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-295/ieu-a-295.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-295/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 11:42:51 2020
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-295/ieu-a-295.vcf.gz ...
Read summary statistics for 122899 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, 50455 SNPs remain.
After merging with regression SNP LD, 50455 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: 2.8368 (0.8192)
Lambda GC: 1.1228
Mean Chi^2: 1.1771
Intercept: 1.0303 (0.023)
Ratio: 0.171 (0.1301)
Analysis finished at Wed Feb  5 11:42:59 2020
Total time elapsed: 8.71s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.7936,
    "inflation_factor": 1.2003,
    "mean_EFFECT": 0.006,
    "n": 2413,
    "n_snps": 122899,
    "n_clumped_hits": 2,
    "n_p_sig": 58,
    "n_mono": 0,
    "n_ns": 0,
    "n_mac": 1677,
    "is_snpid_unique": true,
    "n_miss_EFFECT": 0,
    "n_miss_SE": 0,
    "n_miss_PVAL": 0,
    "n_miss_AF": 887,
    "n_miss_AF_reference": 828,
    "n_est": 2396.7167,
    "ratio_se_n": 0.9966,
    "mean_diff": 0.0099,
    "ratio_diff": 1.9775,
    "sd_y_est1": 2.0379,
    "sd_y_est2": 2.031,
    "r2_sum1": 0.1259,
    "r2_sum2": 0.0303,
    "r2_sum3": 0.0305,
    "r2_sum4": 0.0378,
    "ldsc_nsnp_merge_refpanel_ld": 50455,
    "ldsc_nsnp_merge_regression_ld": 50455,
    "ldsc_observed_scale_h2_beta": 2.8368,
    "ldsc_observed_scale_h2_se": 0.8192,
    "ldsc_intercept_beta": 1.0303,
    "ldsc_intercept_se": 0.023,
    "ldsc_lambda_gc": 1.1228,
    "ldsc_mean_chisq": 1.1771,
    "ldsc_ratio": 0.1711
}

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 122899 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 8.091384e+00 5.772579e+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 7.906774e+07 5.782005e+07 6.34110e+04 3.293228e+07 6.222801e+07 1.176584e+08 2.492107e+08 ▇▅▃▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA 6.029200e-03 3.616333e-01 -6.50653e+00 -6.650200e-02 8.980000e-04 6.706110e-02 6.457640e+00 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 1.562915e-01 3.033112e-01 5.47536e-02 6.310080e-02 7.866690e-02 1.246510e-01 5.687980e+00 ▇▁▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.693456e-01 2.975035e-01 0.00000e+00 2.042434e-01 4.599366e-01 7.265374e-01 9.999940e-01 ▇▆▆▆▆
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.693158e-01 2.975289e-01 0.00000e+00 2.041919e-01 4.598979e-01 7.265338e-01 9.999941e-01 ▇▆▆▆▆
numeric AF 887 0.9927827 NA NA NA NA NA 3.179364e-01 2.866637e-01 5.05000e-04 7.424000e-02 2.268000e-01 5.111000e-01 9.994950e-01 ▇▃▂▂▂
numeric AF_reference 828 0.9932628 NA NA NA NA NA 2.888410e-01 2.571060e-01 1.99700e-04 7.667730e-02 2.092650e-01 4.490810e-01 1.000000e+00 ▇▃▂▂▁
numeric N 0 1.0000000 NA NA NA NA NA 2.413000e+03 0.000000e+00 2.41300e+03 2.413000e+03 2.413000e+03 2.413000e+03 2.413000e+03 ▁▁▇▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 1118275 rs61733845 C T -0.0285351 0.0717970 0.6910365 0.6910420 0.2242 0.185703 2413
1 1120431 rs1320571 G A 0.0039894 0.0721774 0.9559210 0.9559211 0.2091 0.185304 2413
1 1135242 rs9729550 A C 0.0787149 0.0586431 0.1795709 0.1795083 0.4141 0.551917 2413
1 1140435 rs1815606 G T 0.0741141 0.0590633 0.2095970 0.2095423 0.6354 0.712061 2413
1 1163804 rs7515488 C T 0.0692284 0.0784007 0.3772802 0.3772323 0.1591 0.186901 2413
1 1165310 rs11260562 G A 0.0132132 0.1118860 0.9059921 0.9059922 0.0697 0.101837 2413
1 1173611 rs6697886 G A 0.0554656 0.0806344 0.4915571 0.4915377 0.1510 0.220647 2413
1 1186502 rs6603785 A T -0.0380621 0.0807227 0.6372796 0.6372718 0.1542 0.246206 2413
1 1194804 rs11804831 T C -0.0193109 0.0592119 0.7443308 0.7443244 0.6162 0.685903 2413
1 1218086 rs6603788 C T 0.0182077 0.0605141 0.7635017 0.7635033 0.3520 0.469449 2413
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 50960682 rs140524 C T 0.0261469 0.0715150 0.7146559 0.7146530 0.20860 0.230232 2413
22 50966914 rs470119 T C 0.0844683 0.0616205 0.1704932 0.1704428 0.65000 0.554712 2413
22 50971752 rs131794 A C 0.2191170 0.0915137 0.0166782 0.0166493 0.86920 0.832668 2413
22 50988193 rs131779 A G 0.0935036 0.0602664 0.1209740 0.1207808 0.56460 0.580272 2413
22 50999182 rs140518 C T 0.1762010 0.0680450 0.0096525 0.0096122 0.74700 0.765575 2413
22 51078251 rs4040041 C T -0.0655347 0.0601905 0.2762587 0.2762473 0.52020 0.466653 2413
22 51094926 rs9616810 C T -0.0462905 0.0671852 0.4908898 0.4908242 0.27270 0.222444 2413
22 51105556 rs9616812 C T 0.0374914 0.0613558 0.5411766 0.5411671 0.35300 0.362819 2413
22 51109992 rs9628185 T C 0.0439674 0.0612153 0.4726177 0.4726081 0.36250 0.405351 2413
22 51156666 rs9628187 C T -0.0479923 0.1078040 0.6561936 0.6561889 0.07879 0.129992 2413

bcf preview

1   1118275 rs61733845  C   T   .   PASS    AF=0.2242   ES:SE:LP:AF:SS:ID   -0.0285351:0.071797:0.160499:0.2242:2413:rs61733845
1   1120431 rs1320571   G   A   .   PASS    AF=0.2091   ES:SE:LP:AF:SS:ID   0.00398945:0.0721774:0.019578:0.2091:2413:rs1320571
1   1135242 rs9729550   A   C   .   PASS    AF=0.4141   ES:SE:LP:AF:SS:ID   0.0787149:0.0586431:0.745764:0.4141:2413:rs9729550
1   1140435 rs1815606   G   T   .   PASS    AF=0.6354   ES:SE:LP:AF:SS:ID   0.0741141:0.0590633:0.678615:0.6354:2413:rs1815606
1   1163804 rs7515488   C   T   .   PASS    AF=0.1591   ES:SE:LP:AF:SS:ID   0.0692284:0.0784007:0.423336:0.1591:2413:rs7515488
1   1165310 rs11260562  G   A   .   PASS    AF=0.0697   ES:SE:LP:AF:SS:ID   0.0132132:0.111886:0.0428756:0.0697:2413:rs11260562
1   1173611 rs6697886   G   A   .   PASS    AF=0.151    ES:SE:LP:AF:SS:ID   0.0554656:0.0806344:0.308426:0.151:2413:rs6697886
1   1186502 rs6603785   A   T   .   PASS    AF=0.1542   ES:SE:LP:AF:SS:ID   -0.0380621:0.0807227:0.19567:0.1542:2413:rs6603785
1   1194804 rs11804831  T   C   .   PASS    AF=0.6162   ES:SE:LP:AF:SS:ID   -0.0193109:0.0592119:0.128234:0.6162:2413:rs11804831
1   1218086 rs6603788   C   T   .   PASS    AF=0.352    ES:SE:LP:AF:SS:ID   0.0182077:0.0605141:0.11719:0.352:2413:rs6603788
1   1227897 rs3737721   A   G   .   PASS    AF=0.1899   ES:SE:LP:AF:SS:ID   0.0064789:0.0752108:0.0308861:0.1899:2413:rs3737721
1   1231656 rs1749951   G   A   .   PASS    AF=0.09394  ES:SE:LP:AF:SS:ID   -0.0644233:0.100853:0.281537:0.09394:2413:rs1749951
1   1233941 rs1739855   T   C   .   PASS    AF=0.3414   ES:SE:LP:AF:SS:ID   0.0292866:0.0613236:0.198622:0.3414:2413:rs1739855
1   1241529 rs1536168   A   G   .   PASS    AF=0.8862   ES:SE:LP:AF:SS:ID   -0.0429607:0.0910603:0.195797:0.8862:2413:rs1536168
1   1242468 rs2274264   G   A   .   PASS    AF=0.1874   ES:SE:LP:AF:SS:ID   0.0355599:0.0753938:0.195747:0.1874:2413:rs2274264
1   1247494 rs12103 T   C   .   PASS    AF=0.4056   ES:SE:LP:AF:SS:ID   -0.0287871:0.0586248:0.205232:0.4056:2413:rs12103
1   1249187 rs12142199  G   A   .   PASS    AF=0.4045   ES:SE:LP:AF:SS:ID   -0.0301715:0.0586755:0.216733:0.4045:2413:rs12142199
1   1254255 rs62623580  G   A   .   PASS    AF=0.03283  ES:SE:LP:AF:SS:ID   0.219734:0.154127:0.812358:0.03283:2413:rs62623580
1   1335790 rs1240708   A   G   .   PASS    AF=0.5919   ES:SE:LP:AF:SS:ID   0.0350836:0.0589565:0.258216:0.5919:2413:rs1240708
1   1493727 rs880051    G   A   .   PASS    AF=0.5875   ES:SE:LP:AF:SS:ID   0.0799851:0.0598421:0.741427:0.5875:2413:rs880051
1   1497824 rs2296716   C   T   .   PASS    AF=0.2692   ES:SE:LP:AF:SS:ID   0.0830108:0.06739:0.661709:0.2692:2413:rs2296716
1   1611995 rs4074196   A   G   .   PASS    AF=0.4364   ES:SE:LP:AF:SS:ID   -0.0873922:0.0600466:0.837027:0.4364:2413:rs4074196
1   1706160 rs7531583   A   G   .   PASS    AF=0.5141   ES:SE:LP:AF:SS:ID   0.0314234:0.0588448:0.226685:0.5141:2413:rs7531583
1   1721479 rs2272908   C   T   .   PASS    AF=0.3551   ES:SE:LP:AF:SS:ID   -0.00809508:0.0609256:0.0485182:0.3551:2413:rs2272908
1   1723031 rs9660180   G   A   .   PASS    AF=0.3551   ES:SE:LP:AF:SS:ID   -0.00943962:0.0609144:0.0570757:0.3551:2413:rs9660180
1   1781220 rs6681938   T   C   .   PASS    AF=0.1914   ES:SE:LP:AF:SS:ID   -0.0115757:0.0755262:0.056414:0.1914:2413:rs6681938
1   1838516 rs2377037   C   A   .   PASS    AF=0.1556   ES:SE:LP:AF:SS:ID   0.0692048:0.0808384:0.406733:0.1556:2413:rs2377037
1   1840038 rs2474461   T   C   .   PASS    AF=0.7796   ES:SE:LP:AF:SS:ID   0.0770797:0.0721794:0.544132:0.7796:2413:rs2474461
1   1853288 rs1884454   G   T   .   PASS    AF=0.1545   ES:SE:LP:AF:SS:ID   0.0822541:0.0810356:0.508453:0.1545:2413:rs1884454
1   1855319 rs2295362   C   T   .   PASS    AF=0.2702   ES:SE:LP:AF:SS:ID   -0.0593224:0.0666581:0.427642:0.2702:2413:rs2295362
1   1871337 rs16824543  G   A   .   PASS    AF=0.2712   ES:SE:LP:AF:SS:ID   -0.0583395:0.0666592:0.418471:0.2712:2413:rs16824543
1   1873625 rs12758705  G   A   .   PASS    AF=0.1556   ES:SE:LP:AF:SS:ID   0.0773216:0.0806386:0.471522:0.1556:2413:rs12758705
1   1881070 rs4648596   G   A   .   PASS    AF=0.1934   ES:SE:LP:AF:SS:ID   -0.0109287:0.0748695:0.0535748:0.1934:2413:rs4648596
1   1888193 rs3820011   C   A   .   PASS    AF=0.1881   ES:SE:LP:AF:SS:ID   0.059485:0.0753043:0.366951:0.1881:2413:rs3820011
1   2024064 rs2459994   C   T   .   PASS    AF=0.4083   ES:SE:LP:AF:SS:ID   0.00667603:0.0601695:0.0401714:0.4083:2413:rs2459994
1   2146966 rs7512482   T   C   .   PASS    AF=0.2227   ES:SE:LP:AF:SS:ID   0.0611269:0.0697753:0.419036:0.2227:2413:rs7512482
1   2202774 rs6673129   C   T   .   PASS    AF=0.1581   ES:SE:LP:AF:SS:ID   -0.0184093:0.0818593:0.0850928:0.1581:2413:rs6673129
1   2229478 rs12562937  C   T   .   PASS    AF=0.2056   ES:SE:LP:AF:SS:ID   -0.00334133:0.0729466:0.0161636:0.2056:2413:rs12562937
1   2283896 rs2840528   A   G   .   PASS    AF=0.4707   ES:SE:LP:AF:SS:ID   -0.110466:0.0586619:1.22343:0.4707:2413:rs2840528
1   2290143 rs34587196  G   A   .   PASS    AF=0.00202  ES:SE:LP:AF:SS:ID   -0.144117:0.666021:0.0816095:0.00202:2413:rs34587196
1   2404256 rs2494626   C   T   .   PASS    AF=0.2465   ES:SE:LP:AF:SS:ID   0.0588301:0.0675225:0.416112:0.2465:2413:rs2494626
1   2407781 rs78504402  C   T   .   PASS    AF=0.04444  ES:SE:LP:AF:SS:ID   -0.130302:0.144188:0.436285:0.04444:2413:rs78504402
1   2408471 rs115996655 G   A   .   PASS    AF=0.00202  ES:SE:LP:AF:SS:ID   0.399564:0.612007:0.289156:0.00202:2413:rs115996655
1   2408834 rs11588930  G   A   .   PASS    AF=0.02172  ES:SE:LP:AF:SS:ID   -0.0107564:0.197814:0.0192533:0.02172:2413:rs11588930
1   2409892 rs12727342  A   G   .   PASS    AF=0.652    ES:SE:LP:AF:SS:ID   0.00454374:0.0606078:0.0267617:0.652:2413:rs12727342
1   2410789 rs11799501  C   T   .   PASS    AF=0.6081   ES:SE:LP:AF:SS:ID   0.000584641:0.0594244:0.00342266:0.6081:2413:rs11799501
1   2412279 rs4648638   A   T   .   PASS    AF=0.3696   ES:SE:LP:AF:SS:ID   0.00988106:0.0596539:0.0612602:0.3696:2413:rs4648638
1   2412293 rs12731186  C   T   .   PASS    AF=0.09495  ES:SE:LP:AF:SS:ID   0.0488561:0.09894:0.206591:0.09495:2413:rs12731186
1   2413166 rs115810747 A   G   .   PASS    AF=0.008081 ES:SE:LP:AF:SS:ID   0.50717:0.283459:1.1328:0.008081:2413:rs115810747
1   2413464 rs114424485 G   C   .   PASS    AF=0.001515 ES:SE:LP:AF:SS:ID   0.662531:0.665875:0.49513:0.001515:2413:rs114424485