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-972/ieu-a-972.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-972/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 10:11:12 2020
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-972/ieu-a-972.vcf.gz ...
Read summary statistics for 123617 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, 50534 SNPs remain.
After merging with regression SNP LD, 50534 SNPs remain.
WARNING: number of SNPs less than 200k; this is almost always bad.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 2.7077 (1.9525)
Lambda GC: 1.1168
Mean Chi^2: 1.1214
Intercept: 1.0783 (0.0214)
Ratio: 0.6446 (0.1761)
Analysis finished at Tue Feb  4 10:11:27 2020
Total time elapsed: 15.09s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.7839,
    "inflation_factor": 1.1837,
    "mean_EFFECT": 0.0055,
    "n": 739,
    "n_snps": 123617,
    "n_clumped_hits": 0,
    "n_p_sig": 0,
    "n_mono": 0,
    "n_ns": 0,
    "n_mac": 3169,
    "is_snpid_unique": true,
    "n_miss_EFFECT": 0,
    "n_miss_SE": 0,
    "n_miss_PVAL": 0,
    "n_miss_AF": 1184,
    "n_miss_AF_reference": 827,
    "n_est": 739.7228,
    "ratio_se_n": 1.0005,
    "mean_diff": 0.0205,
    "ratio_diff": 1.82,
    "sd_y_est1": 1.9638,
    "sd_y_est2": 1.9647,
    "r2_sum1": 0,
    "r2_sum2": 0,
    "r2_sum3": 0,
    "r2_sum4": 0,
    "ldsc_nsnp_merge_refpanel_ld": 50534,
    "ldsc_nsnp_merge_regression_ld": 50534,
    "ldsc_observed_scale_h2_beta": 2.7077,
    "ldsc_observed_scale_h2_se": 1.9525,
    "ldsc_intercept_beta": 1.0783,
    "ldsc_intercept_se": 0.0214,
    "ldsc_lambda_gc": 1.1168,
    "ldsc_mean_chisq": 1.1214,
    "ldsc_ratio": 0.645
}
 

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 1.000000 5 25 0 123617 0 NA NA NA NA NA NA NA NA
character REF 0 1.000000 1 1 0 4 0 NA NA NA NA NA NA NA NA
character ALT 0 1.000000 1 1 0 4 0 NA NA NA NA NA NA NA NA
numeric CHROM 0 1.000000 NA NA NA NA NA 8.087464e+00 5.769597e+00 1.00000e+00 3.000000e+00 6.000000e+00 1.200000e+01 2.200000e+01 ▇▅▃▂▂
numeric POS 0 1.000000 NA NA NA NA NA 7.901125e+07 5.778993e+07 6.34110e+04 3.290726e+07 6.220920e+07 1.176363e+08 2.492107e+08 ▇▅▃▂▁
numeric EFFECT 0 1.000000 NA NA NA NA NA 5.500200e-03 6.938452e-01 -1.95340e+01 -1.138260e-01 3.518000e-04 1.164190e-01 1.548690e+02 ▇▁▁▁▁
numeric SE 0 1.000000 NA NA NA NA NA 2.437835e-01 4.665800e-01 9.57113e-02 1.102960e-01 1.359580e-01 2.144680e-01 9.428900e+01 ▇▁▁▁▁
numeric PVAL 0 1.000000 NA NA NA NA NA 4.733697e-01 2.941426e-01 1.00000e-07 2.126949e-01 4.630565e-01 7.282458e-01 9.999980e-01 ▇▇▆▆▆
numeric PVAL_ztest 0 1.000000 NA NA NA NA NA 4.732529e-01 2.942450e-01 1.00000e-07 2.124584e-01 4.629811e-01 7.282426e-01 9.999978e-01 ▇▇▆▆▆
numeric AF 1184 0.990422 NA NA NA NA NA 3.178954e-01 2.829672e-01 1.46200e-03 7.749000e-02 2.295000e-01 5.088000e-01 9.985380e-01 ▇▃▂▂▂
numeric AF_reference 827 0.993310 NA NA NA NA NA 2.882265e-01 2.573936e-01 1.99700e-04 7.567890e-02 2.082670e-01 4.482830e-01 1.000000e+00 ▇▃▂▂▁
numeric N 0 1.000000 NA NA NA NA NA 7.390000e+02 0.000000e+00 7.39000e+02 7.390000e+02 7.390000e+02 7.390000e+02 7.390000e+02 ▁▁▇▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 1118275 rs61733845 C T 0.1415570 0.167431 0.3979550 0.3978514 0.09795 0.185703 739
1 1120431 rs1320571 G A 0.1374490 0.165435 0.4061730 0.4060675 0.10820 0.185304 739
1 1135242 rs9729550 A C -0.0057612 0.105540 0.9564670 0.9564670 0.34500 0.551917 739
1 1140435 rs1815606 G T 0.0212465 0.100075 0.8318760 0.8318685 0.43860 0.712061 739
1 1163804 rs7515488 C T 0.1651840 0.143657 0.2503427 0.2502057 0.14470 0.186901 739
1 1165310 rs11260562 G A -0.1996060 0.203532 0.3268820 0.3267355 0.07310 0.101837 739
1 1173611 rs6697886 G A 0.1418880 0.148717 0.3401308 0.3400429 0.13160 0.220647 739
1 1186502 rs6603785 A T 0.0831447 0.160051 0.6034607 0.6034199 0.11400 0.246206 739
1 1194804 rs11804831 T C -0.0893148 0.104467 0.3926748 0.3925749 0.35230 0.685903 739
1 1218086 rs6603788 C T -0.1403310 0.140918 0.3194596 0.3193306 0.16520 0.469449 739
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 50966914 rs470119 T C 0.0129330 0.110443 0.9067791 0.9067799 0.6857 0.5547120 739
22 50971752 rs131794 A C -0.0654140 0.129740 0.6141974 0.6141258 0.8056 0.8326680 739
22 50988193 rs131779 A G -0.0525105 0.110398 0.6343574 0.6343257 0.6477 0.5802720 739
22 50999182 rs140518 C T -0.1261830 0.115017 0.2728048 0.2726059 0.7251 0.7655750 739
22 51078251 rs4040041 C T -0.1030630 0.105613 0.3293002 0.3291362 0.4386 0.4666530 739
22 51094926 rs9616810 C T -0.1089090 0.123591 0.3783337 0.3782069 0.2456 0.2224440 739
22 51105556 rs9616812 C T 0.0255733 0.101460 0.8010011 0.8010001 0.4430 0.3628190 739
22 51109992 rs9628185 T C -0.0112981 0.100978 0.9109140 0.9109132 0.4561 0.4053510 739
22 51134186 rs8135777 A G 1.1448100 2.231460 0.6078816 0.6079291 NA 0.0273562 739
22 51156666 rs9628187 C T -0.0178030 0.142856 0.9008239 0.9008228 0.1652 0.1299920 739

bcf preview

1   1118275 rs61733845  C   T   .   PASS    AF=0.09795  ES:SE:LP:AF:SS:ID   0.141557:0.167431:0.400166:0.09795:739:rs61733845
1   1120431 rs1320571   G   A   .   PASS    AF=0.1082   ES:SE:LP:AF:SS:ID   0.137449:0.165435:0.391289:0.1082:739:rs1320571
1   1135242 rs9729550   A   C   .   PASS    AF=0.345    ES:SE:LP:AF:SS:ID   -0.00576118:0.10554:0.01933:0.345:739:rs9729550
1   1140435 rs1815606   G   T   .   PASS    AF=0.4386   ES:SE:LP:AF:SS:ID   0.0212465:0.100075:0.0799414:0.4386:739:rs1815606
1   1163804 rs7515488   C   T   .   PASS    AF=0.1447   ES:SE:LP:AF:SS:ID   0.165184:0.143657:0.601465:0.1447:739:rs7515488
1   1165310 rs11260562  G   A   .   PASS    AF=0.0731   ES:SE:LP:AF:SS:ID   -0.199606:0.203532:0.485609:0.0731:739:rs11260562
1   1173611 rs6697886   G   A   .   PASS    AF=0.1316   ES:SE:LP:AF:SS:ID   0.141888:0.148717:0.468354:0.1316:739:rs6697886
1   1186502 rs6603785   A   T   .   PASS    AF=0.114    ES:SE:LP:AF:SS:ID   0.0831447:0.160051:0.219351:0.114:739:rs6603785
1   1194804 rs11804831  T   C   .   PASS    AF=0.3523   ES:SE:LP:AF:SS:ID   -0.0893148:0.104467:0.405967:0.3523:739:rs11804831
1   1218086 rs6603788   C   T   .   PASS    AF=0.1652   ES:SE:LP:AF:SS:ID   -0.140331:0.140918:0.495584:0.1652:739:rs6603788
1   1227897 rs3737721   A   G   .   PASS    AF=0.06871  ES:SE:LP:AF:SS:ID   -0.505912:0.225901:1.59598:0.06871:739:rs3737721
1   1231656 rs1749951   G   A   .   PASS    AF=0.05848  ES:SE:LP:AF:SS:ID   0.272591:0.192521:0.804419:0.05848:739:rs1749951
1   1233941 rs1739855   T   C   .   PASS    AF=0.1827   ES:SE:LP:AF:SS:ID   -0.118439:0.132957:0.42812:0.1827:739:rs1739855
1   1241529 rs1536168   A   G   .   PASS    AF=0.91228  ES:SE:LP:AF:SS:ID   -0.124313:0.165371:0.34464:0.91228:739:rs1536168
1   1242468 rs2274264   G   A   .   PASS    AF=0.06433  ES:SE:LP:AF:SS:ID   -0.45324:0.228873:1.31922:0.06433:739:rs2274264
1   1247494 rs12103 T   C   .   PASS    AF=0.6857   ES:SE:LP:AF:SS:ID   0.0722188:0.108585:0.295807:0.6857:739:rs12103
1   1249187 rs12142199  G   A   .   PASS    AF=0.6769   ES:SE:LP:AF:SS:ID   0.0954124:0.108258:0.422235:0.6769:739:rs12142199
1   1254255 rs62623580  G   A   .   PASS    AF=0.04386  ES:SE:LP:AF:SS:ID   -0.0712077:0.255415:0.107687:0.04386:739:rs62623580
1   1335790 rs1240708   A   G   .   PASS    AF=0.3114   ES:SE:LP:AF:SS:ID   -0.0972809:0.111502:0.416765:0.3114:739:rs1240708
1   1493727 rs880051    G   A   .   PASS    AF=0.3816   ES:SE:LP:AF:SS:ID   0.0375228:0.105793:0.140955:0.3816:739:rs880051
1   1497824 rs2296716   C   T   .   PASS    AF=0.1784   ES:SE:LP:AF:SS:ID   0.0155512:0.141171:0.0398699:0.1784:739:rs2296716
1   1611995 rs4074196   A   G   .   PASS    AF=0.3713   ES:SE:LP:AF:SS:ID   0.0413063:0.105586:0.157602:0.3713:739:rs4074196
1   1706160 rs7531583   A   G   .   PASS    AF=0.5673   ES:SE:LP:AF:SS:ID   0.0501823:0.103882:0.201287:0.5673:739:rs7531583
1   1721479 rs2272908   C   T   .   PASS    AF=0.348    ES:SE:LP:AF:SS:ID   -0.0983152:0.106556:0.448238:0.348:739:rs2272908
1   1723031 rs9660180   G   A   .   PASS    AF=0.348    ES:SE:LP:AF:SS:ID   -0.0983152:0.106556:0.448238:0.348:739:rs9660180
1   1781220 rs6681938   T   C   .   PASS    AF=0.2135   ES:SE:LP:AF:SS:ID   -0.0300645:0.125244:0.0913558:0.2135:739:rs6681938
1   1838516 rs2377037   C   A   .   PASS    AF=0.2222   ES:SE:LP:AF:SS:ID   0.175046:0.120002:0.838998:0.2222:739:rs2377037
1   1840038 rs2474461   T   C   .   PASS    AF=0.8874   ES:SE:LP:AF:SS:ID   0.128774:0.164037:0.363959:0.8874:739:rs2474461
1   1853288 rs1884454   G   T   .   PASS    AF=0.2339   ES:SE:LP:AF:SS:ID   0.109188:0.118817:0.44586:0.2339:739:rs1884454
1   1855319 rs2295362   C   T   .   PASS    AF=0.1155   ES:SE:LP:AF:SS:ID   -0.0936867:0.162319:0.248826:0.1155:739:rs2295362
1   1871337 rs16824543  G   A   .   PASS    AF=0.117    ES:SE:LP:AF:SS:ID   -0.108677:0.161063:0.301117:0.117:739:rs16824543
1   1873625 rs12758705  G   A   .   PASS    AF=0.2266   ES:SE:LP:AF:SS:ID   0.115545:0.119998:0.474007:0.2266:739:rs12758705
1   1881070 rs4648596   G   A   .   PASS    AF=0.08626  ES:SE:LP:AF:SS:ID   -0.0466509:0.188122:0.0946619:0.08626:739:rs4648596
1   1888193 rs3820011   C   A   .   PASS    AF=0.2442   ES:SE:LP:AF:SS:ID   0.156525:0.119102:0.723729:0.2442:739:rs3820011
1   2024064 rs2459994   C   T   .   PASS    AF=0.2991   ES:SE:LP:AF:SS:ID   0.0926666:0.113568:0.382337:0.2991:739:rs2459994
1   2146966 rs7512482   T   C   .   PASS    AF=0.2295   ES:SE:LP:AF:SS:ID   0.112949:0.120078:0.459652:0.2295:739:rs7512482
1   2202774 rs6673129   C   T   .   PASS    AF=0.1681   ES:SE:LP:AF:SS:ID   0.186699:0.134568:0.780861:0.1681:739:rs6673129
1   2229478 rs12562937  C   T   .   PASS    AF=0.1711   ES:SE:LP:AF:SS:ID   0.0433926:0.137758:0.123331:0.1711:739:rs12562937
1   2283896 rs2840528   A   G   .   PASS    AF=0.3421   ES:SE:LP:AF:SS:ID   -0.0844577:0.109352:0.356549:0.3421:739:rs2840528
1   2290143 rs34587196  G   A   .   PASS    AF=0.01023  ES:SE:LP:AF:SS:ID   0.677579:0.445052:0.892183:0.01023:739:rs34587196
1   2404256 rs2494626   C   T   .   PASS    AF=0.3202   ES:SE:LP:AF:SS:ID   0.0311582:0.11127:0.1082:0.3202:739:rs2494626
1   2407781 rs78504402  C   T   .   PASS    AF=0.04386  ES:SE:LP:AF:SS:ID   0.100874:0.247804:0.164964:0.04386:739:rs78504402
1   2408471 rs115996655 G   A   .   PASS    AF=0.001462 ES:SE:LP:AF:SS:ID   -3.13999:2.81636:0.576666:0.001462:739:rs115996655
1   2408834 rs11588930  G   A   .   PASS    AF=0.09064  ES:SE:LP:AF:SS:ID   0.184741:0.165781:0.576197:0.09064:739:rs11588930
1   2409892 rs12727342  A   G   .   PASS    AF=0.6477   ES:SE:LP:AF:SS:ID   -0.162962:0.104181:0.928059:0.6477:739:rs12727342
1   2410789 rs11799501  C   T   .   PASS    AF=0.636    ES:SE:LP:AF:SS:ID   -0.134846:0.104284:0.707372:0.636:739:rs11799501
1   2412279 rs4648638   A   T   .   PASS    AF=0.3567   ES:SE:LP:AF:SS:ID   0.171336:0.103517:1.00807:0.3567:739:rs4648638
1   2412293 rs12731186  C   T   .   PASS    AF=0.08918  ES:SE:LP:AF:SS:ID   -0.0335033:0.178417:0.0700449:0.08918:739:rs12731186
1   2413166 rs115810747 A   G   .   PASS    AF=0.004386 ES:SE:LP:AF:SS:ID   0.646944:0.689703:0.457827:0.004386:739:rs115810747
1   2413464 rs114424485 G   C   .   PASS    AF=0.001462 ES:SE:LP:AF:SS:ID   -3.13999:2.81636:0.576666:0.001462:739:rs114424485