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-1108/ieu-a-1108.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-1108/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 19:31:43 2020
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-1108/ieu-a-1108.vcf.gz ...
Read summary statistics for 2419027 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, 1150168 SNPs remain.
After merging with regression SNP LD, 1150168 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0689 (0.0158)
Lambda GC: 1.0313
Mean Chi^2: 1.0373
Intercept: 0.9971 (0.0064)
Ratio < 0 (usually indicates GC correction).
Analysis finished at Tue Feb  4 19:32:12 2020
Total time elapsed: 29.61s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9217,
    "inflation_factor": 1.0335,
    "mean_EFFECT": 0.0005,
    "n": 29633,
    "n_snps": 2419027,
    "n_clumped_hits": 1,
    "n_p_sig": 6,
    "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": 20116,
    "n_est": 29053.4964,
    "ratio_se_n": 0.9902,
    "mean_diff": -0.0002,
    "ratio_diff": 22.6619,
    "sd_y_est1": 2.0343,
    "sd_y_est2": 2.0143,
    "r2_sum1": 0.0041,
    "r2_sum2": 0.001,
    "r2_sum3": 0.001,
    "r2_sum4": 0.001,
    "ldsc_nsnp_merge_refpanel_ld": 1150168,
    "ldsc_nsnp_merge_regression_ld": 1150168,
    "ldsc_observed_scale_h2_beta": 0.0689,
    "ldsc_observed_scale_h2_se": 0.0158,
    "ldsc_intercept_beta": 0.9971,
    "ldsc_intercept_se": 0.0064,
    "ldsc_lambda_gc": 1.0313,
    "ldsc_mean_chisq": 1.0373,
    "ldsc_ratio": -0.0777
}

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 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 3 42 0 2419027 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 8.596383e+00 5.661898e+00 1.0000e+00 4.000000e+00 8.000000e+00 1.200000e+01 2.30000e+01 ▇▅▅▂▂
numeric POS 0 1.0000000 NA NA NA NA NA 7.878698e+07 5.567204e+07 1.1523e+04 3.260193e+07 7.017910e+07 1.143107e+08 2.49219e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA 4.568000e-04 2.858670e-02 -4.6580e-01 -1.490000e-02 3.000000e-04 1.550000e-02 3.99600e-01 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 2.515650e-02 1.296800e-02 1.5600e-02 1.730000e-02 2.010000e-02 2.720000e-02 1.73600e-01 ▇▁▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.949891e-01 2.902241e-01 0.0000e+00 2.425001e-01 4.929002e-01 7.465003e-01 1.00000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.949882e-01 2.902264e-01 0.0000e+00 2.425347e-01 4.929862e-01 7.464277e-01 1.00000e+00 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA 3.645654e-01 2.645349e-01 1.0700e-02 1.374000e-01 2.992000e-01 5.598000e-01 9.89100e-01 ▇▅▃▃▂
numeric AF_reference 20116 0.9916843 NA NA NA NA NA 3.642340e-01 2.541477e-01 1.9970e-04 1.505590e-01 3.037140e-01 5.479230e-01 1.00000e+00 ▇▆▅▃▂
numeric N 0 1.0000000 NA NA NA NA NA 2.963300e+04 0.000000e+00 2.9633e+04 2.963300e+04 2.963300e+04 2.963300e+04 2.96330e+04 ▁▁▇▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 752566 rs3094315 G A 0.0816 0.0368 0.0265699 0.0265964 0.8307 0.718251 29633
1 768448 rs12562034 G A 0.0233 0.0377 0.5363003 0.5365509 0.0991 0.191893 29633
1 785989 rs2980300 T C 0.0785 0.0480 0.1017000 0.1019617 0.8651 0.626997 29633
1 962210 rs3128126 A G -0.0044 0.0346 0.8990000 0.8988077 0.4376 0.305511 29633
1 990380 rs3121561 C T 0.0302 0.0279 0.2796997 0.2790583 0.2785 0.343450 29633
1 998501 rs3813193 G C -0.0053 0.0268 0.8442001 0.8432319 0.1681 0.206669 29633
1 1003629 rs4075116 C T -0.0467 0.0220 0.0337901 0.0337767 0.7395 0.720647 29633
1 1005806 rs3934834 C T -0.0043 0.0245 0.8618000 0.8606788 0.1493 0.223442 29633
1 1017170 rs3766193 C G -0.0278 0.0185 0.1330001 0.1329157 0.5527 0.575479 29633
1 1017197 rs3766192 C T -0.0254 0.0173 0.1410000 0.1420477 0.5633 0.511182 29633
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51196164 rs8136603 A T 0.0339 0.0502 0.4998998 0.4994859 0.0524 0.1427720 29633
22 51212875 rs2238837 A C 0.0408 0.0332 0.2192002 0.2191034 0.3977 0.3724040 29633
22 51216564 rs9616970 T C 0.1160 0.0461 0.0118500 0.0118605 0.1591 0.1563500 29633
22 51222100 rs114553188 G T 0.0489 0.0517 0.3444998 0.3442295 0.0534 0.0880591 29633
22 51223637 rs375798137 G A 0.0498 0.0519 0.3371002 0.3372880 0.0534 0.0788738 29633
23 35921591 rs2204667 C G -0.0210 0.0237 0.3758997 0.3755766 0.1582 NA 29633
23 51666786 rs14115 A G 0.0029 0.0358 0.9352999 0.9354375 0.0544 NA 29633
23 70163799 rs1626496 A C 0.0007 0.0307 0.9811000 0.9818088 0.0857 NA 29633
23 91415872 rs6562597 G A -0.0166 0.0595 0.7805002 0.7802513 0.0225 0.0021192 29633
23 118495837 rs12882977 G A -0.0343 0.0173 0.0477200 0.0474055 0.5024 0.2307280 29633

bcf preview

1   752566  rs3094315   G   A   .   PASS    AF=0.8307   ES:SE:LP:AF:SS:ID   0.0816:0.0368:1.57561:0.8307:29633:rs3094315
1   768448  rs12562034  G   A   .   PASS    AF=0.0991   ES:SE:LP:AF:SS:ID   0.0233:0.0377:0.270592:0.0991:29633:rs12562034
1   785989  rs2980300   T   C   .   PASS    AF=0.8651   ES:SE:LP:AF:SS:ID   0.0785:0.048:0.992679:0.8651:29633:rs2980300
1   962210  rs3128126   A   G   .   PASS    AF=0.4376   ES:SE:LP:AF:SS:ID   -0.0044:0.0346:0.0462403:0.4376:29633:rs3128126
1   990380  rs3121561   C   T   .   PASS    AF=0.2785   ES:SE:LP:AF:SS:ID   0.0302:0.0279:0.553308:0.2785:29633:rs3121561
1   998501  rs3813193   G   C   .   PASS    AF=0.1681   ES:SE:LP:AF:SS:ID   -0.0053:0.0268:0.0735546:0.1681:29633:rs3813193
1   1003629 rs4075116   C   T   .   PASS    AF=0.7395   ES:SE:LP:AF:SS:ID   -0.0467:0.022:1.47121:0.7395:29633:rs4075116
1   1005806 rs3934834   C   T   .   PASS    AF=0.1493   ES:SE:LP:AF:SS:ID   -0.0043:0.0245:0.0645935:0.1493:29633:rs3934834
1   1017170 rs3766193   C   G   .   PASS    AF=0.5527   ES:SE:LP:AF:SS:ID   -0.0278:0.0185:0.876148:0.5527:29633:rs3766193
1   1017197 rs3766192   C   T   .   PASS    AF=0.5633   ES:SE:LP:AF:SS:ID   -0.0254:0.0173:0.850781:0.5633:29633:rs3766192
1   1017587 rs3766191   C   T   .   PASS    AF=0.1427   ES:SE:LP:AF:SS:ID   -0.0116:0.0258:0.186152:0.1427:29633:rs3766191
1   1018562 rs9442371   C   T   .   PASS    AF=0.5726   ES:SE:LP:AF:SS:ID   -0.0214:0.0176:0.652085:0.5726:29633:rs9442371
1   1018704 rs9442372   A   G   .   PASS    AF=0.5723   ES:SE:LP:AF:SS:ID   -0.024:0.0168:0.809949:0.5723:29633:rs9442372
1   1021346 rs10907177  A   G   .   PASS    AF=0.1438   ES:SE:LP:AF:SS:ID   -0.0138:0.0261:0.223807:0.1438:29633:rs10907177
1   1021415 rs3737728   A   G   .   PASS    AF=0.7218   ES:SE:LP:AF:SS:ID   -0.0345:0.0186:1.19915:0.7218:29633:rs3737728
1   1021583 rs10907178  A   C   .   PASS    AF=0.1424   ES:SE:LP:AF:SS:ID   -0.0137:0.0263:0.219539:0.1424:29633:rs10907178
1   1021695 rs9442398   A   G   .   PASS    AF=0.7293   ES:SE:LP:AF:SS:ID   -0.0333:0.0197:1.04407:0.7293:29633:rs9442398
1   1022037 rs6701114   C   T   .   PASS    AF=0.5553   ES:SE:LP:AF:SS:ID   -0.0284:0.0186:0.899974:0.5553:29633:rs6701114
1   1026707 rs4074137   C   A   .   PASS    AF=0.6021   ES:SE:LP:AF:SS:ID   -0.0092:0.0186:0.207748:0.6021:29633:rs4074137
1   1030565 rs6687776   C   T   .   PASS    AF=0.1552   ES:SE:LP:AF:SS:ID   0.023:0.0225:0.512296:0.1552:29633:rs6687776
1   1030633 rs6678318   G   A   .   PASS    AF=0.1547   ES:SE:LP:AF:SS:ID   0.0256:0.0231:0.574303:0.1547:29633:rs6678318
1   1031540 rs9651273   A   G   .   PASS    AF=0.7331   ES:SE:LP:AF:SS:ID   0.012:0.0192:0.272947:0.7331:29633:rs9651273
1   1036959 rs11579015  T   C   .   PASS    AF=0.1089   ES:SE:LP:AF:SS:ID   0.0285:0.0272:0.529884:0.1089:29633:rs11579015
1   1040026 rs6671356   T   C   .   PASS    AF=0.1419   ES:SE:LP:AF:SS:ID   0.0286:0.0244:0.616544:0.1419:29633:rs6671356
1   1046164 rs6666280   C   T   .   PASS    AF=0.1352   ES:SE:LP:AF:SS:ID   0.038:0.0249:0.896881:0.1352:29633:rs6666280
1   1048955 rs4970405   A   G   .   PASS    AF=0.1042   ES:SE:LP:AF:SS:ID   0.0388:0.0274:0.803547:0.1042:29633:rs4970405
1   1049950 rs12726255  A   G   .   PASS    AF=0.1365   ES:SE:LP:AF:SS:ID   0.0322:0.0242:0.73969:0.1365:29633:rs12726255
1   1053452 rs4970409   G   A   .   PASS    AF=0.1057   ES:SE:LP:AF:SS:ID   0.0383:0.0275:0.786482:0.1057:29633:rs4970409
1   1060174 rs7548798   C   T   .   PASS    AF=0.3172   ES:SE:LP:AF:SS:ID   0.0015:0.0209:0.0253502:0.3172:29633:rs7548798
1   1060235 rs7540009   G   A   .   PASS    AF=0.0305   ES:SE:LP:AF:SS:ID   0.0368:0.0561:0.290985:0.0305:29633:rs7540009
1   1060608 rs17160824  G   A   .   PASS    AF=0.1152   ES:SE:LP:AF:SS:ID   0.0364:0.0277:0.723308:0.1152:29633:rs17160824
1   1061115 rs17160826  T   C   .   PASS    AF=0.105    ES:SE:LP:AF:SS:ID   0.0396:0.0278:0.813609:0.105:29633:rs17160826
1   1061152 rs12748370  T   C   .   PASS    AF=0.1049   ES:SE:LP:AF:SS:ID   0.0398:0.0278:0.818156:0.1049:29633:rs12748370
1   1061166 rs11807848  T   C   .   PASS    AF=0.4067   ES:SE:LP:AF:SS:ID   0.0173:0.0186:0.451365:0.4067:29633:rs11807848
1   1062015 rs9659914   C   T   .   PASS    AF=0.03 ES:SE:LP:AF:SS:ID   0.0196:0.0592:0.130827:0.03:29633:rs9659914
1   1062638 rs9442373   C   A   .   PASS    AF=0.5525   ES:SE:LP:AF:SS:ID   -0.0106:0.0179:0.254613:0.5525:29633:rs9442373
1   1064535 rs6682475   G   C   .   PASS    AF=0.7183   ES:SE:LP:AF:SS:ID   -0.0291:0.0257:0.58956:0.7183:29633:rs6682475
1   1064979 rs2298217   C   T   .   PASS    AF=0.1466   ES:SE:LP:AF:SS:ID   0.0261:0.0235:0.573326:0.1466:29633:rs2298217
1   1066029 rs12145826  G   A   .   PASS    AF=0.0741   ES:SE:LP:AF:SS:ID   -0.0196:0.0423:0.191451:0.0741:29633:rs12145826
1   1066403 rs10907182  T   C   .   PASS    AF=0.629    ES:SE:LP:AF:SS:ID   -0.0316:0.0213:0.859492:0.629:29633:rs10907182
1   1071118 rs10907183  G   C   .   PASS    AF=0.6455   ES:SE:LP:AF:SS:ID   -0.0385:0.0229:1.02784:0.6455:29633:rs10907183
1   1077064 rs4970357   C   A   .   PASS    AF=0.9166   ES:SE:LP:AF:SS:ID   0.0122:0.0412:0.114808:0.9166:29633:rs4970357
1   1079198 rs11260603  T   C   .   PASS    AF=0.2296   ES:SE:LP:AF:SS:ID   0.036:0.0282:0.692932:0.2296:29633:rs11260603
1   1087683 rs9442380   T   C   .   PASS    AF=0.9198   ES:SE:LP:AF:SS:ID   -0.0046:0.0335:0.0501223:0.9198:29633:rs9442380
1   1089262 rs4970358   A   G   .   PASS    AF=0.9535   ES:SE:LP:AF:SS:ID   0.0081:0.0485:0.0618807:0.9535:29633:rs4970358
1   1094738 rs4970362   A   G   .   PASS    AF=0.6327   ES:SE:LP:AF:SS:ID   -0.0288:0.0203:0.805486:0.6327:29633:rs4970362
1   1097335 rs9442385   T   G   .   PASS    AF=0.9336   ES:SE:LP:AF:SS:ID   -0.0018:0.0349:0.0180908:0.9336:29633:rs9442385
1   1099342 rs9660710   A   C   .   PASS    AF=0.9335   ES:SE:LP:AF:SS:ID   -0.0096:0.0328:0.114017:0.9335:29633:rs9660710
1   1100217 rs1891905   C   T   .   PASS    AF=0.9558   ES:SE:LP:AF:SS:ID   0.0205:0.0513:0.161592:0.9558:29633:rs1891905
1   1106473 rs4970420   G   A   .   PASS    AF=0.1777   ES:SE:LP:AF:SS:ID   -0.0397:0.0271:0.844664:0.1777:29633:rs4970420