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-971/ieu-a-971.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-971/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 20:58:29 2020
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-971/ieu-a-971.vcf.gz ...
Read summary statistics for 122374 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, 50453 SNPs remain.
After merging with regression SNP LD, 50453 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: 2.832 (0.8395)
Lambda GC: 1.1301
Mean Chi^2: 1.1754
Intercept: 1.0393 (0.0222)
Ratio: 0.2243 (0.1269)
Analysis finished at Tue Feb  4 20:58:38 2020
Total time elapsed: 9.1s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.7935,
    "inflation_factor": 1.2088,
    "mean_EFFECT": 0.0026,
    "n": 2229,
    "n_snps": 122374,
    "n_clumped_hits": 3,
    "n_p_sig": 68,
    "n_mono": 0,
    "n_ns": 0,
    "n_mac": 1594,
    "is_snpid_unique": true,
    "n_miss_EFFECT": 0,
    "n_miss_SE": 0,
    "n_miss_PVAL": 0,
    "n_miss_AF": 675,
    "n_miss_AF_reference": 820,
    "n_est": 2215.3985,
    "ratio_se_n": 0.9969,
    "mean_diff": 0.0106,
    "ratio_diff": 2.0083,
    "sd_y_est1": 2.011,
    "sd_y_est2": 2.0048,
    "r2_sum1": 0.1993,
    "r2_sum2": 0.0493,
    "r2_sum3": 0.0496,
    "r2_sum4": 0.0591,
    "ldsc_nsnp_merge_refpanel_ld": 50453,
    "ldsc_nsnp_merge_regression_ld": 50453,
    "ldsc_observed_scale_h2_beta": 2.832,
    "ldsc_observed_scale_h2_se": 0.8395,
    "ldsc_intercept_beta": 1.0393,
    "ldsc_intercept_se": 0.0222,
    "ldsc_lambda_gc": 1.1301,
    "ldsc_mean_chisq": 1.1754,
    "ldsc_ratio": 0.2241
}

Flags

name value
af_correlation FALSE
inflation_factor TRUE
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 122374 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 8.091294e+00 5.771330e+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 7.906529e+07 5.779353e+07 6.34110e+04 3.294106e+07 6.222787e+07 1.176462e+08 2.492107e+08 ▇▅▃▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA 2.560800e-03 3.539183e-01 -7.23861e+00 -7.005200e-02 -7.857000e-04 6.873260e-02 8.730950e+00 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 1.545531e-01 2.878999e-01 5.64362e-02 6.478450e-02 8.067440e-02 1.264990e-01 6.722150e+00 ▇▁▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.675236e-01 2.973471e-01 0.00000e+00 2.031888e-01 4.583408e-01 7.232085e-01 9.999860e-01 ▇▆▆▆▆
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.674862e-01 2.973789e-01 0.00000e+00 2.031099e-01 4.583109e-01 7.232055e-01 9.999865e-01 ▇▆▆▆▆
numeric AF 675 0.9944841 NA NA NA NA NA 3.186157e-01 2.864837e-01 5.05000e-04 7.509000e-02 2.275000e-01 5.121000e-01 9.994950e-01 ▇▃▂▂▂
numeric AF_reference 820 0.9932992 NA NA NA NA NA 2.897543e-01 2.568443e-01 1.99700e-04 7.807510e-02 2.106630e-01 4.500800e-01 1.000000e+00 ▇▃▂▂▁
numeric N 0 1.0000000 NA NA NA NA NA 2.229000e+03 0.000000e+00 2.22900e+03 2.229000e+03 2.229000e+03 2.229000e+03 2.229000e+03 ▁▁▇▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 1118275 rs61733845 C T -0.0419953 0.0736530 0.5685531 0.5685572 0.2242 0.185703 2229
1 1120431 rs1320571 G A 0.0218949 0.0740415 0.7674516 0.7674507 0.2091 0.185304 2229
1 1135242 rs9729550 A C 0.0926863 0.0602591 0.1241069 0.1240170 0.4141 0.551917 2229
1 1140435 rs1815606 G T 0.0913379 0.0606849 0.1323771 0.1322939 0.6354 0.712061 2229
1 1163804 rs7515488 C T 0.0656200 0.0803853 0.4143688 0.4143180 0.1591 0.186901 2229
1 1165310 rs11260562 G A 0.0370921 0.1142550 0.7454543 0.7454512 0.0697 0.101837 2229
1 1173611 rs6697886 G A 0.0607528 0.0825384 0.4617246 0.4616972 0.1510 0.220647 2229
1 1186502 rs6603785 A T -0.0330266 0.0827583 0.6898458 0.6898394 0.1542 0.246206 2229
1 1194804 rs11804831 T C -0.0026494 0.0607462 0.9652111 0.9652114 0.6162 0.685903 2229
1 1218086 rs6603788 C T 0.0296845 0.0621494 0.6329115 0.6329126 0.3520 0.469449 2229
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 50960682 rs140524 C T 0.0437473 0.0732101 0.5501473 0.5501347 0.20860 0.230232 2229
22 50966914 rs470119 T C 0.0752954 0.0634122 0.2351332 0.2350714 0.65000 0.554712 2229
22 50971752 rs131794 A C 0.2070520 0.0940744 0.0277984 0.0277404 0.86920 0.832668 2229
22 50988193 rs131779 A G 0.1211360 0.0617528 0.0499747 0.0498059 0.56460 0.580272 2229
22 50999182 rs140518 C T 0.1717830 0.0698189 0.0139380 0.0138779 0.74700 0.765575 2229
22 51078251 rs4040041 C T -0.0670422 0.0617787 0.2778549 0.2778334 0.52020 0.466653 2229
22 51094926 rs9616810 C T -0.0496912 0.0690310 0.4716914 0.4716242 0.27270 0.222444 2229
22 51105556 rs9616812 C T 0.0510562 0.0630707 0.4182423 0.4182233 0.35300 0.362819 2229
22 51109992 rs9628185 T C 0.0602187 0.0628933 0.3383530 0.3383281 0.36250 0.405351 2229
22 51156666 rs9628187 C T -0.0611959 0.1106130 0.5801069 0.5800968 0.07879 0.129992 2229

bcf preview

1   1118275 rs61733845  C   T   .   PASS    AF=0.2242   ES:SE:LP:AF:SS:ID   -0.0419953:0.073653:0.245229:0.2242:2229:rs61733845
1   1120431 rs1320571   G   A   .   PASS    AF=0.2091   ES:SE:LP:AF:SS:ID   0.0218949:0.0740415:0.114949:0.2091:2229:rs1320571
1   1135242 rs9729550   A   C   .   PASS    AF=0.4141   ES:SE:LP:AF:SS:ID   0.0926863:0.0602591:0.906204:0.4141:2229:rs9729550
1   1140435 rs1815606   G   T   .   PASS    AF=0.6354   ES:SE:LP:AF:SS:ID   0.0913379:0.0606849:0.878187:0.6354:2229:rs1815606
1   1163804 rs7515488   C   T   .   PASS    AF=0.1591   ES:SE:LP:AF:SS:ID   0.06562:0.0803853:0.382613:0.1591:2229:rs7515488
1   1165310 rs11260562  G   A   .   PASS    AF=0.0697   ES:SE:LP:AF:SS:ID   0.0370921:0.114255:0.127579:0.0697:2229:rs11260562
1   1173611 rs6697886   G   A   .   PASS    AF=0.151    ES:SE:LP:AF:SS:ID   0.0607528:0.0825384:0.335617:0.151:2229:rs6697886
1   1186502 rs6603785   A   T   .   PASS    AF=0.1542   ES:SE:LP:AF:SS:ID   -0.0330266:0.0827583:0.161248:0.1542:2229:rs6603785
1   1194804 rs11804831  T   C   .   PASS    AF=0.6162   ES:SE:LP:AF:SS:ID   -0.00264944:0.0607462:0.0153777:0.6162:2229:rs11804831
1   1218086 rs6603788   C   T   .   PASS    AF=0.352    ES:SE:LP:AF:SS:ID   0.0296845:0.0621494:0.198657:0.352:2229:rs6603788
1   1227897 rs3737721   A   G   .   PASS    AF=0.1899   ES:SE:LP:AF:SS:ID   0.00144501:0.077381:0.00651924:0.1899:2229:rs3737721
1   1231656 rs1749951   G   A   .   PASS    AF=0.09394  ES:SE:LP:AF:SS:ID   -0.0565859:0.103413:0.233399:0.09394:2229:rs1749951
1   1233941 rs1739855   T   C   .   PASS    AF=0.3414   ES:SE:LP:AF:SS:ID   0.0424548:0.0629051:0.301245:0.3414:2229:rs1739855
1   1241529 rs1536168   A   G   .   PASS    AF=0.8862   ES:SE:LP:AF:SS:ID   -0.0624953:0.09292:0.299952:0.8862:2229:rs1536168
1   1242468 rs2274264   G   A   .   PASS    AF=0.1874   ES:SE:LP:AF:SS:ID   0.0334437:0.0776342:0.176126:0.1874:2229:rs2274264
1   1247494 rs12103 T   C   .   PASS    AF=0.4056   ES:SE:LP:AF:SS:ID   -0.0349846:0.0600815:0.251516:0.4056:2229:rs12103
1   1249187 rs12142199  G   A   .   PASS    AF=0.4045   ES:SE:LP:AF:SS:ID   -0.0352088:0.0601181:0.253278:0.4045:2229:rs12142199
1   1254255 rs62623580  G   A   .   PASS    AF=0.03283  ES:SE:LP:AF:SS:ID   0.275297:0.155454:1.11533:0.03283:2229:rs62623580
1   1335790 rs1240708   A   G   .   PASS    AF=0.5919   ES:SE:LP:AF:SS:ID   0.0364795:0.0604605:0.262584:0.5919:2229:rs1240708
1   1493727 rs880051    G   A   .   PASS    AF=0.5875   ES:SE:LP:AF:SS:ID   0.0628922:0.0613305:0.515457:0.5875:2229:rs880051
1   1497824 rs2296716   C   T   .   PASS    AF=0.2692   ES:SE:LP:AF:SS:ID   0.0715157:0.0692039:0.520943:0.2692:2229:rs2296716
1   1611995 rs4074196   A   G   .   PASS    AF=0.4364   ES:SE:LP:AF:SS:ID   -0.0680563:0.0616624:0.569014:0.4364:2229:rs4074196
1   1706160 rs7531583   A   G   .   PASS    AF=0.5141   ES:SE:LP:AF:SS:ID   0.0458822:0.06057:0.347962:0.5141:2229:rs7531583
1   1721479 rs2272908   C   T   .   PASS    AF=0.3551   ES:SE:LP:AF:SS:ID   0.00277499:0.0623921:0.0156865:0.3551:2229:rs2272908
1   1723031 rs9660180   G   A   .   PASS    AF=0.3551   ES:SE:LP:AF:SS:ID   0.00134994:0.0623806:0.00756358:0.3551:2229:rs9660180
1   1781220 rs6681938   T   C   .   PASS    AF=0.1914   ES:SE:LP:AF:SS:ID   -1.49e-05:0.0774582:6.64521e-05:0.1914:2229:rs6681938
1   1838516 rs2377037   C   A   .   PASS    AF=0.1556   ES:SE:LP:AF:SS:ID   0.077816:0.0826976:0.459952:0.1556:2229:rs2377037
1   1840038 rs2474461   T   C   .   PASS    AF=0.7796   ES:SE:LP:AF:SS:ID   0.0715658:0.0742109:0.474976:0.7796:2229:rs2474461
1   1853288 rs1884454   G   T   .   PASS    AF=0.1545   ES:SE:LP:AF:SS:ID   0.0768451:0.0832441:0.448562:0.1545:2229:rs1884454
1   1855319 rs2295362   C   T   .   PASS    AF=0.2702   ES:SE:LP:AF:SS:ID   -0.0406856:0.0680528:0.25966:0.2702:2229:rs2295362
1   1871337 rs16824543  G   A   .   PASS    AF=0.2712   ES:SE:LP:AF:SS:ID   -0.0382669:0.0680714:0.24106:0.2712:2229:rs16824543
1   1873625 rs12758705  G   A   .   PASS    AF=0.1556   ES:SE:LP:AF:SS:ID   0.0721614:0.0828134:0.41613:0.1556:2229:rs12758705
1   1881070 rs4648596   G   A   .   PASS    AF=0.1934   ES:SE:LP:AF:SS:ID   0.0250321:0.0763667:0.128967:0.1934:2229:rs4648596
1   1888193 rs3820011   C   A   .   PASS    AF=0.1881   ES:SE:LP:AF:SS:ID   0.0793391:0.0774294:0.514884:0.1881:2229:rs3820011
1   2024064 rs2459994   C   T   .   PASS    AF=0.4083   ES:SE:LP:AF:SS:ID   -0.00390016:0.0616634:0.0224735:0.4083:2229:rs2459994
1   2146966 rs7512482   T   C   .   PASS    AF=0.2227   ES:SE:LP:AF:SS:ID   0.0312187:0.0715213:0.178824:0.2227:2229:rs7512482
1   2202774 rs6673129   C   T   .   PASS    AF=0.1581   ES:SE:LP:AF:SS:ID   0.00686268:0.0837746:0.0293226:0.1581:2229:rs6673129
1   2229478 rs12562937  C   T   .   PASS    AF=0.2056   ES:SE:LP:AF:SS:ID   0.0148019:0.0753046:0.0735706:0.2056:2229:rs12562937
1   2283896 rs2840528   A   G   .   PASS    AF=0.4707   ES:SE:LP:AF:SS:ID   -0.12669:0.0601231:1.45356:0.4707:2229:rs2840528
1   2290143 rs34587196  G   A   .   PASS    AF=0.00202  ES:SE:LP:AF:SS:ID   -0.267402:0.696297:0.154309:0.00202:2229:rs34587196
1   2404256 rs2494626   C   T   .   PASS    AF=0.2465   ES:SE:LP:AF:SS:ID   0.0646527:0.0691184:0.456442:0.2465:2229:rs2494626
1   2407781 rs78504402  C   T   .   PASS    AF=0.04444  ES:SE:LP:AF:SS:ID   -0.126725:0.14743:0.40885:0.04444:2229:rs78504402
1   2408471 rs115996655 G   A   .   PASS    AF=0.00202  ES:SE:LP:AF:SS:ID   0.389991:0.620506:0.275972:0.00202:2229:rs115996655
1   2408834 rs11588930  G   A   .   PASS    AF=0.02172  ES:SE:LP:AF:SS:ID   0.0320197:0.200971:0.0587808:0.02172:2229:rs11588930
1   2409892 rs12727342  A   G   .   PASS    AF=0.652    ES:SE:LP:AF:SS:ID   -0.011622:0.0622499:0.0696134:0.652:2229:rs12727342
1   2410789 rs11799501  C   T   .   PASS    AF=0.6081   ES:SE:LP:AF:SS:ID   -0.0183958:0.060919:0.11766:0.6081:2229:rs11799501
1   2412279 rs4648638   A   T   .   PASS    AF=0.3696   ES:SE:LP:AF:SS:ID   0.0253515:0.0611903:0.168352:0.3696:2229:rs4648638
1   2412293 rs12731186  C   T   .   PASS    AF=0.09495  ES:SE:LP:AF:SS:ID   0.0347778:0.101557:0.135479:0.09495:2229:rs12731186
1   2413166 rs115810747 A   G   .   PASS    AF=0.008081 ES:SE:LP:AF:SS:ID   0.461806:0.286252:0.971551:0.008081:2229:rs115810747
1   2413464 rs114424485 G   C   .   PASS    AF=0.001515 ES:SE:LP:AF:SS:ID   0.639802:0.671526:0.467546:0.001515:2229:rs114424485