▇
numeric AF 1980 0.9989781 NA NA NA NA NA 4.006891e-01 2.388596e-01 8.0000e-03 1.920000e-01 3.560000e-01 5.830000e-01 9.920000e-01 ▇▇▆▅▂
numeric AF_reference 15677 0.9919091 NA NA NA NA NA 3.973105e-01 2.296970e-01 1.9970e-04 2.058710e-01 3.554310e-01 5.686900e-01 1.000000e+00 ▆▇▆▃▂
numeric N 0 1.0000000 NA NA NA NA NA 8.318405e+03 1.586951e+03 4.8297e+03 7.017600e+03 8.852890e+03 9.711520e+03 1.025500e+04 ▂▂▃▃▇

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 990380 rs3121561 C T 0.0190 0.058 0.7499995 0.7432246 0.267 0.343450 7269.22
1 998501 rs3813193 G C -0.0140 0.064 0.8300000 0.8268448 0.150 0.206669 5609.80
1 1003629 rs4075116 C T 0.0019 0.042 0.9599999 0.9639175 0.737 0.720647 8555.64
1 1017170 rs3766193 C G -0.0092 0.038 0.8100000 0.8086986 0.569 0.575479 9578.74
1 1017197 rs3766192 C T -0.0044 0.036 0.9000000 0.9027230 0.576 0.511182 9627.99
1 1018562 rs9442371 C T -0.0048 0.036 0.8900000 0.8939298 0.592 0.530152 9627.99
1 1018704 rs9442372 A G -0.0048 0.036 0.8900000 0.8939298 0.602 0.611022 9625.89
1 1021415 rs3737728 A G -0.0086 0.038 0.8200001 0.8209558 0.717 0.812700 8965.00
1 1021695 rs9442398 A G 0.0014 0.041 0.9699999 0.9727605 0.725 0.727236 8827.74
1 1022037 rs6701114 C T -0.0150 0.039 0.7099994 0.7005224 0.567 0.586661 9031.01
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51162059 rs10451 G A 0.0670 0.043 0.1199999 0.1192002 0.284 0.3865810 6230.41
22 51163138 rs715586 C T 0.0920 0.053 0.0860003 0.0825905 0.150 0.0902556 6766.00
22 51165664 rs8137951 G A 0.0560 0.035 0.1100001 0.1095986 0.275 0.4063500 9148.00
22 51171693 rs756638 G A -0.0610 0.037 0.0929994 0.0992196 0.283 0.3049120 7570.00
22 51183017 rs58651371 C T -0.1400 0.069 0.0439997 0.0424598 0.267 0.4137380 6277.00
22 51212875 rs2238837 A C 0.0670 0.049 0.1700000 0.1715166 0.392 0.3724040 7440.00
22 51216564 rs9616970 T C -0.0440 0.079 0.5700002 0.5775534 0.150 0.1563500 6080.00
22 51217134 rs117417021 A G 0.0560 0.049 0.2500000 0.2530979 0.442 0.2671730 7629.00
23 35921591 rs2204667 C G 0.0052 0.049 0.9199999 0.9154852 0.167 NA 6882.00
23 118495837 rs12882977 G A -0.0120 0.030 0.6999999 0.6891565 0.509 0.2307280 10030.00

bcf preview

1   990380  rs3121561   C   T   .   PASS    AF=0.267    ES:SE:LP:AF:SS:ID   0.019:0.058:0.124939:0.267:7269.22:rs3121561
1   998501  rs3813193   G   C   .   PASS    AF=0.15 ES:SE:LP:AF:SS:ID   -0.014:0.064:0.0809219:0.15:5609.8:rs3813193
1   1003629 rs4075116   C   T   .   PASS    AF=0.737    ES:SE:LP:AF:SS:ID   0.0019:0.042:0.0177288:0.737:8555.64:rs4075116
1   1017170 rs3766193   C   G   .   PASS    AF=0.569    ES:SE:LP:AF:SS:ID   -0.0092:0.038:0.091515:0.569:9578.74:rs3766193
1   1017197 rs3766192   C   T   .   PASS    AF=0.576    ES:SE:LP:AF:SS:ID   -0.0044:0.036:0.0457575:0.576:9627.99:rs3766192
1   1018562 rs9442371   C   T   .   PASS    AF=0.592    ES:SE:LP:AF:SS:ID   -0.0048:0.036:0.05061:0.592:9627.99:rs9442371
1   1018704 rs9442372   A   G   .   PASS    AF=0.602    ES:SE:LP:AF:SS:ID   -0.0048:0.036:0.05061:0.602:9625.89:rs9442372
1   1021415 rs3737728   A   G   .   PASS    AF=0.717    ES:SE:LP:AF:SS:ID   -0.0086:0.038:0.0861861:0.717:8965:rs3737728
1   1021695 rs9442398   A   G   .   PASS    AF=0.725    ES:SE:LP:AF:SS:ID   0.0014:0.041:0.0132283:0.725:8827.74:rs9442398
1   1022037 rs6701114   C   T   .   PASS    AF=0.567    ES:SE:LP:AF:SS:ID   -0.015:0.039:0.148742:0.567:9031.01:rs6701114
1   1026707 rs4074137   C   A   .   PASS    AF=0.6  ES:SE:LP:AF:SS:ID   0.053:0.042:0.677781:0.6:6656.64:rs4074137
1   1031540 rs9651273   A   G   .   PASS    AF=0.658    ES:SE:LP:AF:SS:ID   0.013:0.045:0.113509:0.658:6247:rs9651273
1   1046164 rs6666280   C   T   .   PASS    AF=0.067    ES:SE:LP:AF:SS:ID   -0.026:0.065:0.161151:0.067:5808:rs6666280
1   1049950 rs12726255  A   G   .   PASS    AF=0.067    ES:SE:LP:AF:SS:ID   -0.024:0.065:0.148742:0.067:5807:rs12726255
1   1061166 rs11807848  T   C   .   PASS    AF=0.412    ES:SE:LP:AF:SS:ID   0.015:0.044:0.142668:0.412:6665.63:rs11807848
1   1062638 rs9442373   C   A   .   PASS    AF=0.552    ES:SE:LP:AF:SS:ID   -0.028:0.045:0.275724:0.552:6434.87:rs9442373
1   1064535 rs6682475   G   C   .   PASS    AF=0.754    ES:SE:LP:AF:SS:ID   -0.024:0.062:0.154902:0.754:5948.41:rs6682475
1   1066403 rs10907182  T   C   .   PASS    AF=0.675    ES:SE:LP:AF:SS:ID   -0.029:0.05:0.251812:0.675:6254.85:rs10907182
1   1071118 rs10907183  G   C   .   PASS    AF=0.683    ES:SE:LP:AF:SS:ID   -0.036:0.054:0.30103:0.683:6049.04:rs10907183
1   1077064 rs4970357   C   A   .   PASS    AF=0.924    ES:SE:LP:AF:SS:ID   -0.13:0.095:0.769551:0.924:4830.4:rs4970357
1   1087683 rs9442380   T   C   .   PASS    AF=0.912    ES:SE:LP:AF:SS:ID   -0.071:0.086:0.387216:0.912:5361.3:rs9442380
1   1121794 rs11260549  G   A   .   PASS    AF=0.125    ES:SE:LP:AF:SS:ID   0.028:0.064:0.180456:0.125:4962:rs11260549
1   1124663 rs6684820   G   A   .   PASS    AF=0.267    ES:SE:LP:AF:SS:ID   -0.03:0.04:0.337242:0.267:8580.76:rs6684820
1   1125553 rs10907174  A   T   .   PASS    AF=0.225    ES:SE:LP:AF:SS:ID   -0.0006:0.045:0.00436481:0.225:7813.78:rs10907174
1   1129672 rs11260554  G   T   .   PASS    AF=0.125    ES:SE:LP:AF:SS:ID   0.042:0.064:0.283997:0.125:4956:rs11260554
1   1130727 rs10907175  A   C   .   PASS    AF=0.1  ES:SE:LP:AF:SS:ID   0.024:0.073:0.124939:0.1:4891.9:rs10907175
1   1135242 rs9729550   A   C   .   PASS    AF=0.275    ES:SE:LP:AF:SS:ID   -0.034:0.039:0.420216:0.275:8734:rs9729550
1   1140435 rs1815606   G   T   .   PASS    AF=0.31 ES:SE:LP:AF:SS:ID   -0.043:0.044:0.468521:0.31:6388.14:rs1815606
1   1156131 rs2887286   T   C   .   PASS    AF=0.183    ES:SE:LP:AF:SS:ID   0.083:0.052:0.958607:0.183:6443:rs2887286
1   1158277 rs3813199   G   A   .   PASS    AF=0.1  ES:SE:LP:AF:SS:ID   -0.0051:0.07:0.0268721:0.1:5117:rs3813199
1   1162435 rs3766186   C   A   .   PASS    AF=0.1  ES:SE:LP:AF:SS:ID   -0.015:0.072:0.0757207:0.1:4891:rs3766186
1   1163804 rs7515488   C   T   .   PASS    AF=0.15 ES:SE:LP:AF:SS:ID   -0.064:0.056:0.60206:0.15:6580:rs7515488
1   1194804 rs11804831  T   C   .   PASS    AF=0.208    ES:SE:LP:AF:SS:ID   -0.024:0.049:0.207608:0.208:7678:rs11804831
1   1249187 rs12142199  G   A   .   PASS    AF=0.775    ES:SE:LP:AF:SS:ID   0.041:0.054:0.346787:0.775:6044.47:rs12142199
1   1388289 rs1781145   A   C   .   PASS    AF=0.144    ES:SE:LP:AF:SS:ID   0.0037:0.07:0.0177288:0.144:6532.88:rs1781145
1   1474304 rs1571150   C   A   .   PASS    AF=0.3  ES:SE:LP:AF:SS:ID   0.022:0.035:0.275724:0.3:9135.46:rs1571150
1   1477244 rs7290  T   C   .   PASS    AF=0.25 ES:SE:LP:AF:SS:ID   -0.0004:0.044:0.00436481:0.25:6186.98:rs7290
1   1478153 rs3766180   T   C   .   PASS    AF=0.242    ES:SE:LP:AF:SS:ID   0.0094:0.036:0.102373:0.242:8972.99:rs3766180
1   1478180 rs3766178   T   C   .   PASS    AF=0.242    ES:SE:LP:AF:SS:ID   0.015:0.036:0.173925:0.242:9055.99:rs3766178
1   1479333 rs7533  A   G   .   PASS    AF=0.246    ES:SE:LP:AF:SS:ID   -0.0015:0.044:0.0132283:0.246:6187:rs7533
1   1481348 rs3766177   T   C   .   PASS    AF=0.317    ES:SE:LP:AF:SS:ID   0.042:0.039:0.552842:0.317:8762.25:rs3766177
1   1483010 rs7517401   G   A   .   PASS    AF=0.283    ES:SE:LP:AF:SS:ID   0.021:0.036:0.244125:0.283:9058.19:rs7517401
1   1486834 rs3128342   C   A   .   PASS    AF=0.333    ES:SE:LP:AF:SS:ID   -0.0031:0.033:0.0362122:0.333:10049:rs3128342
1   1489670 rs7531530   C   T   .   PASS    AF=0.25 ES:SE:LP:AF:SS:ID   0.033:0.039:0.39794:0.25:8430.87:rs7531530
1   1489928 rs7366884   T   C   .   PASS    AF=0.25 ES:SE:LP:AF:SS:ID   0.033:0.039:0.39794:0.25:8430.88:rs7366884
1   1493727 rs880051    G   A   .   PASS    AF=0.188    ES:SE:LP:AF:SS:ID   0.049:0.05:0.49485:0.188:5920.97:rs880051
1   1497201 rs3766169   A   C   .   PASS    AF=0.246    ES:SE:LP:AF:SS:ID   0.0084:0.036:0.091515:0.246:8989:rs3766169
1   1497824 rs2296716   C   T   .   PASS    AF=0.083    ES:SE:LP:AF:SS:ID   0.088:0.066:0.744727:0.083:5787:rs2296716
1   1499298 rs9439468   A   G   .   PASS    AF=0.31 ES:SE:LP:AF:SS:ID   0.024:0.034:0.309804:0.31:9198:rs9439468
1   1500941 rs6603791   A   G   .   PASS    AF=0.3  ES:SE:LP:AF:SS:ID   0.023:0.034:0.30103:0.3:9194.99:rs6603791