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-970/ieu-a-970.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-970/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 11:38:45 2020
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-970/ieu-a-970.vcf.gz ...
Read summary statistics for 124474 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, 50573 SNPs remain.
After merging with regression SNP LD, 50573 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: 2.8265 (0.3127)
Lambda GC: 2.2022
Mean Chi^2: 4.0888
Intercept: 1.2875 (0.0577)
Ratio: 0.0931 (0.0187)
Analysis finished at Wed Feb  5 11:38:54 2020
Total time elapsed: 9.45s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.7668,
    "inflation_factor": 2.5645,
    "mean_EFFECT": -0.0006,
    "n": 47745,
    "n_snps": 124474,
    "n_clumped_hits": 88,
    "n_p_sig": 3733,
    "n_mono": 0,
    "n_ns": 0,
    "n_mac": 29,
    "is_snpid_unique": true,
    "n_miss_EFFECT": 0,
    "n_miss_SE": 0,
    "n_miss_PVAL": 0,
    "n_miss_AF": 0,
    "n_miss_AF_reference": 840,
    "n_est": 47965.9545,
    "ratio_se_n": 1.0023,
    "mean_diff": 0.0007,
    "ratio_diff": 1.9566,
    "sd_y_est1": 1.9795,
    "sd_y_est2": 1.984,
    "r2_sum1": 0.6643,
    "r2_sum2": 0.1695,
    "r2_sum3": 0.1688,
    "r2_sum4": 0.1705,
    "ldsc_nsnp_merge_refpanel_ld": 50573,
    "ldsc_nsnp_merge_regression_ld": 50573,
    "ldsc_observed_scale_h2_beta": 2.8265,
    "ldsc_observed_scale_h2_se": 0.3127,
    "ldsc_intercept_beta": 1.2875,
    "ldsc_intercept_se": 0.0577,
    "ldsc_lambda_gc": 2.2022,
    "ldsc_mean_chisq": 4.0888,
    "ldsc_ratio": 0.0931
}

Flags

name value
af_correlation FALSE
inflation_factor TRUE
n FALSE
is_snpid_non_unique FALSE
mean_EFFECT_nonfinite FALSE
mean_EFFECT_05 FALSE
mean_EFFECT_01 FALSE
mean_chisq TRUE
n_p_sig TRUE
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 5 25 0 124474 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 8.085865e+00 5.768649e+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 7.906188e+07 5.778011e+07 6.34110e+04 3.292806e+07 6.222332e+07 1.176462e+08 2.492107e+08 ▇▅▃▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA -6.411000e-04 5.633520e-02 -1.10304e+00 -2.285080e-02 -3.878000e-04 2.228210e-02 1.058540e+00 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 2.702680e-02 2.967630e-02 1.23244e-02 1.381470e-02 1.717040e-02 2.722270e-02 9.404370e-01 ▇▁▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 3.524185e-01 3.164045e-01 0.00000e+00 4.509410e-02 2.800838e-01 6.185905e-01 9.999573e-01 ▇▃▂▂▂
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 3.524185e-01 3.164045e-01 0.00000e+00 4.509300e-02 2.800825e-01 6.185905e-01 9.999573e-01 ▇▃▂▂▂
numeric AF 0 1.0000000 NA NA NA NA NA 3.128062e-01 2.827421e-01 1.49000e-05 7.263250e-02 2.226000e-01 5.004000e-01 9.999850e-01 ▇▃▂▂▂
numeric AF_reference 840 0.9932516 NA NA NA NA NA 2.869068e-01 2.575957e-01 1.99700e-04 7.428120e-02 2.066690e-01 4.466850e-01 1.000000e+00 ▇▃▂▂▁
numeric N 0 1.0000000 NA NA NA NA NA 4.774500e+04 0.000000e+00 4.77450e+04 4.774500e+04 4.774500e+04 4.774500e+04 4.774500e+04 ▁▁▇▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 1118275 rs61733845 C T 0.0192020 0.0320018 0.5484866 0.5484871 0.04416 0.185703 47745
1 1120431 rs1320571 G A 0.0098475 0.0314857 0.7544614 0.7544620 0.04653 0.185304 47745
1 1135242 rs9729550 A C 0.0433147 0.0147194 0.0032537 0.0032537 0.25870 0.551917 47745
1 1140435 rs1815606 G T 0.0405531 0.0142165 0.0043371 0.0043372 0.31790 0.712061 47745
1 1163804 rs7515488 C T 0.0906364 0.0173110 0.0000002 0.0000002 0.14860 0.186901 47745
1 1165310 rs11260562 G A 0.0903556 0.0264339 0.0006304 0.0006304 0.05560 0.101837 47745
1 1173611 rs6697886 G A 0.0994688 0.0178792 0.0000000 0.0000000 0.13730 0.220647 47745
1 1186502 rs6603785 A T 0.1069210 0.0189560 0.0000000 0.0000000 0.11950 0.246206 47745
1 1194804 rs11804831 T C 0.0910417 0.0160841 0.0000000 0.0000000 0.18560 0.685903 47745
1 1218086 rs6603788 C T 0.0747598 0.0230269 0.0011678 0.0011678 0.07697 0.469449 47745
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 50966914 rs470119 T C -0.0557607 0.0127581 0.0000124 0.0000124 0.609800 0.5547120 47745
22 50971752 rs131794 A C -0.0685185 0.0151700 0.0000063 0.0000063 0.791900 0.8326680 47745
22 50988193 rs131779 A G -0.0208810 0.0136947 0.1273210 0.1273214 0.657900 0.5802720 47745
22 50999182 rs140518 C T -0.0408692 0.0137477 0.0029509 0.0029509 0.696600 0.7655750 47745
22 51078251 rs4040041 C T 0.0088169 0.0132207 0.5048345 0.5048343 0.373100 0.4666530 47745
22 51094926 rs9616810 C T 0.0411207 0.0151862 0.0067736 0.0067737 0.218600 0.2224440 47745
22 51105556 rs9616812 C T -0.0223395 0.0128789 0.0828171 0.0828150 0.483200 0.3628190 47745
22 51109992 rs9628185 T C -0.0289028 0.0130478 0.0267498 0.0267500 0.484300 0.4053510 47745
22 51134186 rs8135777 A G -0.4247410 0.3102890 0.1710437 0.1710443 0.000446 0.0273562 47745
22 51156666 rs9628187 C T -0.0061069 0.0163022 0.7079523 0.7079536 0.203200 0.1299920 47745

bcf preview

1   1118275 rs61733845  C   T   .   PASS    AF=0.04416  ES:SE:LP:AF:SS:ID   0.019202:0.0320018:0.260834:0.04416:47745:rs61733845
1   1120431 rs1320571   G   A   .   PASS    AF=0.04653  ES:SE:LP:AF:SS:ID   0.00984751:0.0314857:0.122363:0.04653:47745:rs1320571
1   1135242 rs9729550   A   C   .   PASS    AF=0.2587   ES:SE:LP:AF:SS:ID   0.0433147:0.0147194:2.48762:0.2587:47745:rs9729550
1   1140435 rs1815606   G   T   .   PASS    AF=0.3179   ES:SE:LP:AF:SS:ID   0.0405531:0.0142165:2.3628:0.3179:47745:rs1815606
1   1163804 rs7515488   C   T   .   PASS    AF=0.1486   ES:SE:LP:AF:SS:ID   0.0906364:0.017311:6.78439:0.1486:47745:rs7515488
1   1165310 rs11260562  G   A   .   PASS    AF=0.0556   ES:SE:LP:AF:SS:ID   0.0903556:0.0264339:3.20036:0.0556:47745:rs11260562
1   1173611 rs6697886   G   A   .   PASS    AF=0.1373   ES:SE:LP:AF:SS:ID   0.0994688:0.0178792:7.57742:0.1373:47745:rs6697886
1   1186502 rs6603785   A   T   .   PASS    AF=0.1195   ES:SE:LP:AF:SS:ID   0.106921:0.018956:7.77064:0.1195:47745:rs6603785
1   1194804 rs11804831  T   C   .   PASS    AF=0.1856   ES:SE:LP:AF:SS:ID   0.0910417:0.0160841:7.82086:0.1856:47745:rs11804831
1   1218086 rs6603788   C   T   .   PASS    AF=0.07697  ES:SE:LP:AF:SS:ID   0.0747598:0.0230269:2.93262:0.07697:47745:rs6603788
1   1227897 rs3737721   A   G   .   PASS    AF=0.002436 ES:SE:LP:AF:SS:ID   0.0517328:0.0945477:0.233388:0.002436:47745:rs3737721
1   1231656 rs1749951   G   A   .   PASS    AF=0.04028  ES:SE:LP:AF:SS:ID   0.062385:0.0329014:1.23699:0.04028:47745:rs1749951
1   1233941 rs1739855   T   C   .   PASS    AF=0.07333  ES:SE:LP:AF:SS:ID   0.0662944:0.0237983:2.27233:0.07333:47745:rs1739855
1   1241529 rs1536168   A   G   .   PASS    AF=0.95394  ES:SE:LP:AF:SS:ID   -0.0688144:0.0302075:1.64353:0.95394:47745:rs1536168
1   1242468 rs2274264   G   A   .   PASS    AF=0.002467 ES:SE:LP:AF:SS:ID   0.0503525:0.100315:0.210625:0.002467:47745:rs2274264
1   1247494 rs12103 T   C   .   PASS    AF=0.8166   ES:SE:LP:AF:SS:ID   -0.0995588:0.0162944:9.00158:0.8166:47745:rs12103
1   1249187 rs12142199  G   A   .   PASS    AF=0.8026   ES:SE:LP:AF:SS:ID   -0.0983383:0.0159317:9.17249:0.8026:47745:rs12142199
1   1254255 rs62623580  G   A   .   PASS    AF=0.007606 ES:SE:LP:AF:SS:ID   0.115117:0.0702762:0.993929:0.007606:47745:rs62623580
1   1335790 rs1240708   A   G   .   PASS    AF=0.1737   ES:SE:LP:AF:SS:ID   0.0958588:0.0164435:8.25517:0.1737:47745:rs1240708
1   1493727 rs880051    G   A   .   PASS    AF=0.232    ES:SE:LP:AF:SS:ID   0.0561188:0.0148341:3.80998:0.232:47745:rs880051
1   1497824 rs2296716   C   T   .   PASS    AF=0.1208   ES:SE:LP:AF:SS:ID   0.0331484:0.019684:1.03538:0.1208:47745:rs2296716
1   1611995 rs4074196   A   G   .   PASS    AF=0.4414   ES:SE:LP:AF:SS:ID   -0.0129163:0.0144783:0.429071:0.4414:47745:rs4074196
1   1706160 rs7531583   A   G   .   PASS    AF=0.77 ES:SE:LP:AF:SS:ID   -0.0411673:0.0147257:2.28566:0.77:47745:rs7531583
1   1721479 rs2272908   C   T   .   PASS    AF=0.4974   ES:SE:LP:AF:SS:ID   -0.0583209:0.0125715:5.45608:0.4974:47745:rs2272908
1   1723031 rs9660180   G   A   .   PASS    AF=0.4974   ES:SE:LP:AF:SS:ID   -0.0585612:0.012573:5.49515:0.4974:47745:rs9660180
1   1781220 rs6681938   T   C   .   PASS    AF=0.2996   ES:SE:LP:AF:SS:ID   -0.04139:0.0142526:2.4337:0.2996:47745:rs6681938
1   1838516 rs2377037   C   A   .   PASS    AF=0.2747   ES:SE:LP:AF:SS:ID   0.0408188:0.0142903:2.36807:0.2747:47745:rs2377037
1   1840038 rs2474461   T   C   .   PASS    AF=0.95331  ES:SE:LP:AF:SS:ID   -0.121137:0.0293899:4.42476:0.95331:47745:rs2474461
1   1853288 rs1884454   G   T   .   PASS    AF=0.2694   ES:SE:LP:AF:SS:ID   0.0391229:0.0143493:2.1937:0.2694:47745:rs1884454
1   1855319 rs2295362   C   T   .   PASS    AF=0.0452   ES:SE:LP:AF:SS:ID   0.0744716:0.0304297:1.84189:0.0452:47745:rs2295362
1   1871337 rs16824543  G   A   .   PASS    AF=0.04241  ES:SE:LP:AF:SS:ID   0.0706185:0.0313929:1.61118:0.04241:47745:rs16824543
1   1873625 rs12758705  G   A   .   PASS    AF=0.2651   ES:SE:LP:AF:SS:ID   0.037465:0.0145693:1.99458:0.2651:47745:rs12758705
1   1881070 rs4648596   G   A   .   PASS    AF=0.04073  ES:SE:LP:AF:SS:ID   0.0764288:0.0329815:1.68854:0.04073:47745:rs4648596
1   1888193 rs3820011   C   A   .   PASS    AF=0.2698   ES:SE:LP:AF:SS:ID   0.0342737:0.0145362:1.73559:0.2698:47745:rs3820011
1   2024064 rs2459994   C   T   .   PASS    AF=0.1824   ES:SE:LP:AF:SS:ID   0.0207617:0.0169543:0.656127:0.1824:47745:rs2459994
1   2146966 rs7512482   T   C   .   PASS    AF=0.1674   ES:SE:LP:AF:SS:ID   -0.021892:0.0178823:0.655871:0.1674:47745:rs7512482
1   2202774 rs6673129   C   T   .   PASS    AF=0.1651   ES:SE:LP:AF:SS:ID   0.0231766:0.0179545:0.70607:0.1651:47745:rs6673129
1   2229478 rs12562937  C   T   .   PASS    AF=0.1998   ES:SE:LP:AF:SS:ID   0.0451627:0.0164414:2.22066:0.1998:47745:rs12562937
1   2283896 rs2840528   A   G   .   PASS    AF=0.4158   ES:SE:LP:AF:SS:ID   0.0162644:0.0131999:0.661766:0.4158:47745:rs2840528
1   2290143 rs34587196  G   A   .   PASS    AF=0.01202  ES:SE:LP:AF:SS:ID   0.0886126:0.0597007:0.860957:0.01202:47745:rs34587196
1   2404256 rs2494626   C   T   .   PASS    AF=0.2884   ES:SE:LP:AF:SS:ID   -0.00187853:0.0153883:0.0443895:0.2884:47745:rs2494626
1   2407781 rs78504402  C   T   .   PASS    AF=0.06862  ES:SE:LP:AF:SS:ID   -0.0437856:0.0270384:0.977309:0.06862:47745:rs78504402
1   2408471 rs115996655 G   A   .   PASS    AF=0.007814 ES:SE:LP:AF:SS:ID   -0.002633:0.0681198:0.0136012:0.007814:47745:rs115996655
1   2408834 rs11588930  G   A   .   PASS    AF=0.101    ES:SE:LP:AF:SS:ID   0.0279766:0.0232268:0.641306:0.101:47745:rs11588930
1   2409892 rs12727342  A   G   .   PASS    AF=0.6229   ES:SE:LP:AF:SS:ID   0.0354679:0.0138191:1.98841:0.6229:47745:rs12727342
1   2410789 rs11799501  C   T   .   PASS    AF=0.5834   ES:SE:LP:AF:SS:ID   0.0444544:0.0137203:2.92261:0.5834:47745:rs11799501
1   2412279 rs4648638   A   T   .   PASS    AF=0.388    ES:SE:LP:AF:SS:ID   -0.038505:0.0137544:2.29085:0.388:47745:rs4648638
1   2412293 rs12731186  C   T   .   PASS    AF=0.1211   ES:SE:LP:AF:SS:ID   0.0329436:0.0196216:1.03075:0.1211:47745:rs12731186
1   2413166 rs115810747 A   G   .   PASS    AF=0.04094  ES:SE:LP:AF:SS:ID   0.0181816:0.0355888:0.215073:0.04094:47745:rs115810747
1   2413464 rs114424485 G   C   .   PASS    AF=0.008958 ES:SE:LP:AF:SS:ID   0.0488255:0.066777:0.332852:0.008958:47745:rs114424485