IEU GWAS QC Report

name	value
id	ieu-a-1112
pmid	27992413
year	2017
mr	1
note	NULL
trait	Primary sclerosing cholangitis
category	Disease
subcategory	Autoimmune / inflammatory
population	Mixed
sex	Males and females
ncase	2871
ncontrol	12019
sample_size	14890
nsnp	7891603
sd	NULL
priority	1
author	Ji
group_name	public
access	public
build	HG19/GRCh37

name	value
gwas_id	ieu-a-1112
bcf_file	ieu-a-1112.vcf.gz
qc_metrics_file	qc_metrics.json
metadata	metadata.json
refdata	1kg_v3_nomult.bcf
compile_time	2020-05-09 23:35 BST
build_version	run_igd-8f4f4c9-2020-05-09

manhattan_plot

qq_plot

af_plot

pz_plot

beta_std_plot

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}

*********************************************************************
* 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-1112/ieu-a-1112.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-1112/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 08:36:09 2020
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-1112/ieu-a-1112.vcf.gz ...
Read summary statistics for 6288120 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, 760985 SNPs remain.
After merging with regression SNP LD, 760985 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.301 (0.0455)
Lambda GC: 1.0094
Mean Chi^2: 1.0396
Intercept: 0.9452 (0.0078)
Ratio < 0 (usually indicates GC correction).
Analysis finished at Wed Feb  5 08:37:14 2020
Total time elapsed: 1.0m:5.31s

{
    "af_correlation": 0.9422,
    "inflation_factor": 1.0744,
    "mean_EFFECT": -0.002,
    "n": 14890,
    "n_snps": 6288120,
    "n_clumped_hits": 18,
    "n_p_sig": 13857,
    "n_mono": 0,
    "n_ns": 364426,
    "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": 167149,
    "n_est": 14879.1299,
    "ratio_se_n": 0.9996,
    "mean_diff": 0.0018,
    "ratio_diff": 2.9812,
    "sd_y_est1": 2.6357,
    "sd_y_est2": 2.6347,
    "r2_sum1": 1.1019,
    "r2_sum2": 0.1586,
    "r2_sum3": 0.1587,
    "r2_sum4": 0.1464,
    "ldsc_nsnp_merge_refpanel_ld": 760985,
    "ldsc_nsnp_merge_regression_ld": 760985,
    "ldsc_observed_scale_h2_beta": 0.301,
    "ldsc_observed_scale_h2_se": 0.0455,
    "ldsc_intercept_beta": 0.9452,
    "ldsc_intercept_se": 0.0078,
    "ldsc_lambda_gc": 1.0094,
    "ldsc_mean_chisq": 1.0396,
    "ldsc_ratio": -1.3838
}

name	value
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	TRUE
miss_EFFECT	FALSE
miss_SE	FALSE
miss_PVAL	FALSE
ldsc_ratio	FALSE
ldsc_intercept_beta	FALSE
n_clumped_hits	FALSE
r2_sum1	TRUE
r2_sum2	FALSE
r2_sum3	FALSE
r2_sum4	FALSE

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 $\beta_j$

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
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	47	0	6288120	0	NA	NA	NA	NA	NA	NA	NA	NA
character	REF	0	1.0000000	1	49	0	18685	0	NA	NA	NA	NA	NA	NA	NA	NA
character	ALT	0	1.0000000	1	40	0	7851	0	NA	NA	NA	NA	NA	NA	NA	NA
numeric	CHROM	0	1.0000000	NA	NA	NA	NA	NA	8.756854e+00	6.015344e+00	1.00000	4.000000e+00	8.000000e+00	1.300000e+01	2.30000e+01	▇▅▅▂▂
numeric	POS	0	1.0000000	NA	NA	NA	NA	NA	7.798949e+07	5.499881e+07	302.00000	3.244481e+07	6.967919e+07	1.128368e+08	2.49205e+08	▇▆▅▂▁
numeric	EFFECT	0	1.0000000	NA	NA	NA	NA	NA	-1.963700e-03	8.056120e-02	-3.09802	-3.536710e-02	0.000000e+00	3.440140e-02	3.35536e+00	▁▁▇▁▁
numeric	SE	0	1.0000000	NA	NA	NA	NA	NA	6.559130e-02	4.348140e-02	0.02300	3.500000e-02	4.700000e-02	8.200000e-02	7.02000e-01	▇▁▁▁▁
numeric	PVAL	0	1.0000000	NA	NA	NA	NA	NA	4.877571e-01	2.931908e-01	0.00000	2.310766e-01	4.844802e-01	7.420634e-01	1.00000e+00	▇▇▇▇▇
numeric	PVAL_ztest	0	1.0000000	NA	NA	NA	NA	NA	4.977882e-01	2.907681e-01	0.00000	2.461506e-01	4.980163e-01	7.489516e-01	1.00000e+00	▇▇▇▇▇
numeric	AF	0	1.0000000	NA	NA	NA	NA	NA	2.540005e-01	2.642542e-01	0.01000	4.000000e-02	1.500000e-01	4.000000e-01	9.90000e-01	▇▂▂▁▁
numeric	AF_reference	167149	0.9734183	NA	NA	NA	NA	NA	2.538424e-01	2.513709e-01	0.00000	5.051920e-02	1.633390e-01	3.945690e-01	1.00000e+00	▇▃▂▁▁
numeric	N	0	1.0000000	NA	NA	NA	NA	NA	1.489000e+04	0.000000e+00	14890.00000	1.489000e+04	1.489000e+04	1.489000e+04	1.48900e+04	▁▁▇▁▁

CHROM	POS	ID	REF	ALT	EFFECT	SE	PVAL	PVAL_ztest	AF	AF_reference	N
CHROM	POS	ID	REF	ALT	EFFECT	SE	PVAL	PVAL_ztest	AF	AF_reference	N
1	748332	rs182373484	T	C	-0.0732505	0.206	0.6966987	0.7221514	0.01	0.0013978	14890
1	761752	rs1057213	C	T	-0.0227395	0.043	0.5829885	0.5969265	0.86	0.7490020	14890
1	764191	rs7515915	T	G	0.0246926	0.042	0.5561834	0.5565866	0.14	0.2220450	14890
1	769138	rs59306077	CAT	C	0.0266419	0.042	0.5169172	0.5258649	0.14	0.2332270	14890
1	769223	rs60320384	C	G	0.0266419	0.042	0.5158115	0.5258649	0.14	0.1912940	14890
1	771823	rs2977605	T	C	-0.0237165	0.042	0.5586168	0.5722924	0.86	0.7503990	14890
1	772755	rs2905039	A	C	-0.0237165	0.042	0.5625576	0.5722924	0.86	0.7551920	14890
1	775181	rs61768182	A	G	0.0237165	0.042	0.5599058	0.5722924	0.14	0.2272360	14890
1	776556	rs151160018	C	T	-0.1034590	0.182	0.5355845	0.5697253	0.01	0.0015974	14890
1	778745	rs1055606	A	G	0.0276152	0.042	0.5062721	0.5108564	0.14	0.2106630	14890

CHROM	POS	ID	REF	ALT	EFFECT	SE	PVAL	PVAL_ztest	AF	AF_reference	N
CHROM	POS	ID	REF	ALT	EFFECT	SE	PVAL	PVAL_ztest	AF	AF_reference	N
23	154653820	rs181977483	A	G	-0.1980310	0.114	0.0664676	0.0823670	0.02	0.0301987	14890
23	154661750	rs140976899	C	G	0.1124350	0.065	0.0763080	0.0836715	0.03	0.0238411	14890
23	154683663	rs5940510	C	T	0.0079682	0.032	0.7882682	0.8033567	0.74	0.6278150	14890
23	154741935	rs6642272	A	C	0.0639133	0.054	0.2202363	0.2365795	0.76	0.5835760	14890
23	154826774	rs782306	G	A	0.0363319	0.028	0.1826712	0.1944359	0.76	0.6384110	14890
23	154866751	rs191379385	C	T	0.1016540	0.065	0.1069109	0.1178392	0.03	0.0386755	14890
23	154878253	rs141771419	A	G	-0.0898407	0.088	0.2866481	0.3072937	0.02	0.0060927	14890
23	154885405	rs563690	G	A	0.0372958	0.028	0.1718502	0.1828625	0.76	0.6378810	14890
23	154894936	rs148915445	T	C	-0.1914460	0.113	0.0727394	0.0902249	0.02	0.0307285	14890
23	154902105	rs696316	G	T	0.0372958	0.028	0.1719428	0.1828625	0.76	0.6360260	14890

1   748332  rs182373484 T   C   .   PASS    AF=0.01 ES:SE:LP:AF:SS:ID   -0.0732505:0.206:0.156955:0.01:14890:rs182373484
1   761752  rs1057213   C   T   .   PASS    AF=0.86 ES:SE:LP:AF:SS:ID   -0.0227395:0.043:0.23434:0.86:14890:rs1057213
1   764191  rs7515915   T   G   .   PASS    AF=0.14 ES:SE:LP:AF:SS:ID   0.0246926:0.042:0.254782:0.14:14890:rs7515915
1   769138  rs59306077  CAT C   .   PASS    AF=0.14 ES:SE:LP:AF:SS:ID   0.0266419:0.042:0.286579:0.14:14890:rs59306077
1   769223  rs60320384  C   G   .   PASS    AF=0.14 ES:SE:LP:AF:SS:ID   0.0266419:0.042:0.287509:0.14:14890:rs60320384
1   771823  rs2977605   T   C   .   PASS    AF=0.86 ES:SE:LP:AF:SS:ID   -0.0237165:0.042:0.252886:0.86:14890:rs2977605
1   772755  rs2905039   A   C   .   PASS    AF=0.86 ES:SE:LP:AF:SS:ID   -0.0237165:0.042:0.249833:0.86:14890:rs2905039
1   775181  rs61768182  A   G   .   PASS    AF=0.14 ES:SE:LP:AF:SS:ID   0.0237165:0.042:0.251885:0.14:14890:rs61768182
1   776556  rs151160018 C   T   .   PASS    AF=0.01 ES:SE:LP:AF:SS:ID   -0.103459:0.182:0.271172:0.01:14890:rs151160018
1   778745  rs1055606   A   G   .   PASS    AF=0.14 ES:SE:LP:AF:SS:ID   0.0276152:0.042:0.295616:0.14:14890:rs1055606
1   780785  rs2977612   T   A   .   PASS    AF=0.86 ES:SE:LP:AF:SS:ID   -0.0382587:0.049:0.376324:0.86:14890:rs2977612
1   782981  rs6594026   C   T   .   PASS    AF=0.14 ES:SE:LP:AF:SS:ID   0.0353671:0.049:0.332078:0.14:14890:rs6594026
1   783318  rs6686696   A   G   .   PASS    AF=0.14 ES:SE:LP:AF:SS:ID   0.0266419:0.042:0.277918:0.14:14890:rs6686696
1   785050  rs2905062   G   A   .   PASS    AF=0.86 ES:SE:LP:AF:SS:ID   -0.0372958:0.049:0.357233:0.86:14890:rs2905062
1   786995  rs61768202  G   A   .   PASS    AF=0.14 ES:SE:LP:AF:SS:ID   0.0276152:0.042:0.302274:0.14:14890:rs61768202
1   787121  rs12077234  T   A   .   PASS    AF=0.14 ES:SE:LP:AF:SS:ID   0.0421012:0.049:0.418708:0.14:14890:rs12077234
1   787151  rs2519065   G   A   .   PASS    AF=0.14 ES:SE:LP:AF:SS:ID   0.0372958:0.049:0.354208:0.14:14890:rs2519065
1   787606  rs3863622   G   T   .   PASS    AF=0.14 ES:SE:LP:AF:SS:ID   0.0285875:0.042:0.305992:0.14:14890:rs3863622
1   787844  rs2905053   C   T   .   PASS    AF=0.86 ES:SE:LP:AF:SS:ID   -0.0401818:0.049:0.396625:0.86:14890:rs2905053
1   791191  rs111818025 G   A   .   PASS    AF=0.14 ES:SE:LP:AF:SS:ID   -0.0198026:0.085:0.0913778:0.14:14890:rs111818025
1   794332  rs12127425  G   A   .   PASS    AF=0.08 ES:SE:LP:AF:SS:ID   0.0852598:0.064:0.762341:0.08:14890:rs12127425
1   795222  rs12131377  C   G   .   PASS    AF=0.08 ES:SE:LP:AF:SS:ID   0.0760347:0.064:0.650351:0.08:14890:rs12131377
1   796100  rs12132398  C   T   .   PASS    AF=0.08 ES:SE:LP:AF:SS:ID   0.0723207:0.065:0.607311:0.08:14890:rs12132398
1   797281  rs76631953  G   C   .   PASS    AF=0.08 ES:SE:LP:AF:SS:ID   0.07139:0.065:0.59429:0.08:14890:rs76631953
1   797325  rs111739932 T   C   .   PASS    AF=0.08 ES:SE:LP:AF:SS:ID   0.076961:0.064:0.661816:0.08:14890:rs111739932
1   798026  rs4951864   C   T   .   PASS    AF=0.92 ES:SE:LP:AF:SS:ID   -0.0778865:0.064:0.677925:0.92:14890:rs4951864
1   799499  rs147634896 T   C   .   PASS    AF=0.08 ES:SE:LP:AF:SS:ID   0.0741794:0.064:0.63186:0.08:14890:rs147634896
1   801661  rs12132974  C   T   .   PASS    AF=0.08 ES:SE:LP:AF:SS:ID   0.0934903:0.064:0.87534:0.08:14890:rs12132974
1   801680  rs12134490  A   C   .   PASS    AF=0.08 ES:SE:LP:AF:SS:ID   0.0934903:0.064:0.875339:0.08:14890:rs12134490
1   802398  rs111444624 C   T   .   PASS    AF=0.08 ES:SE:LP:AF:SS:ID   0.0778865:0.065:0.667009:0.08:14890:rs111444624
1   802856  rs139867617 C   T   .   PASS    AF=0.08 ES:SE:LP:AF:SS:ID   0.0843411:0.064:0.755688:0.08:14890:rs139867617
1   814870  rs149628520 T   G   .   PASS    AF=0.01 ES:SE:LP:AF:SS:ID   -0.0334348:0.181:0.0742062:0.01:14890:rs149628520
1   832359  rs9697294   C   T   .   PASS    AF=0.02 ES:SE:LP:AF:SS:ID   -0.116894:0.129:0.473484:0.02:14890:rs9697294
1   833223  rs13303211  C   T   .   PASS    AF=0.23 ES:SE:LP:AF:SS:ID   0.0139029:0.04:0.136444:0.23:14890:rs13303211
1   833302  rs28752186  C   T   .   PASS    AF=0.23 ES:SE:LP:AF:SS:ID   0.0109399:0.04:0.109614:0.23:14890:rs28752186
1   833824  rs28484835  T   C   .   PASS    AF=0.23 ES:SE:LP:AF:SS:ID   0.0139029:0.04:0.145004:0.23:14890:rs28484835
1   833927  rs28593608  T   C   .   PASS    AF=0.21 ES:SE:LP:AF:SS:ID   0.0305292:0.042:0.342691:0.21:14890:rs28593608
1   834056  rs28482280  A   C   .   PASS    AF=0.02 ES:SE:LP:AF:SS:ID   -0.131028:0.124:0.579868:0.02:14890:rs28482280
1   834198  rs28385272  T   C   .   PASS    AF=0.21 ES:SE:LP:AF:SS:ID   0.0314987:0.042:0.35907:0.21:14890:rs28385272
1   834263  rs143031236 C   T   .   PASS    AF=0.02 ES:SE:LP:AF:SS:ID   -0.10075:0.13:0.386585:0.02:14890:rs143031236
1   834637  rs34941678  AC  A   .   PASS    AF=0.02 ES:SE:LP:AF:SS:ID   -0.128393:0.124:0.564263:0.02:14890:rs34941678
1   834832  rs4411087   G   C   .   PASS    AF=0.23 ES:SE:LP:AF:SS:ID   0.0129162:0.04:0.134617:0.23:14890:rs4411087
1   834928  rs4422949   A   G   .   PASS    AF=0.21 ES:SE:LP:AF:SS:ID   0.0266419:0.041:0.288483:0.21:14890:rs4422949
1   834956  rs7518581   G   A   .   PASS    AF=0.02 ES:SE:LP:AF:SS:ID   -0.116004:0.125:0.488604:0.02:14890:rs7518581
1   834999  rs28570054  G   A   .   PASS    AF=0.21 ES:SE:LP:AF:SS:ID   0.0266419:0.041:0.285011:0.21:14890:rs28570054
1   836529  rs28731045  C   G   .   PASS    AF=0.21 ES:SE:LP:AF:SS:ID   0.0285875:0.041:0.318259:0.21:14890:rs28731045
1   837553  rs112791300 GGTGT   G   .   PASS    AF=0.02 ES:SE:LP:AF:SS:ID   -0.120446:0.13:0.492798:0.02:14890:rs112791300
1   838329  rs144685080 G   GC  .   PASS    AF=0.21 ES:SE:LP:AF:SS:ID   0.0314987:0.041:0.355331:0.21:14890:rs144685080
1   838387  rs4970384   T   C   .   PASS    AF=0.21 ES:SE:LP:AF:SS:ID   0.0276152:0.041:0.300077:0.21:14890:rs4970384
1   838665  rs28678693  T   C   .   PASS    AF=0.02 ES:SE:LP:AF:SS:ID   -0.107957:0.127:0.436144:0.02:14890:rs28678693

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