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-14/ieu-a-14.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-14/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 11:42:09 2020
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-14/ieu-a-14.vcf.gz ...
Read summary statistics for 123070 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, 50535 SNPs remain.
After merging with regression SNP LD, 50535 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: 5.7571 (2.4899)
Lambda GC: 1.1029
Mean Chi^2: 1.0944
Intercept: 1.0313 (0.0196)
Ratio: 0.3312 (0.208)
Analysis finished at Wed Feb  5 11:42:19 2020
Total time elapsed: 9.45s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.7836,
    "inflation_factor": 1.1313,
    "mean_EFFECT": -0.0273,
    "n": 493,
    "n_snps": 123070,
    "n_clumped_hits": 0,
    "n_p_sig": 0,
    "n_mono": 0,
    "n_ns": 0,
    "n_mac": 5481,
    "is_snpid_unique": true,
    "n_miss_EFFECT": 0,
    "n_miss_SE": 0,
    "n_miss_PVAL": 0,
    "n_miss_AF": 632,
    "n_miss_AF_reference": 817,
    "n_est": 491.9723,
    "ratio_se_n": 0.999,
    "mean_diff": 0.0476,
    "ratio_diff": 2.0842,
    "sd_y_est1": 2.1611,
    "sd_y_est2": 2.1589,
    "r2_sum1": 0,
    "r2_sum2": 0,
    "r2_sum3": 0,
    "r2_sum4": 0,
    "ldsc_nsnp_merge_refpanel_ld": 50535,
    "ldsc_nsnp_merge_regression_ld": 50535,
    "ldsc_observed_scale_h2_beta": 5.7571,
    "ldsc_observed_scale_h2_se": 2.4899,
    "ldsc_intercept_beta": 1.0313,
    "ldsc_intercept_se": 0.0196,
    "ldsc_lambda_gc": 1.1029,
    "ldsc_mean_chisq": 1.0944,
    "ldsc_ratio": 0.3316
}

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 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 5 25 0 123070 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 8.089421e+00 5.769799e+00 1.00000e+00 3.000000e+00 6.000000e+00 1.200000e+01 2.200000e+01 ▇▅▃▂▂
numeric POS 0 1.0000000 NA NA NA NA NA 7.897569e+07 5.780595e+07 6.34110e+04 3.284347e+07 6.218967e+07 1.176290e+08 2.492107e+08 ▇▅▃▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA -2.734480e-02 6.185919e-01 -7.14214e+00 -1.514282e-01 1.936000e-04 1.482620e-01 6.533830e+00 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 3.331126e-01 5.048964e-01 1.27047e-01 1.481158e-01 1.827730e-01 2.882960e-01 7.872680e+00 ▇▁▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.793605e-01 2.919904e-01 1.90000e-06 2.202901e-01 4.731224e-01 7.312203e-01 9.999980e-01 ▇▇▇▆▆
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.793576e-01 2.919931e-01 1.90000e-06 2.203118e-01 4.731413e-01 7.312287e-01 9.999980e-01 ▇▇▇▆▆
numeric AF 632 0.9948647 NA NA NA NA NA 3.179635e-01 2.830549e-01 1.46200e-03 7.749000e-02 2.295000e-01 5.088000e-01 9.985380e-01 ▇▃▂▂▂
numeric AF_reference 817 0.9933615 NA NA NA NA NA 2.891334e-01 2.571852e-01 1.99700e-04 7.687700e-02 2.094650e-01 4.494810e-01 9.998000e-01 ▇▃▂▂▁
numeric N 0 1.0000000 NA NA NA NA NA 4.930000e+02 0.000000e+00 4.93000e+02 4.930000e+02 4.930000e+02 4.930000e+02 4.930000e+02 ▁▁▇▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 1118275 rs61733845 C T 0.3044080 0.200171 0.1282599 0.1283252 0.09795 0.185703 493
1 1120431 rs1320571 G A 0.4831020 0.199465 0.0155643 0.0154358 0.10820 0.185304 493
1 1135242 rs9729550 A C 0.0675147 0.139784 0.6291222 0.6291007 0.34500 0.551917 493
1 1140435 rs1815606 G T 0.0972288 0.135197 0.4720500 0.4720399 0.43860 0.712061 493
1 1163804 rs7515488 C T 0.2474120 0.186196 0.1839891 0.1839233 0.14470 0.186901 493
1 1165310 rs11260562 G A 0.1421320 0.261886 0.5873203 0.5873194 0.07310 0.101837 493
1 1173611 rs6697886 G A 0.0577609 0.202428 0.7753968 0.7753833 0.13160 0.220647 493
1 1186502 rs6603785 A T -0.0237657 0.220841 0.9142989 0.9143015 0.11400 0.246206 493
1 1194804 rs11804831 T C -0.0133696 0.141942 0.9249580 0.9249578 0.35230 0.685903 493
1 1218086 rs6603788 C T -0.0046248 0.184474 0.9799990 0.9799990 0.16520 0.469449 493
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 50960682 rs140524 C T -0.3995530 0.236323 0.0907194 0.0908927 0.1243 0.230232 493
22 50966914 rs470119 T C 0.1436590 0.148217 0.3324681 0.3324216 0.6857 0.554712 493
22 50971752 rs131794 A C 0.0545451 0.173960 0.7538727 0.7538631 0.8056 0.832668 493
22 50988193 rs131779 A G -0.0003492 0.148173 0.9981190 0.9981194 0.6477 0.580272 493
22 50999182 rs140518 C T -0.0601457 0.152331 0.6929278 0.6929642 0.7251 0.765575 493
22 51078251 rs4040041 C T 0.1431470 0.146906 0.3298268 0.3298519 0.4386 0.466653 493
22 51094926 rs9616810 C T -0.0509961 0.161672 0.7524437 0.7524357 0.2456 0.222444 493
22 51105556 rs9616812 C T -0.0171318 0.141211 0.9034350 0.9034371 0.4430 0.362819 493
22 51109992 rs9628185 T C -0.0796575 0.140730 0.5712787 0.5713729 0.4561 0.405351 493
22 51156666 rs9628187 C T -0.0893607 0.189426 0.6371255 0.6371091 0.1652 0.129992 493

bcf preview

1   1118275 rs61733845  C   T   .   PASS    AF=0.09795  ES:SE:LP:AF:SS:ID   0.304408:0.200171:0.891909:0.09795:493:rs61733845
1   1120431 rs1320571   G   A   .   PASS    AF=0.1082   ES:SE:LP:AF:SS:ID   0.483102:0.199465:1.80787:0.1082:493:rs1320571
1   1135242 rs9729550   A   C   .   PASS    AF=0.345    ES:SE:LP:AF:SS:ID   0.0675147:0.139784:0.201265:0.345:493:rs9729550
1   1140435 rs1815606   G   T   .   PASS    AF=0.4386   ES:SE:LP:AF:SS:ID   0.0972288:0.135197:0.326012:0.4386:493:rs1815606
1   1163804 rs7515488   C   T   .   PASS    AF=0.1447   ES:SE:LP:AF:SS:ID   0.247412:0.186196:0.735208:0.1447:493:rs7515488
1   1165310 rs11260562  G   A   .   PASS    AF=0.0731   ES:SE:LP:AF:SS:ID   0.142132:0.261886:0.231125:0.0731:493:rs11260562
1   1173611 rs6697886   G   A   .   PASS    AF=0.1316   ES:SE:LP:AF:SS:ID   0.0577609:0.202428:0.110476:0.1316:493:rs6697886
1   1186502 rs6603785   A   T   .   PASS    AF=0.114    ES:SE:LP:AF:SS:ID   -0.0237657:0.220841:0.0389118:0.114:493:rs6603785
1   1194804 rs11804831  T   C   .   PASS    AF=0.3523   ES:SE:LP:AF:SS:ID   -0.0133696:0.141942:0.033878:0.3523:493:rs11804831
1   1218086 rs6603788   C   T   .   PASS    AF=0.1652   ES:SE:LP:AF:SS:ID   -0.00462479:0.184474:0.00877437:0.1652:493:rs6603788
1   1227897 rs3737721   A   G   .   PASS    AF=0.06871  ES:SE:LP:AF:SS:ID   -0.313423:0.287194:0.560472:0.06871:493:rs3737721
1   1231656 rs1749951   G   A   .   PASS    AF=0.05848  ES:SE:LP:AF:SS:ID   -0.00644466:0.292951:0.00768998:0.05848:493:rs1749951
1   1233941 rs1739855   T   C   .   PASS    AF=0.1827   ES:SE:LP:AF:SS:ID   -0.0836405:0.179763:0.192649:0.1827:493:rs1739855
1   1241529 rs1536168   A   G   .   PASS    AF=0.91228  ES:SE:LP:AF:SS:ID   -0.0798628:0.2357:0.133872:0.91228:493:rs1536168
1   1242468 rs2274264   G   A   .   PASS    AF=0.06433  ES:SE:LP:AF:SS:ID   -0.186844:0.283588:0.292443:0.06433:493:rs2274264
1   1247494 rs12103 T   C   .   PASS    AF=0.6857   ES:SE:LP:AF:SS:ID   -0.16869:0.144004:0.617193:0.6857:493:rs12103
1   1249187 rs12142199  G   A   .   PASS    AF=0.6769   ES:SE:LP:AF:SS:ID   -0.142432:0.143662:0.492846:0.6769:493:rs12142199
1   1254255 rs62623580  G   A   .   PASS    AF=0.04386  ES:SE:LP:AF:SS:ID   0.138181:0.32358:0.174345:0.04386:493:rs62623580
1   1335790 rs1240708   A   G   .   PASS    AF=0.3114   ES:SE:LP:AF:SS:ID   0.20587:0.146469:0.796192:0.3114:493:rs1240708
1   1493727 rs880051    G   A   .   PASS    AF=0.3816   ES:SE:LP:AF:SS:ID   0.0724923:0.143607:0.212024:0.3816:493:rs880051
1   1497824 rs2296716   C   T   .   PASS    AF=0.1784   ES:SE:LP:AF:SS:ID   0.186087:0.184897:0.5027:0.1784:493:rs2296716
1   1611995 rs4074196   A   G   .   PASS    AF=0.3713   ES:SE:LP:AF:SS:ID   0.0703648:0.142084:0.207264:0.3713:493:rs4074196
1   1706160 rs7531583   A   G   .   PASS    AF=0.5673   ES:SE:LP:AF:SS:ID   -0.023082:0.132284:0.0647533:0.5673:493:rs7531583
1   1721479 rs2272908   C   T   .   PASS    AF=0.348    ES:SE:LP:AF:SS:ID   -0.13062:0.145359:0.433034:0.348:493:rs2272908
1   1723031 rs9660180   G   A   .   PASS    AF=0.348    ES:SE:LP:AF:SS:ID   -0.13062:0.145359:0.433034:0.348:493:rs9660180
1   1781220 rs6681938   T   C   .   PASS    AF=0.2135   ES:SE:LP:AF:SS:ID   -0.449079:0.187177:1.78486:0.2135:493:rs6681938
1   1838516 rs2377037   C   A   .   PASS    AF=0.2222   ES:SE:LP:AF:SS:ID   0.123808:0.161066:0.354499:0.2222:493:rs2377037
1   1840038 rs2474461   T   C   .   PASS    AF=0.8874   ES:SE:LP:AF:SS:ID   0.177236:0.226172:0.363355:0.8874:493:rs2474461
1   1853288 rs1884454   G   T   .   PASS    AF=0.2339   ES:SE:LP:AF:SS:ID   0.0921622:0.162418:0.243789:0.2339:493:rs1884454
1   1855319 rs2295362   C   T   .   PASS    AF=0.1155   ES:SE:LP:AF:SS:ID   -0.05953:0.213359:0.107777:0.1155:493:rs2295362
1   1871337 rs16824543  G   A   .   PASS    AF=0.117    ES:SE:LP:AF:SS:ID   -0.0381066:0.211595:0.0669786:0.117:493:rs16824543
1   1873625 rs12758705  G   A   .   PASS    AF=0.2266   ES:SE:LP:AF:SS:ID   0.0976096:0.163347:0.259517:0.2266:493:rs12758705
1   1881070 rs4648596   G   A   .   PASS    AF=0.08626  ES:SE:LP:AF:SS:ID   -0.0572353:0.250071:0.0867405:0.08626:493:rs4648596
1   1888193 rs3820011   C   A   .   PASS    AF=0.2442   ES:SE:LP:AF:SS:ID   0.134855:0.157908:0.405378:0.2442:493:rs3820011
1   2024064 rs2459994   C   T   .   PASS    AF=0.2991   ES:SE:LP:AF:SS:ID   0.462293:0.144451:2.86465:0.2991:493:rs2459994
1   2146966 rs7512482   T   C   .   PASS    AF=0.2295   ES:SE:LP:AF:SS:ID   -0.051066:0.163672:0.122032:0.2295:493:rs7512482
1   2202774 rs6673129   C   T   .   PASS    AF=0.1681   ES:SE:LP:AF:SS:ID   0.311486:0.177921:1.0971:0.1681:493:rs6673129
1   2229478 rs12562937  C   T   .   PASS    AF=0.1711   ES:SE:LP:AF:SS:ID   -0.0182659:0.189139:0.0347677:0.1711:493:rs12562937
1   2283896 rs2840528   A   G   .   PASS    AF=0.3421   ES:SE:LP:AF:SS:ID   0.0507646:0.14296:0.14115:0.3421:493:rs2840528
1   2290143 rs34587196  G   A   .   PASS    AF=0.01023  ES:SE:LP:AF:SS:ID   0.837395:0.535087:0.92953:0.01023:493:rs34587196
1   2404256 rs2494626   C   T   .   PASS    AF=0.3202   ES:SE:LP:AF:SS:ID   -0.227789:0.154916:0.848879:0.3202:493:rs2494626
1   2407781 rs78504402  C   T   .   PASS    AF=0.04386  ES:SE:LP:AF:SS:ID   -0.0327782:0.34723:0.0339555:0.04386:493:rs78504402
1   2408471 rs115996655 G   A   .   PASS    AF=0.001462 ES:SE:LP:AF:SS:ID   -3.05881:4.30567:0.321045:0.001462:493:rs115996655
1   2408834 rs11588930  G   A   .   PASS    AF=0.09064  ES:SE:LP:AF:SS:ID   -0.0838144:0.246964:0.134111:0.09064:493:rs11588930
1   2409892 rs12727342  A   G   .   PASS    AF=0.6477   ES:SE:LP:AF:SS:ID   -0.0553453:0.142521:0.156176:0.6477:493:rs12727342
1   2410789 rs11799501  C   T   .   PASS    AF=0.636    ES:SE:LP:AF:SS:ID   -0.0910177:0.141417:0.283856:0.636:493:rs11799501
1   2412279 rs4648638   A   T   .   PASS    AF=0.3567   ES:SE:LP:AF:SS:ID   0.146122:0.141831:0.517488:0.3567:493:rs4648638
1   2412293 rs12731186  C   T   .   PASS    AF=0.08918  ES:SE:LP:AF:SS:ID   -0.45515:0.276851:1.00018:0.08918:493:rs12731186
1   2413166 rs115810747 A   G   .   PASS    AF=0.004386 ES:SE:LP:AF:SS:ID   0.644863:0.704513:0.443677:0.004386:493:rs115810747
1   2413464 rs114424485 G   C   .   PASS    AF=0.001462 ES:SE:LP:AF:SS:ID   -3.05881:4.30567:0.321045:0.001462:493:rs114424485