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-1025/ieu-a-1025.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-1025/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 11:40:57 2020
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-1025/ieu-a-1025.vcf.gz ...
Read summary statistics for 154065 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, 54116 SNPs remain.
After merging with regression SNP LD, 54116 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: 1.543 (0.1782)
Lambda GC: 1.4103
Mean Chi^2: 2.1641
Intercept: 1.0067 (0.0511)
Ratio: 0.0057 (0.0439)
Analysis finished at Wed Feb  5 11:41:06 2020
Total time elapsed: 9.17s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.7603,
    "inflation_factor": 1.4921,
    "mean_EFFECT": 0.0073,
    "n": 38589,
    "n_snps": 154065,
    "n_clumped_hits": 49,
    "n_p_sig": 3795,
    "n_mono": 0,
    "n_ns": 0,
    "n_mac": 0,
    "is_snpid_unique": true,
    "n_miss_EFFECT": 0,
    "n_miss_SE": 0,
    "n_miss_PVAL": 0,
    "n_miss_AF": 1579,
    "n_miss_AF_reference": 3050,
    "n_est": 37582.3615,
    "ratio_se_n": 0.9869,
    "mean_diff": -0.0027,
    "ratio_diff": 9.3243,
    "sd_y_est1": 2.3275,
    "sd_y_est2": 2.297,
    "r2_sum1": 0.4662,
    "r2_sum2": 0.086,
    "r2_sum3": 0.0884,
    "r2_sum4": 0.0871,
    "ldsc_nsnp_merge_refpanel_ld": 54116,
    "ldsc_nsnp_merge_regression_ld": 54116,
    "ldsc_observed_scale_h2_beta": 1.543,
    "ldsc_observed_scale_h2_se": 0.1782,
    "ldsc_intercept_beta": 1.0067,
    "ldsc_intercept_se": 0.0511,
    "ldsc_lambda_gc": 1.4103,
    "ldsc_mean_chisq": 2.1641,
    "ldsc_ratio": 0.0058
}

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 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 154065 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 8.015039e+00 5.772324e+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 7.967614e+07 5.809695e+07 6.26140e+04 3.304457e+07 6.224941e+07 1.186846e+08 2.492107e+08 ▇▅▃▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA 7.333400e-03 1.743802e-01 -2.97960e+00 -2.566770e-02 9.995000e-04 2.664190e-02 3.021400e+00 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 9.073750e-02 2.153153e-01 1.61703e-02 1.819420e-02 2.405630e-02 4.784590e-02 1.598820e+00 ▇▁▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.288599e-01 3.150262e-01 0.00000e+00 1.299999e-01 4.100001e-01 7.040006e-01 1.000000e+00 ▇▅▅▅▅
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.283768e-01 3.148295e-01 0.00000e+00 1.300279e-01 4.093842e-01 7.033391e-01 1.000000e+00 ▇▅▅▅▅
numeric AF 1579 0.9897511 NA NA NA NA NA 2.991951e-01 2.930464e-01 1.00000e-04 4.660000e-02 1.976000e-01 4.881000e-01 9.999000e-01 ▇▃▂▂▂
numeric AF_reference 3050 0.9802032 NA NA NA NA NA 2.719871e-01 2.644386e-01 0.00000e+00 5.091850e-02 1.831070e-01 4.295130e-01 1.000000e+00 ▇▃▂▁▁
numeric N 0 1.0000000 NA NA NA NA NA 3.858900e+04 0.000000e+00 3.85890e+04 3.858900e+04 3.858900e+04 3.858900e+04 3.858900e+04 ▁▁▇▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 1118275 rs61733845 C T -0.0119286 0.0405296 0.7620001 0.7685147 0.0414 0.185703 38589
1 1120431 rs1320571 G A 0.0256677 0.0385181 0.5090003 0.5051681 0.0438 0.185304 38589
1 1135242 rs9729550 A C 0.0009995 0.0186028 0.9680001 0.9571515 0.2744 0.551917 38589
1 1140435 rs1815606 G T 0.0029955 0.0175476 0.8739999 0.8644536 0.3286 0.712061 38589
1 1163804 rs7515488 C T 0.0198026 0.0227407 0.3810000 0.3838634 0.1597 0.186901 38589
1 1165310 rs11260562 G A 0.0109399 0.0353122 0.7630008 0.7567092 0.0606 0.101837 38589
1 1173611 rs6697886 G A 0.0256677 0.0236259 0.2819999 0.2772923 0.1483 0.220647 38589
1 1186502 rs6603785 A T 0.0148886 0.0251288 0.5510005 0.5535215 0.1314 0.246206 38589
1 1194804 rs11804831 T C 0.0029955 0.0210906 0.8770000 0.8870559 0.1908 0.685903 38589
1 1218086 rs6603788 C T 0.0049875 0.0304355 0.8620001 0.8698316 0.0767 0.469449 38589
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 50966914 rs470119 T C -0.0639133 0.0167576 0.0001510 0.0001367 0.6108 0.5547120 38589
22 50971752 rs131794 A C -0.0620354 0.0199006 0.0020200 0.0018254 0.7899 0.8326680 38589
22 50988193 rs131779 A G -0.0334348 0.0172766 0.0550998 0.0529578 0.6554 0.5802720 38589
22 50999182 rs140518 C T -0.0285875 0.0178396 0.1060000 0.1090508 0.6930 0.7655750 38589
22 51078251 rs4040041 C T -0.0049875 0.0175126 0.7929997 0.7757995 0.3793 0.4666530 38589
22 51094926 rs9616810 C T 0.0069756 0.0197499 0.7279994 0.7239406 0.2229 0.2224440 38589
22 51105556 rs9616812 C T -0.0019980 0.0162832 0.8860000 0.9023422 0.4758 0.3628190 38589
22 51109992 rs9628185 T C 0.0009995 0.0165626 0.9519999 0.9518794 0.4798 0.4053510 38589
22 51134186 rs8135777 A G 0.6318040 0.4491650 0.1590000 0.1595404 0.0005 0.0273562 38589
22 51156666 rs9628187 C T -0.0059821 0.0205409 0.7809999 0.7708775 0.2083 0.1299920 38589

bcf preview

1   1118275 rs61733845  C   T   .   PASS    AF=0.0414   ES:SE:LP:AF:SS:ID   -0.0119286:0.0405296:0.118045:0.0414:38589:rs61733845
1   1120431 rs1320571   G   A   .   PASS    AF=0.0438   ES:SE:LP:AF:SS:ID   0.0256677:0.0385181:0.293282:0.0438:38589:rs1320571
1   1135242 rs9729550   A   C   .   PASS    AF=0.2744   ES:SE:LP:AF:SS:ID   0.0009995:0.0186028:0.0141246:0.2744:38589:rs9729550
1   1140435 rs1815606   G   T   .   PASS    AF=0.3286   ES:SE:LP:AF:SS:ID   0.00299551:0.0175476:0.0584886:0.3286:38589:rs1815606
1   1163804 rs7515488   C   T   .   PASS    AF=0.1597   ES:SE:LP:AF:SS:ID   0.0198026:0.0227407:0.419075:0.1597:38589:rs7515488
1   1165310 rs11260562  G   A   .   PASS    AF=0.0606   ES:SE:LP:AF:SS:ID   0.0109399:0.0353122:0.117475:0.0606:38589:rs11260562
1   1173611 rs6697886   G   A   .   PASS    AF=0.1483   ES:SE:LP:AF:SS:ID   0.0256677:0.0236259:0.549751:0.1483:38589:rs6697886
1   1186502 rs6603785   A   T   .   PASS    AF=0.1314   ES:SE:LP:AF:SS:ID   0.0148886:0.0251288:0.258848:0.1314:38589:rs6603785
1   1194804 rs11804831  T   C   .   PASS    AF=0.1908   ES:SE:LP:AF:SS:ID   0.00299551:0.0210906:0.0570004:0.1908:38589:rs11804831
1   1218086 rs6603788   C   T   .   PASS    AF=0.0767   ES:SE:LP:AF:SS:ID   0.00498754:0.0304355:0.0644927:0.0767:38589:rs6603788
1   1227897 rs3737721   A   G   .   PASS    AF=0.0007   ES:SE:LP:AF:SS:ID   0.0843411:0.163398:0.218963:0.0007:38589:rs3737721
1   1231656 rs1749951   G   A   .   PASS    AF=0.0391   ES:SE:LP:AF:SS:ID   -0.0148886:0.0424267:0.137869:0.0391:38589:rs1749951
1   1233941 rs1739855   T   C   .   PASS    AF=0.0758   ES:SE:LP:AF:SS:ID   -0.0198026:0.0314909:0.278189:0.0758:38589:rs1739855
1   1241529 rs1536168   A   G   .   PASS    AF=0.9539   ES:SE:LP:AF:SS:ID   0.0188218:0.039788:0.193142:0.9539:38589:rs1536168
1   1242468 rs2274264   G   A   .   PASS    AF=0.0007   ES:SE:LP:AF:SS:ID   0.0573251:0.16421:0.137272:0.0007:38589:rs2274264
1   1247494 rs12103 T   C   .   PASS    AF=0.8187   ES:SE:LP:AF:SS:ID   0.00697561:0.0248212:0.113509:0.8187:38589:rs12103
1   1249187 rs12142199  G   A   .   PASS    AF=0.7881   ES:SE:LP:AF:SS:ID   -0.0009995:0.0206436:0.0163737:0.7881:38589:rs12142199
1   1254255 rs62623580  G   A   .   PASS    AF=0.0071   ES:SE:LP:AF:SS:ID   -0.0363319:0.094899:0.153663:0.0071:38589:rs62623580
1   1335790 rs1240708   A   G   .   PASS    AF=0.1857   ES:SE:LP:AF:SS:ID   -0.0198026:0.023765:0.38934:0.1857:38589:rs1240708
1   1493727 rs880051    G   A   .   PASS    AF=0.2422   ES:SE:LP:AF:SS:ID   -0.001998:0.0198485:0.0366845:0.2422:38589:rs880051
1   1497824 rs2296716   C   T   .   PASS    AF=0.123    ES:SE:LP:AF:SS:ID   0.0344014:0.0253957:0.747147:0.123:38589:rs2296716
1   1611995 rs4074196   A   G   .   PASS    AF=0.447    ES:SE:LP:AF:SS:ID   0.00299551:0.0165296:0.0710923:0.447:38589:rs4074196
1   1706160 rs7531583   A   G   .   PASS    AF=0.7739   ES:SE:LP:AF:SS:ID   -0.0295588:0.0193089:0.89279:0.7739:38589:rs7531583
1   1721479 rs2272908   C   T   .   PASS    AF=0.5026   ES:SE:LP:AF:SS:ID   -0.0411419:0.0164007:1.89963:0.5026:38589:rs2272908
1   1723031 rs9660180   G   A   .   PASS    AF=0.5021   ES:SE:LP:AF:SS:ID   -0.0421012:0.016385:1.96257:0.5021:38589:rs9660180
1   1781220 rs6681938   T   C   .   PASS    AF=0.3033   ES:SE:LP:AF:SS:ID   -0.0207825:0.0179794:0.621602:0.3033:38589:rs6681938
1   1838516 rs2377037   C   A   .   PASS    AF=0.272    ES:SE:LP:AF:SS:ID   0.0256677:0.0181493:0.782516:0.272:38589:rs2377037
1   1840038 rs2474461   T   C   .   PASS    AF=0.9595   ES:SE:LP:AF:SS:ID   -0.00498754:0.040303:0.0457575:0.9595:38589:rs2474461
1   1849530 rs4459050   T   C   .   PASS    AF=0.0458   ES:SE:LP:AF:SS:ID   -0.0685928:0.144514:0.197226:0.0458:38589:rs4459050
1   1853288 rs1884454   G   T   .   PASS    AF=0.2693   ES:SE:LP:AF:SS:ID   0.0188218:0.0187752:0.493495:0.2693:38589:rs1884454
1   1855319 rs2295362   C   T   .   PASS    AF=0.0381   ES:SE:LP:AF:SS:ID   0.00598207:0.0400285:0.0525663:0.0381:38589:rs2295362
1   1871337 rs16824543  G   A   .   PASS    AF=0.0348   ES:SE:LP:AF:SS:ID   0.0207825:0.0409439:0.207608:0.0348:38589:rs16824543
1   1873625 rs12758705  G   A   .   PASS    AF=0.2667   ES:SE:LP:AF:SS:ID   0.0276152:0.0186107:0.853872:0.2667:38589:rs12758705
1   1881070 rs4648596   G   A   .   PASS    AF=0.0324   ES:SE:LP:AF:SS:ID   -0.001998:0.0417213:0.0181814:0.0324:38589:rs4648596
1   1888193 rs3820011   C   A   .   PASS    AF=0.2795   ES:SE:LP:AF:SS:ID   0.0129162:0.0183823:0.312471:0.2795:38589:rs3820011
1   2146966 rs7512482   T   C   .   PASS    AF=0.163    ES:SE:LP:AF:SS:ID   -0.0119286:0.0219334:0.220404:0.163:38589:rs7512482
1   2202774 rs6673129   C   T   .   PASS    AF=0.156    ES:SE:LP:AF:SS:ID   0.00498754:0.0228375:0.078834:0.156:38589:rs6673129
1   2229478 rs12562937  C   T   .   PASS    AF=0.2073   ES:SE:LP:AF:SS:ID   -0.00995033:0.0207021:0.209012:0.2073:38589:rs12562937
1   2283896 rs2840528   A   G   .   PASS    AF=0.4258   ES:SE:LP:AF:SS:ID   0.00697561:0.0172158:0.171985:0.4258:38589:rs2840528
1   2286127 rs4648832   G   C   .   PASS    AF=0.1918   ES:SE:LP:AF:SS:ID   -0.0168571:0.0253181:0.301899:0.1918:38589:rs4648832
1   2290143 rs34587196  G   A   .   PASS    AF=0.0119   ES:SE:LP:AF:SS:ID   0.0363319:0.0754464:0.20204:0.0119:38589:rs34587196
1   2359862 rs10910073  C   A   .   PASS    AF=0.2909   ES:SE:LP:AF:SS:ID   0.0109399:0.0249879:0.174574:0.2909:38589:rs10910073
1   2404256 rs2494626   C   T   .   PASS    AF=0.2877   ES:SE:LP:AF:SS:ID   0.001998:0.021621:0.0409586:0.2877:38589:rs2494626
1   2407781 rs78504402  C   T   .   PASS    AF=0.0796   ES:SE:LP:AF:SS:ID   -0.1441:0.033769:4.66959:0.0796:38589:rs78504402
1   2408471 rs115996655 G   A   .   PASS    AF=0.0071   ES:SE:LP:AF:SS:ID   0.0421012:0.0907546:0.19044:0.0071:38589:rs115996655
1   2408834 rs11588930  G   A   .   PASS    AF=0.1021   ES:SE:LP:AF:SS:ID   0.0119286:0.0271964:0.180456:0.1021:38589:rs11588930
1   2409235 rs12045425  G   A   .   PASS    AF=0.0001   ES:SE:LP:AF:SS:ID   0.0843411:0.381981:0.083546:0.0001:38589:rs12045425
1   2409276 rs12049628  A   G   .   PASS    AF=0.6101   ES:SE:LP:AF:SS:ID   0.0009995:0.0180927:0.011441:0.6101:38589:rs12049628
1   2409340 rs144283296 G   C   .   PASS    AF=0.991    ES:SE:LP:AF:SS:ID   -0.08158:0.114954:0.319664:0.991:38589:rs144283296
1   2409892 rs12727342  A   G   .   PASS    AF=0.6168   ES:SE:LP:AF:SS:ID   0.001998:0.0173017:0.048177:0.6168:38589:rs12727342