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IEU GWAS information

Trait: fatty acid binding protein 4.

name	value
id	PROT-b-71
trait	fatty acid binding protein 4
pmid	28369058
year	2018
author	Folkersen L
population	European
sex	Males and Females
sample_size	3394
build	HG19/GRCh37
group_name	public
access	public
nsnp	5270646
mr	1
category	Immune system
subcategory	Protein
batch	PROT-b

Report information

name	value
gwas_id	prot-b-71
bcf_file	prot-b-71.vcf.gz
qc_metrics_file	qc_metrics.json
metadata	metadata.json
refdata	1kg_v3_nomult.bcf
compile_time	2020-05-09 18:45 BST
build_version	run_igd-8f4f4c9-2020-05-09

Summary

Summary {data-width=650}

Manhattan plot

manhattan_plot

QQ plot

qq_plot

AF plot

af_plot

P-Z plot

pz_plot

beta_std plot

beta_std_plot

Metadata

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    "FORMAT.2": "<ID=LP,Number=A,Type=Float,Description=\"-log10 p-value for effect estimate\">",
    "FORMAT.3": "<ID=AF,Number=A,Type=Float,Description=\"Alternate allele frequency in the association study\">",
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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/folkersen-pqtl-gwas-import/processed/PROT-b-71/PROT-b-71.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/folkersen-pqtl-gwas-import/processed/PROT-b-71/ldsc.txt \
--w-ld-chr /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/reference/eur_w_ld_chr/ 

Beginning analysis at Mon Oct 28 22:10:24 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/folkersen-pqtl-gwas-import/processed/PROT-b-71/PROT-b-71.vcf.gz ...
Read summary statistics for 5135036 SNPs.
Dropped 1 SNPs with duplicated rs numbers.
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, 759193 SNPs remain.
After merging with regression SNP LD, 759193 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.2227 (0.163)
Lambda GC: 1.0122
Mean Chi^2: 1.0142
Intercept: 0.9969 (0.0093)
Ratio < 0 (usually indicates GC correction).
Analysis finished at Mon Oct 28 22:11:13 2019
Total time elapsed: 49.11s

QC metrics

Metrics

{
    "af_correlation": 0.9563,
    "inflation_factor": 0.9981,
    "mean_EFFECT": 0.007,
    "n": "-Inf",
    "n_snps": 5135036,
    "n_clumped_hits": 3,
    "n_p_sig": 137,
    "n_mono": 545,
    "n_ns": 317497,
    "n_mac": 0,
    "is_snpid_unique": false,
    "n_miss_EFFECT": 0,
    "n_miss_SE": 0,
    "n_miss_PVAL": 0,
    "n_miss_AF": 0,
    "n_miss_AF_reference": 377170,
    "n_est": "NA",
    "ratio_se_n": "NA",
    "mean_diff": "NaN",
    "ratio_diff": "NaN",
    "sd_y_est1": "NaN",
    "sd_y_est2": "NA",
    "r2_sum1": 0,
    "r2_sum2": 0,
    "r2_sum3": 0,
    "r2_sum4": 0,
    "ldsc_nsnp_merge_refpanel_ld": 759193,
    "ldsc_nsnp_merge_regression_ld": 759193,
    "ldsc_observed_scale_h2_beta": 0.2227,
    "ldsc_observed_scale_h2_se": 0.163,
    "ldsc_intercept_beta": 0.9969,
    "ldsc_intercept_se": 0.0093,
    "ldsc_lambda_gc": 1.0122,
    "ldsc_mean_chisq": 1.0142,
    "ldsc_ratio": -0.2183
}

Flags

name	value
af_correlation	FALSE
inflation_factor	FALSE
n	TRUE
is_snpid_non_unique	TRUE
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	logical.mean	logical.count	numeric.mean	numeric.sd	numeric.p0	numeric.p25	numeric.p50	numeric.p75	numeric.p100	numeric.hist
character	ID	0	1.0000000	3	58	0	5135032	0	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA
character	REF	0	1.0000000	1	3	0	80	0	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA
character	ALT	0	1.0000000	1	3	0	80	0	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA
logical	N	5135036	0.0000000	NA	NA	NA	NA	NA	NaN	:	NA	NA	NA	NA	NA	NA	NA	NA
numeric	CHROM	0	1.0000000	NA	NA	NA	NA	NA	NA	NA	8.356760e+00	5.629048e+00	1.0000	3.000000e+00	7.000000e+00	1.200000e+01	2.200000e+01	▇▅▃▂▂
numeric	POS	0	1.0000000	NA	NA	NA	NA	NA	NA	NA	7.977423e+07	5.495317e+07	29422.0000	3.532730e+07	7.050636e+07	1.143548e+08	2.492183e+08	▇▇▅▂▁
numeric	EFFECT	0	1.0000000	NA	NA	NA	NA	NA	NA	NA	6.991500e-03	2.662899e-01	-8.0421	-3.660000e-02	4.000000e-04	3.750000e-02	2.034390e+01	▁▇▁▁▁
numeric	SE	0	1.0000000	NA	NA	NA	NA	NA	NA	NA	1.325986e-01	2.390849e-01	0.0233	3.380000e-02	4.740000e-02	1.082000e-01	3.316800e+00	▇▁▁▁▁
numeric	PVAL	0	1.0000000	NA	NA	NA	NA	NA	NA	NA	4.996583e-01	2.891165e-01	0.0000	2.487001e-01	5.003997e-01	7.498994e-01	1.000000e+00	▇▇▇▇▇
numeric	PVAL_ztest	0	1.0000000	NA	NA	NA	NA	NA	NA	NA	4.994963e-01	2.892150e-01	0.0000	2.484680e-01	5.002409e-01	7.498474e-01	1.000000e+00	▇▇▇▇▇
numeric	AF	0	1.0000000	NA	NA	NA	NA	NA	NA	NA	2.781589e-01	2.817943e-01	0.0000	3.560000e-02	1.762000e-01	4.617000e-01	1.000000e+00	▇▃▂▂▁
numeric	AF_reference	377170	0.9265497	NA	NA	NA	NA	NA	NA	NA	2.522964e-01	2.538675e-01	0.0000	3.654150e-02	1.659350e-01	4.039540e-01	1.000000e+00	▇▃▂▁▁

Head and tail

CHROM	POS	ID	REF	ALT	EFFECT	SE	PVAL	PVAL_ztest	AF	AF_reference	N
1	780785	rs2977612	T	A	0.0401	0.0464	0.3870998	0.3874648	0.8252	0.669329	NA
1	782981	rs6594026	C	T	-0.0396	0.0457	0.3870000	0.3862046	0.1534	0.297923	NA
1	783318	rs6686696	A	G	-0.0620	0.0717	0.3870998	0.3871957	0.0799	0.183107	NA
1	785050	rs2905062	G	A	0.0294	0.0340	0.3870998	0.3872002	0.8365	0.626997	NA
1	785989	rs2980300	T	C	0.0326	0.0377	0.3870998	0.3871917	0.8083	0.626997	NA
1	787121	rs12077234	T	A	-0.0516	0.0596	0.3870000	0.3866153	0.1319	NA	NA
1	787399	rs2905055	G	T	0.0399	0.0461	0.3870000	0.3867591	0.8001	0.646366	NA
1	787685	rs2905054	G	T	0.0382	0.0441	0.3871997	0.3863733	0.7668	0.622204	NA
1	787844	rs2905053	C	T	0.0415	0.0479	0.3870000	0.3862773	0.8114	0.651757	NA
1	790758	1_790758_GTA_G	G	GTA	0.0441	0.0509	0.3870000	0.3862683	0.7799	NA	NA

CHROM	POS	ID	REF	ALT	EFFECT	SE	PVAL	PVAL_ztest	AF	AF_reference	N
22	51163039	rs715584	G	T	-0.0113	0.0301	0.7079001	0.7073516	0.4131	0.4736420	NA
22	51163138	rs715586	C	T	0.0089	0.0361	0.8045999	0.8052663	0.1273	0.0902556	NA
22	51163910	rs192700691	C	T	-0.0464	0.1073	0.6657007	0.6654272	0.0304	0.0295527	NA
22	51164109	rs5770995	G	C	-0.0132	0.0283	0.6410000	0.6409070	0.4411	0.5109820	NA
22	51164115	rs5770996	C	T	-0.0128	0.0284	0.6514994	0.6522027	0.4446	0.5147760	NA
22	51164287	rs6009957	T	C	-0.0154	0.0273	0.5737002	0.5726843	0.3052	0.4155350	NA
22	51165664	rs8137951	G	A	-0.0147	0.0266	0.5815004	0.5805157	0.2954	0.4063500	NA
22	51171693	rs756638	G	A	0.0479	0.0387	0.2154001	0.2158176	0.3046	0.3049120	NA
22	51175626	rs3810648	A	G	-0.0176	0.0603	0.7706000	0.7703830	0.0735	0.1084270	NA
22	51178090	rs2285395	G	A	-0.0168	0.0572	0.7695999	0.7689823	0.0481	0.0666933	NA

bcf preview

1   780785  rs2977612   T   A   .   PASS    AF=0.8252   ES:SE:LP:AF:ID  0.0401:0.0464:0.412177:0.8252:rs2977612
1   782981  rs6594026   C   T   .   PASS    AF=0.1534   ES:SE:LP:AF:ID  -0.0396:0.0457:0.412289:0.1534:rs6594026
1   783318  rs6686696   A   G   .   PASS    AF=0.0799   ES:SE:LP:AF:ID  -0.062:0.0717:0.412177:0.0799:rs6686696
1   785050  rs2905062   G   A   .   PASS    AF=0.8365   ES:SE:LP:AF:ID  0.0294:0.034:0.412177:0.8365:rs2905062
1   785989  rs2980300   T   C   .   PASS    AF=0.8083   ES:SE:LP:AF:ID  0.0326:0.0377:0.412177:0.8083:rs2980300
1   787121  rs12077234  T   A   .   PASS    AF=0.1319   ES:SE:LP:AF:ID  -0.0516:0.0596:0.412289:0.1319:rs12077234
1   787399  rs2905055   G   T   .   PASS    AF=0.8001   ES:SE:LP:AF:ID  0.0399:0.0461:0.412289:0.8001:rs2905055
1   787685  rs2905054   G   T   .   PASS    AF=0.7668   ES:SE:LP:AF:ID  0.0382:0.0441:0.412065:0.7668:rs2905054
1   787844  rs2905053   C   T   .   PASS    AF=0.8114   ES:SE:LP:AF:ID  0.0415:0.0479:0.412289:0.8114:rs2905053
1   790758  1_790758_GTA_G  G   GTA .   PASS    AF=0.7799   ES:SE:LP:AF:ID  0.0441:0.0509:0.412289:0.7799:1_790758_GTA_G
1   1108637 rs4970421   G   A   .   PASS    AF=0.0713   ES:SE:LP:AF:ID  -0.0514:0.0757:0.303644:0.0713:rs4970421
1   1112982 rs6671609   C   T   .   PASS    AF=0.1436   ES:SE:LP:AF:ID  -0.0209:0.0601:0.137809:0.1436:rs6671609
1   1115994 rs13376597  G   A   .   PASS    AF=0.1429   ES:SE:LP:AF:ID  -0.0203:0.0581:0.138824:0.1429:rs13376597
1   1116231 rs13374146  T   C   .   PASS    AF=0.0678   ES:SE:LP:AF:ID  -0.0444:0.0612:0.32929:0.0678:rs13374146
1   1117398 rs12097586  A   G   .   PASS    AF=0.4246   ES:SE:LP:AF:ID  0.0347:0.0437:0.36947:0.4246:rs12097586
1   1117486 rs13376670  A   G   .   PASS    AF=0.1481   ES:SE:LP:AF:ID  -0.0176:0.0571:0.120503:0.1481:rs13376670
1   1118275 rs61733845  C   T   .   PASS    AF=0.05 ES:SE:LP:AF:ID  -0.0492:0.0576:0.405386:0.05:rs61733845
1   1118578 rs111290899 G   A   .   PASS    AF=0.0504   ES:SE:LP:AF:ID  -0.0504:0.0588:0.407379:0.0504:rs111290899
1   1119657 rs4560982   G   C   .   PASS    AF=0.4012   ES:SE:LP:AF:ID  0.0434:0.0392:0.572189:0.4012:rs4560982
1   1119858 rs1320565   C   T   .   PASS    AF=0.1126   ES:SE:LP:AF:ID  0.0131:0.0603:0.0819697:0.1126:rs1320565
1   1120431 rs1320571   G   A   .   PASS    AF=0.0525   ES:SE:LP:AF:ID  0.0454:0.0551:0.387428:0.0525:rs1320571
1   1121014 rs3813204   G   A   .   PASS    AF=0.1364   ES:SE:LP:AF:ID  0.0671:0.057:0.621239:0.1364:rs3813204
1   1121341 rs4297230   C   T   .   PASS    AF=0.1422   ES:SE:LP:AF:ID  0.0636:0.0557:0.59568:0.1422:rs4297230
1   1121358 rs80057011  A   C   .   PASS    AF=0.0928   ES:SE:LP:AF:ID  0.0413:0.0656:0.276626:0.0928:rs80057011
1   1121480 rs12063663  T   C   .   PASS    AF=0.0923   ES:SE:LP:AF:ID  0.0375:0.0654:0.246494:0.0923:rs12063663
1   1121625 rs4081334   C   G   .   PASS    AF=0.1418   ES:SE:LP:AF:ID  0.0631:0.0552:0.597567:0.1418:rs4081334
1   1121657 rs11260548  T   C   .   PASS    AF=0.2302   ES:SE:LP:AF:ID  0.0412:0.0371:0.572514:0.2302:rs11260548
1   1121715 rs4081333   C   T   .   PASS    AF=0.0882   ES:SE:LP:AF:ID  0.0355:0.0643:0.235525:0.0882:rs4081333
1   1121794 rs11260549  G   A   .   PASS    AF=0.1326   ES:SE:LP:AF:ID  0.0648:0.055:0.622148:0.1326:rs11260549
1   1121835 rs57346441  C   CTG .   PASS    AF=0.2304   ES:SE:LP:AF:ID  0.0402:0.0363:0.571217:0.2304:1_1121835_C_CTG
1   1122024 rs4314833   T   C   .   PASS    AF=0.1279   ES:SE:LP:AF:ID  0.0682:0.056:0.650722:0.1279:rs4314833
1   1122196 rs4634847   A   G   .   PASS    AF=0.1342   ES:SE:LP:AF:ID  0.0652:0.0547:0.631341:0.1342:rs4634847
1   1122283 rs12064046  T   G   .   PASS    AF=0.0862   ES:SE:LP:AF:ID  0.0343:0.0638:0.228192:0.0862:rs12064046
1   1122319 rs7415847   C   T   .   PASS    AF=0.1199   ES:SE:LP:AF:ID  0.0733:0.0598:0.656591:0.1199:rs7415847
1   1122468 rs7545694   T   C   .   PASS    AF=0.2031   ES:SE:LP:AF:ID  0.0452:0.04:0.589054:0.2031:rs7545694
1   1122516 rs11260551  G   A   .   PASS    AF=0.1274   ES:SE:LP:AF:ID  0.0673:0.0558:0.641114:0.1274:rs11260551
1   1122539 rs12063897  A   G   .   PASS    AF=0.0866   ES:SE:LP:AF:ID  0.035:0.063:0.237697:0.0866:rs12063897
1   1122915 rs28595293  A   G   .   PASS    AF=0.2718   ES:SE:LP:AF:ID  0.0413:0.032:0.707744:0.2718:rs28595293
1   1122916 rs28460227  A   G   .   PASS    AF=0.0856   ES:SE:LP:AF:ID  0.0343:0.0631:0.231066:0.0856:rs28460227
1   1122937 rs28648687  G   A   .   PASS    AF=0.0856   ES:SE:LP:AF:ID  0.0344:0.0631:0.231806:0.0856:rs28648687
1   1123106 rs12401472  G   A   .   PASS    AF=0.128    ES:SE:LP:AF:ID  0.0669:0.0554:0.643592:0.128:rs12401472
1   1123434 rs12066716  T   A   .   PASS    AF=0.1323   ES:SE:LP:AF:ID  0.0507:0.0537:0.462055:0.1323:rs12066716
1   1124257 rs10907172  A   G   .   PASS    AF=0.1273   ES:SE:LP:AF:ID  0.0666:0.0552:0.643592:0.1273:rs10907172
1   1124399 rs10907173  C   G   .   PASS    AF=0.1324   ES:SE:LP:AF:ID  0.0639:0.054:0.626353:0.1324:rs10907173
1   1124663 rs6684820   G   A   .   PASS    AF=0.2737   ES:SE:LP:AF:ID  0.0404:0.0313:0.705754:0.2737:rs6684820
1   1124819 rs6694487   C   T   .   PASS    AF=0.0867   ES:SE:LP:AF:ID  0.0344:0.0625:0.235525:0.0867:rs6694487
1   1124891 rs61768485  G   A   .   PASS    AF=0.1266   ES:SE:LP:AF:ID  0.0665:0.055:0.644166:0.1266:rs61768485
1   1125110 rs12124436  T   C   .   PASS    AF=0.1248   ES:SE:LP:AF:ID  0.0656:0.0547:0.636952:0.1248:rs12124436
1   1125220 rs12065129  C   T   .   PASS    AF=0.0864   ES:SE:LP:AF:ID  0.0341:0.0619:0.235002:0.0864:rs12065129
1   1125348 rs12029885  T   C   .   PASS    AF=0.1261   ES:SE:LP:AF:ID  0.0664:0.0552:0.640354:0.1261:rs12029885