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-1110/ieu-a-1110.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-1110/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 17:01:10 2020
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-1110/ieu-a-1110.vcf.gz ...
Read summary statistics for 2410558 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, 1149458 SNPs remain.
After merging with regression SNP LD, 1149458 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0215 (0.0223)
Lambda GC: 1.0165
Mean Chi^2: 1.0315
Intercept: 1.0225 (0.0062)
Ratio: 0.7128 (0.1974)
Analysis finished at Tue Feb  4 17:01:34 2020
Total time elapsed: 23.64s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9216,
    "inflation_factor": 1.0117,
    "mean_EFFECT": 0.0035,
    "n": 21143,
    "n_snps": 2410558,
    "n_clumped_hits": 1,
    "n_p_sig": 13,
    "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": 0,
    "n_miss_AF_reference": 19710,
    "n_est": 20765.6367,
    "ratio_se_n": 0.991,
    "mean_diff": -0.0026,
    "ratio_diff": 281.5786,
    "sd_y_est1": 3.6579,
    "sd_y_est2": 3.6251,
    "r2_sum1": 0.0284,
    "r2_sum2": 0.0021,
    "r2_sum3": 0.0022,
    "r2_sum4": 0.0023,
    "ldsc_nsnp_merge_refpanel_ld": 1149458,
    "ldsc_nsnp_merge_regression_ld": 1149458,
    "ldsc_observed_scale_h2_beta": 0.0215,
    "ldsc_observed_scale_h2_se": 0.0223,
    "ldsc_intercept_beta": 1.0225,
    "ldsc_intercept_se": 0.0062,
    "ldsc_lambda_gc": 1.0165,
    "ldsc_mean_chisq": 1.0315,
    "ldsc_ratio": 0.7143
}

Flags

name value
af_correlation FALSE
inflation_factor FALSE
n FALSE
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 TRUE
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 3 42 0 2410558 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 8.596131e+00 5.659320e+00 1.0000e+00 4.000000e+00 8.000000e+00 1.200000e+01 2.300000e+01 ▇▅▅▂▂
numeric POS 0 1.0000000 NA NA NA NA NA 7.877445e+07 5.565397e+07 1.1523e+04 3.260151e+07 7.017923e+07 1.142756e+08 2.492107e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA 3.537600e-03 5.952530e-02 -8.1540e-01 -2.920000e-02 2.300000e-03 3.460000e-02 8.410000e-01 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 5.288100e-02 2.615720e-02 3.3000e-02 3.680000e-02 4.270000e-02 5.740000e-02 3.826000e-01 ▇▁▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.974358e-01 2.905350e-01 0.0000e+00 2.449001e-01 4.974999e-01 7.494005e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.974357e-01 2.905357e-01 0.0000e+00 2.448967e-01 4.975232e-01 7.494446e-01 1.000000e+00 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA 3.653545e-01 2.633802e-01 1.0500e-02 1.407000e-01 3.001000e-01 5.602000e-01 9.893000e-01 ▇▅▃▃▂
numeric AF_reference 19710 0.9918235 NA NA NA NA NA 3.647143e-01 2.538176e-01 1.9970e-04 1.513580e-01 3.043130e-01 5.483230e-01 1.000000e+00 ▇▆▅▃▂
numeric N 0 1.0000000 NA NA NA NA NA 2.114300e+04 0.000000e+00 2.1143e+04 2.114300e+04 2.114300e+04 2.114300e+04 2.114300e+04 ▁▁▇▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 752566 rs3094315 G A 0.1361 0.0689 0.0482903 0.0482311 0.8349 0.718251 21143
1 768448 rs12562034 G A 0.0675 0.0671 0.3150003 0.3144342 0.1010 0.191893 21143
1 785989 rs2980300 T C 0.1127 0.0987 0.2535000 0.2535189 0.8703 0.626997 21143
1 990380 rs3121561 C T 0.0222 0.0566 0.6944005 0.6948911 0.2763 0.343450 21143
1 998501 rs3813193 G C -0.0159 0.0546 0.7703002 0.7708916 0.1651 0.206669 21143
1 1003629 rs4075116 C T -0.0654 0.0462 0.1564999 0.1568972 0.7385 0.720647 21143
1 1005806 rs3934834 C T -0.0077 0.0495 0.8766001 0.8763834 0.1488 0.223442 21143
1 1017170 rs3766193 C G -0.0517 0.0386 0.1802001 0.1804476 0.5512 0.575479 21143
1 1017197 rs3766192 C T -0.0416 0.0357 0.2442002 0.2439113 0.5598 0.511182 21143
1 1017587 rs3766191 C T -0.0250 0.0520 0.6308005 0.6306805 0.1440 0.171126 21143
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51175626 rs3810648 A G 0.0400 0.0709 0.5728000 0.5726351 0.1077 0.1084270 21143
22 51178090 rs2285395 G A 0.0246 0.0753 0.7440995 0.7438999 0.1116 0.0666933 21143
22 51196164 rs8136603 A T 0.0628 0.1086 0.5629995 0.5630826 0.0523 0.1427720 21143
22 51222100 rs114553188 G T 0.1854 0.1207 0.1246000 0.1245286 0.0547 0.0880591 21143
22 51223637 rs375798137 G A 0.1858 0.1208 0.1238999 0.1240292 0.0547 0.0788738 21143
23 35921591 rs2204667 C G -0.0779 0.0541 0.1498001 0.1498883 0.1563 NA 21143
23 51666786 rs14115 A G 0.0559 0.0749 0.4560999 0.4554690 0.0568 NA 21143
23 70163799 rs1626496 A C 0.1410 0.0649 0.0298703 0.0298125 0.0816 NA 21143
23 91415872 rs6562597 G A -0.0657 0.1247 0.5981994 0.5982877 0.0226 0.0021192 21143
23 118495837 rs12882977 G A -0.1033 0.0386 0.0073680 0.0074470 0.4980 0.2307280 21143

bcf preview

1   752566  rs3094315   G   A   .   PASS    AF=0.8349   ES:SE:LP:AF:SS:ID   0.1361:0.0689:1.31614:0.8349:21143:rs3094315
1   768448  rs12562034  G   A   .   PASS    AF=0.101    ES:SE:LP:AF:SS:ID   0.0675:0.0671:0.501689:0.101:21143:rs12562034
1   785989  rs2980300   T   C   .   PASS    AF=0.8703   ES:SE:LP:AF:SS:ID   0.1127:0.0987:0.596022:0.8703:21143:rs2980300
1   990380  rs3121561   C   T   .   PASS    AF=0.2763   ES:SE:LP:AF:SS:ID   0.0222:0.0566:0.15839:0.2763:21143:rs3121561
1   998501  rs3813193   G   C   .   PASS    AF=0.1651   ES:SE:LP:AF:SS:ID   -0.0159:0.0546:0.11334:0.1651:21143:rs3813193
1   1003629 rs4075116   C   T   .   PASS    AF=0.7385   ES:SE:LP:AF:SS:ID   -0.0654:0.0462:0.805486:0.7385:21143:rs4075116
1   1005806 rs3934834   C   T   .   PASS    AF=0.1488   ES:SE:LP:AF:SS:ID   -0.0077:0.0495:0.0571985:0.1488:21143:rs3934834
1   1017170 rs3766193   C   G   .   PASS    AF=0.5512   ES:SE:LP:AF:SS:ID   -0.0517:0.0386:0.744245:0.5512:21143:rs3766193
1   1017197 rs3766192   C   T   .   PASS    AF=0.5598   ES:SE:LP:AF:SS:ID   -0.0416:0.0357:0.612254:0.5598:21143:rs3766192
1   1017587 rs3766191   C   T   .   PASS    AF=0.144    ES:SE:LP:AF:SS:ID   -0.025:0.052:0.200108:0.144:21143:rs3766191
1   1018562 rs9442371   C   T   .   PASS    AF=0.5681   ES:SE:LP:AF:SS:ID   -0.0297:0.0363:0.383735:0.5681:21143:rs9442371
1   1018704 rs9442372   A   G   .   PASS    AF=0.5678   ES:SE:LP:AF:SS:ID   -0.0372:0.0349:0.542724:0.5678:21143:rs9442372
1   1021346 rs10907177  A   G   .   PASS    AF=0.1451   ES:SE:LP:AF:SS:ID   -0.0314:0.0526:0.259006:0.1451:21143:rs10907177
1   1021415 rs3737728   A   G   .   PASS    AF=0.7196   ES:SE:LP:AF:SS:ID   -0.0681:0.0389:1.09832:0.7196:21143:rs3737728
1   1021583 rs10907178  A   C   .   PASS    AF=0.1434   ES:SE:LP:AF:SS:ID   -0.0363:0.0535:0.302771:0.1434:21143:rs10907178
1   1021695 rs9442398   A   G   .   PASS    AF=0.7275   ES:SE:LP:AF:SS:ID   -0.0689:0.0412:1.02604:0.7275:21143:rs9442398
1   1022037 rs6701114   C   T   .   PASS    AF=0.5541   ES:SE:LP:AF:SS:ID   -0.0552:0.0388:0.809108:0.5541:21143:rs6701114
1   1026707 rs4074137   C   A   .   PASS    AF=0.5952   ES:SE:LP:AF:SS:ID   -0.0283:0.0389:0.329847:0.5952:21143:rs4074137
1   1030565 rs6687776   C   T   .   PASS    AF=0.1585   ES:SE:LP:AF:SS:ID   0.0141:0.0468:0.117191:0.1585:21143:rs6687776
1   1030633 rs6678318   G   A   .   PASS    AF=0.1571   ES:SE:LP:AF:SS:ID   0.0102:0.0478:0.0806604:0.1571:21143:rs6678318
1   1031540 rs9651273   A   G   .   PASS    AF=0.7303   ES:SE:LP:AF:SS:ID   -0.0222:0.04:0.237847:0.7303:21143:rs9651273
1   1036959 rs11579015  T   C   .   PASS    AF=0.1129   ES:SE:LP:AF:SS:ID   0.0047:0.057:0.0296531:0.1129:21143:rs11579015
1   1040026 rs6671356   T   C   .   PASS    AF=0.1433   ES:SE:LP:AF:SS:ID   0.0137:0.0511:0.103033:0.1433:21143:rs6671356
1   1046164 rs6666280   C   T   .   PASS    AF=0.137    ES:SE:LP:AF:SS:ID   0.0276:0.0519:0.225629:0.137:21143:rs6666280
1   1048955 rs4970405   A   G   .   PASS    AF=0.108    ES:SE:LP:AF:SS:ID   0.0181:0.0571:0.12384:0.108:21143:rs4970405
1   1049950 rs12726255  A   G   .   PASS    AF=0.138    ES:SE:LP:AF:SS:ID   0.0191:0.0502:0.152242:0.138:21143:rs12726255
1   1053452 rs4970409   G   A   .   PASS    AF=0.1092   ES:SE:LP:AF:SS:ID   0.0179:0.0573:0.122283:0.1092:21143:rs4970409
1   1060174 rs7548798   C   T   .   PASS    AF=0.3138   ES:SE:LP:AF:SS:ID   0.0221:0.042:0.222356:0.3138:21143:rs7548798
1   1060235 rs7540009   G   A   .   PASS    AF=0.0298   ES:SE:LP:AF:SS:ID   0.0946:0.1192:0.369064:0.0298:21143:rs7540009
1   1060608 rs17160824  G   A   .   PASS    AF=0.1198   ES:SE:LP:AF:SS:ID   0.0019:0.0576:0.0113965:0.1198:21143:rs17160824
1   1061115 rs17160826  T   C   .   PASS    AF=0.1087   ES:SE:LP:AF:SS:ID   0.0174:0.0577:0.117419:0.1087:21143:rs17160826
1   1061152 rs12748370  T   C   .   PASS    AF=0.1087   ES:SE:LP:AF:SS:ID   0.0176:0.0577:0.119072:0.1087:21143:rs12748370
1   1061166 rs11807848  T   C   .   PASS    AF=0.4072   ES:SE:LP:AF:SS:ID   0.0237:0.0369:0.282912:0.4072:21143:rs11807848
1   1062015 rs9659914   C   T   .   PASS    AF=0.029    ES:SE:LP:AF:SS:ID   0.0851:0.1248:0.304869:0.029:21143:rs9659914
1   1062638 rs9442373   C   A   .   PASS    AF=0.5529   ES:SE:LP:AF:SS:ID   -0.0257:0.0359:0.324313:0.5529:21143:rs9442373
1   1064535 rs6682475   G   C   .   PASS    AF=0.7184   ES:SE:LP:AF:SS:ID   -0.0238:0.0524:0.187087:0.7184:21143:rs6682475
1   1064979 rs2298217   C   T   .   PASS    AF=0.1497   ES:SE:LP:AF:SS:ID   0.0353:0.0484:0.332267:0.1497:21143:rs2298217
1   1066029 rs12145826  G   A   .   PASS    AF=0.075    ES:SE:LP:AF:SS:ID   0.024:0.074:0.127378:0.075:21143:rs12145826
1   1066403 rs10907182  T   C   .   PASS    AF=0.6252   ES:SE:LP:AF:SS:ID   -0.0697:0.0445:0.931443:0.6252:21143:rs10907182
1   1071118 rs10907183  G   C   .   PASS    AF=0.6416   ES:SE:LP:AF:SS:ID   -0.0741:0.0468:0.94424:0.6416:21143:rs10907183
1   1077064 rs4970357   C   A   .   PASS    AF=0.9179   ES:SE:LP:AF:SS:ID   -0.0251:0.0907:0.10696:0.9179:21143:rs4970357
1   1079198 rs11260603  T   C   .   PASS    AF=0.2292   ES:SE:LP:AF:SS:ID   0.0786:0.0555:0.805208:0.2292:21143:rs11260603
1   1087683 rs9442380   T   C   .   PASS    AF=0.9248   ES:SE:LP:AF:SS:ID   -0.0049:0.0703:0.0247061:0.9248:21143:rs9442380
1   1089262 rs4970358   A   G   .   PASS    AF=0.9533   ES:SE:LP:AF:SS:ID   0.047:0.1065:0.181246:0.9533:21143:rs4970358
1   1094738 rs4970362   A   G   .   PASS    AF=0.6382   ES:SE:LP:AF:SS:ID   -0.0262:0.0399:0.291069:0.6382:21143:rs4970362
1   1097335 rs9442385   T   G   .   PASS    AF=0.9328   ES:SE:LP:AF:SS:ID   0.0171:0.0789:0.0816551:0.9328:21143:rs9442385
1   1099342 rs9660710   A   C   .   PASS    AF=0.9317   ES:SE:LP:AF:SS:ID   -0.0047:0.0704:0.0239712:0.9317:21143:rs9660710
1   1100217 rs1891905   C   T   .   PASS    AF=0.9566   ES:SE:LP:AF:SS:ID   0.0494:0.1183:0.169989:0.9566:21143:rs1891905
1   1119858 rs1320565   C   T   .   PASS    AF=0.0768   ES:SE:LP:AF:SS:ID   -0.0627:0.0729:0.40927:0.0768:21143:rs1320565
1   1120431 rs1320571   G   A   .   PASS    AF=0.0365   ES:SE:LP:AF:SS:ID   -0.1164:0.1238:0.459796:0.0365:21143:rs1320571