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-1063/ieu-a-1063.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-1063/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 18:48:22 2020
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-1063/ieu-a-1063.vcf.gz ...
Read summary statistics for 2380395 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, 1124589 SNPs remain.
After merging with regression SNP LD, 1124589 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: -0.1437 (0.2939)
Lambda GC: 0.9999
Mean Chi^2: 0.99
Intercept: 0.994 (0.0062)
Ratio: NA (mean chi^2 < 1)
Analysis finished at Tue Feb  4 18:48:50 2020
Total time elapsed: 28.7s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9211,
    "inflation_factor": 1,
    "mean_EFFECT": 1.0166e-07,
    "n": 1382,
    "n_snps": 2380395,
    "n_clumped_hits": 0,
    "n_p_sig": 0,
    "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": 19711,
    "n_est": 1361.8483,
    "ratio_se_n": 0.9927,
    "mean_diff": -0,
    "ratio_diff": 1.0004,
    "sd_y_est1": 1.0631,
    "sd_y_est2": 1.0553,
    "r2_sum1": 0,
    "r2_sum2": 0,
    "r2_sum3": 0,
    "r2_sum4": 0,
    "ldsc_nsnp_merge_refpanel_ld": 1124589,
    "ldsc_nsnp_merge_regression_ld": 1124589,
    "ldsc_observed_scale_h2_beta": "NA",
    "ldsc_observed_scale_h2_se": "NA",
    "ldsc_intercept_beta": 0.994,
    "ldsc_intercept_se": 0.0062,
    "ldsc_lambda_gc": 0.9999,
    "ldsc_mean_chisq": 0.99,
    "ldsc_ratio": 0.6
}

Flags

name value
af_correlation FALSE
inflation_factor FALSE
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 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 2380395 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 8.567027e+00 5.647690e+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 7.886815e+07 5.555610e+07 1.1523e+04 3.280602e+07 7.033413e+07 1.142314e+08 2.49219e+08 ▇▇▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA 1.000000e-07 6.729150e-02 -1.0210e+00 -3.600000e-02 0.000000e+00 3.600000e-02 1.12100e+00 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 6.076000e-02 3.013440e-02 3.7000e-02 4.200000e-02 4.900000e-02 6.600000e-02 4.31000e-01 ▇▁▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 5.010490e-01 2.884221e-01 9.0000e-07 2.500000e-01 5.000000e-01 7.499995e-01 1.00000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 5.010597e-01 2.884278e-01 8.0000e-07 2.515194e-01 5.003666e-01 7.511881e-01 1.00000e+00 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA 3.610335e-01 2.714024e-01 7.7410e-03 1.264000e-01 2.974000e-01 5.597000e-01 9.92105e-01 ▇▅▃▃▂
numeric AF_reference 19711 0.9917194 NA NA NA NA NA 3.640189e-01 2.543581e-01 1.9970e-04 1.501600e-01 3.033150e-01 5.479230e-01 1.00000e+00 ▇▆▅▃▂
numeric N 0 1.0000000 NA NA NA NA NA 1.382000e+03 0.000000e+00 1.3820e+03 1.382000e+03 1.382000e+03 1.382000e+03 1.38200e+03 ▁▁▇▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 998501 rs3813193 G C -0.083 0.057 0.1430000 0.1453538 0.1458 0.206669 1382
1 1003629 rs4075116 C T 0.002 0.046 0.9699999 0.9653203 0.7230 0.720647 1382
1 1005806 rs3934834 C T -0.083 0.057 0.1430000 0.1453538 0.1453 0.223442 1382
1 1017587 rs3766191 C T -0.063 0.062 0.3100002 0.3095679 0.1223 0.171126 1382
1 1018562 rs9442371 C T 0.026 0.043 0.5400003 0.5454108 0.5992 0.530152 1382
1 1018704 rs9442372 A G 0.026 0.043 0.5400003 0.5454108 0.5992 0.611022 1382
1 1021346 rs10907177 A G -0.043 0.064 0.5099998 0.5016633 0.1160 0.178914 1382
1 1021415 rs3737728 A G 0.001 0.045 0.9800000 0.9822707 0.7157 0.812700 1382
1 1021583 rs10907178 A C -0.043 0.064 0.5099998 0.5016633 0.1158 0.173722 1382
1 1021695 rs9442398 A G 0.003 0.045 0.9500000 0.9468471 0.7173 0.727236 1382
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51196164 rs8136603 A T -0.033 0.090 0.7099994 0.7138677 0.05146 0.1427720 1382
22 51216564 rs9616970 T C -0.032 0.068 0.6400000 0.6379348 0.10620 0.1563500 1382
22 51222100 rs114553188 G T -0.033 0.087 0.6999999 0.7044574 0.05358 0.0880591 1382
22 51223637 rs375798137 G A -0.033 0.087 0.6999999 0.7044574 0.05358 0.0788738 1382
22 51229805 rs9616985 T C -0.003 0.096 0.9699999 0.9750702 0.05201 0.0730831 1382
23 35921591 rs2204667 C G 0.100 0.052 0.0580003 0.0544704 0.16820 NA 1382
23 51666786 rs14115 A G 0.012 0.099 0.9000000 0.9035230 0.04909 NA 1382
23 70163799 rs1626496 A C -0.096 0.079 0.2200002 0.2242937 0.07646 NA 1382
23 91415872 rs6562597 G A -0.161 0.141 0.2500000 0.2535189 0.02562 0.0021192 1382
23 118495837 rs12882977 G A 0.012 0.041 0.7800007 0.7697645 0.48150 0.2307280 1382

bcf preview

1   998501  rs3813193   G   C   .   PASS    AF=0.1458   ES:SE:LP:AF:SS:ID   -0.083:0.057:0.844664:0.1458:1382:rs3813193
1   1003629 rs4075116   C   T   .   PASS    AF=0.723    ES:SE:LP:AF:SS:ID   0.002:0.046:0.0132283:0.723:1382:rs4075116
1   1005806 rs3934834   C   T   .   PASS    AF=0.1453   ES:SE:LP:AF:SS:ID   -0.083:0.057:0.844664:0.1453:1382:rs3934834
1   1017587 rs3766191   C   T   .   PASS    AF=0.1223   ES:SE:LP:AF:SS:ID   -0.063:0.062:0.508638:0.1223:1382:rs3766191
1   1018562 rs9442371   C   T   .   PASS    AF=0.5992   ES:SE:LP:AF:SS:ID   0.026:0.043:0.267606:0.5992:1382:rs9442371
1   1018704 rs9442372   A   G   .   PASS    AF=0.5992   ES:SE:LP:AF:SS:ID   0.026:0.043:0.267606:0.5992:1382:rs9442372
1   1021346 rs10907177  A   G   .   PASS    AF=0.116    ES:SE:LP:AF:SS:ID   -0.043:0.064:0.29243:0.116:1382:rs10907177
1   1021415 rs3737728   A   G   .   PASS    AF=0.7157   ES:SE:LP:AF:SS:ID   0.001:0.045:0.00877392:0.7157:1382:rs3737728
1   1021583 rs10907178  A   C   .   PASS    AF=0.1158   ES:SE:LP:AF:SS:ID   -0.043:0.064:0.29243:0.1158:1382:rs10907178
1   1021695 rs9442398   A   G   .   PASS    AF=0.7173   ES:SE:LP:AF:SS:ID   0.003:0.045:0.0222764:0.7173:1382:rs9442398
1   1022037 rs6701114   C   T   .   PASS    AF=0.577    ES:SE:LP:AF:SS:ID   0.028:0.042:0.29243:0.577:1382:rs6701114
1   1026707 rs4074137   C   A   .   PASS    AF=0.6037   ES:SE:LP:AF:SS:ID   0.04:0.041:0.481486:0.6037:1382:rs4074137
1   1030565 rs6687776   C   T   .   PASS    AF=0.1593   ES:SE:LP:AF:SS:ID   0.013:0.054:0.09691:0.1593:1382:rs6687776
1   1030633 rs6678318   G   A   .   PASS    AF=0.1593   ES:SE:LP:AF:SS:ID   0.013:0.054:0.09691:0.1593:1382:rs6678318
1   1031540 rs9651273   A   G   .   PASS    AF=0.7284   ES:SE:LP:AF:SS:ID   0.062:0.045:0.769551:0.7284:1382:rs9651273
1   1036959 rs11579015  T   C   .   PASS    AF=0.1021   ES:SE:LP:AF:SS:ID   -0.004:0.067:0.0222764:0.1021:1382:rs11579015
1   1040026 rs6671356   T   C   .   PASS    AF=0.1349   ES:SE:LP:AF:SS:ID   0.001:0.058:0.00877392:0.1349:1382:rs6671356
1   1046164 rs6666280   C   T   .   PASS    AF=0.1355   ES:SE:LP:AF:SS:ID   -0.006:0.058:0.0362122:0.1355:1382:rs6666280
1   1048955 rs4970405   A   G   .   PASS    AF=0.1072   ES:SE:LP:AF:SS:ID   0:0.066:0.00436481:0.1072:1382:rs4970405
1   1049950 rs12726255  A   G   .   PASS    AF=0.1372   ES:SE:LP:AF:SS:ID   0.001:0.057:0.00877392:0.1372:1382:rs12726255
1   1053452 rs4970409   G   A   .   PASS    AF=0.1075   ES:SE:LP:AF:SS:ID   0.003:0.065:0.0177288:0.1075:1382:rs4970409
1   1060174 rs7548798   C   T   .   PASS    AF=0.3125   ES:SE:LP:AF:SS:ID   -0.047:0.043:0.568636:0.3125:1382:rs7548798
1   1060235 rs7540009   G   A   .   PASS    AF=0.02786  ES:SE:LP:AF:SS:ID   -0.033:0.12:0.102373:0.02786:1382:rs7540009
1   1060608 rs17160824  G   A   .   PASS    AF=0.1027   ES:SE:LP:AF:SS:ID   0.048:0.067:0.327902:0.1027:1382:rs17160824
1   1061115 rs17160826  T   C   .   PASS    AF=0.1021   ES:SE:LP:AF:SS:ID   0.05:0.067:0.346787:0.1021:1382:rs17160826
1   1061152 rs12748370  T   C   .   PASS    AF=0.1021   ES:SE:LP:AF:SS:ID   0.05:0.067:0.346787:0.1021:1382:rs12748370
1   1061166 rs11807848  T   C   .   PASS    AF=0.4147   ES:SE:LP:AF:SS:ID   -0.027:0.041:0.283997:0.4147:1382:rs11807848
1   1062015 rs9659914   C   T   .   PASS    AF=0.02642  ES:SE:LP:AF:SS:ID   0.017:0.125:0.05061:0.02642:1382:rs9659914
1   1062638 rs9442373   C   A   .   PASS    AF=0.5409   ES:SE:LP:AF:SS:ID   0.033:0.041:0.376751:0.5409:1382:rs9442373
1   1064535 rs6682475   G   C   .   PASS    AF=0.8132   ES:SE:LP:AF:SS:ID   -0.022:0.051:0.173925:0.8132:1382:rs6682475
1   1064979 rs2298217   C   T   .   PASS    AF=0.1509   ES:SE:LP:AF:SS:ID   0.031:0.055:0.244125:0.1509:1382:rs2298217
1   1077064 rs4970357   C   A   .   PASS    AF=0.93957  ES:SE:LP:AF:SS:ID   -0.107:0.086:0.677781:0.93957:1382:rs4970357
1   1087683 rs9442380   T   C   .   PASS    AF=0.93533  ES:SE:LP:AF:SS:ID   -0.085:0.082:0.522879:0.93533:1382:rs9442380
1   1089262 rs4970358   A   G   .   PASS    AF=0.95481  ES:SE:LP:AF:SS:ID   -0.018:0.099:0.0655015:0.95481:1382:rs4970358
1   1097335 rs9442385   T   G   .   PASS    AF=0.93543  ES:SE:LP:AF:SS:ID   -0.085:0.082:0.522879:0.93543:1382:rs9442385
1   1099342 rs9660710   A   C   .   PASS    AF=0.93543  ES:SE:LP:AF:SS:ID   -0.085:0.082:0.522879:0.93543:1382:rs9660710
1   1100217 rs1891905   C   T   .   PASS    AF=0.95598  ES:SE:LP:AF:SS:ID   -0.096:0.103:0.455932:0.95598:1382:rs1891905
1   1121014 rs3813204   G   A   .   PASS    AF=0.1091   ES:SE:LP:AF:SS:ID   0.02:0.067:0.113509:0.1091:1382:rs3813204
1   1121794 rs11260549  G   A   .   PASS    AF=0.1139   ES:SE:LP:AF:SS:ID   0.043:0.065:0.30103:0.1139:1382:rs11260549
1   1124663 rs6684820   G   A   .   PASS    AF=0.232    ES:SE:LP:AF:SS:ID   0.012:0.049:0.09691:0.232:1382:rs6684820
1   1125553 rs10907174  A   T   .   PASS    AF=0.1904   ES:SE:LP:AF:SS:ID   0.009:0.053:0.0655015:0.1904:1382:rs10907174
1   1129672 rs11260554  G   T   .   PASS    AF=0.1134   ES:SE:LP:AF:SS:ID   0.036:0.065:0.236572:0.1134:1382:rs11260554
1   1130727 rs10907175  A   C   .   PASS    AF=0.08009  ES:SE:LP:AF:SS:ID   0.006:0.076:0.0268721:0.08009:1382:rs10907175
1   1135242 rs9729550   A   C   .   PASS    AF=0.233    ES:SE:LP:AF:SS:ID   0.012:0.049:0.09691:0.233:1382:rs9729550
1   1138913 rs3819001   T   C   .   PASS    AF=0.04252  ES:SE:LP:AF:SS:ID   0.001:0.098:0.00436481:0.04252:1382:rs3819001
1   1140435 rs1815606   G   T   .   PASS    AF=0.2674   ES:SE:LP:AF:SS:ID   0.024:0.047:0.221849:0.2674:1382:rs1815606
1   1143657 rs3753348   C   G   .   PASS    AF=0.04396  ES:SE:LP:AF:SS:ID   0.001:0.096:0.00436481:0.04396:1382:rs3753348
1   1146785 rs2298209   G   C   .   PASS    AF=0.01779  ES:SE:LP:AF:SS:ID   0.066:0.148:0.187087:0.01779:1382:rs2298209
1   1151300 rs3813200   C   T   .   PASS    AF=0.02682  ES:SE:LP:AF:SS:ID   -0.072:0.122:0.259637:0.02682:1382:rs3813200
1   1152631 rs11721 C   A   .   PASS    AF=0.09388  ES:SE:LP:AF:SS:ID   0.077:0.069:0.568636:0.09388:1382:rs11721