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IEU GWAS information

Trait: Years of schooling.

name	value
id	ieu-a-1001
pmid	27225129
year	2016
mr	1
note	NULL
trait	Years of schooling
category	Risk factor
subcategory	Education
population	European
sex	Males and females
ncase	NULL
ncontrol	NULL
sample_size	293723
nsnp	8146841
sd	3.71
priority	1
author	Okbay
group_name	public
access	public
build	HG19/GRCh37

Report information

name	value
gwas_id	ieu-a-1001
bcf_file	ieu-a-1001.vcf.gz
qc_metrics_file	qc_metrics.json
metadata	metadata.json
refdata	1kg_v3_nomult.bcf
compile_time	2020-05-10 12:14 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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}

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-1001/ieu-a-1001.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-1001/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 09:21:18 2020
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-1001/ieu-a-1001.vcf.gz ...
Read summary statistics for 8018495 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, 1282601 SNPs remain.
After merging with regression SNP LD, 1282601 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.127 (0.0041)
Lambda GC: 1.2365
Mean Chi^2: 1.6581
Intercept: 0.9282 (0.0086)
Ratio < 0 (usually indicates GC correction).
Analysis finished at Wed Feb  5 09:22:40 2020
Total time elapsed: 1.0m:22.23s

QC metrics

Metrics

{
    "af_correlation": 0.9404,
    "inflation_factor": 1.3537,
    "mean_EFFECT": -0,
    "n": 293723,
    "n_snps": 8018495,
    "n_clumped_hits": 73,
    "n_p_sig": 4961,
    "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": 111882,
    "n_est": 284551.0968,
    "ratio_se_n": 0.9843,
    "mean_diff": 2.117e-06,
    "ratio_diff": 1.4495,
    "sd_y_est1": 1.0331,
    "sd_y_est2": 1.0168,
    "r2_sum1": 0.0094,
    "r2_sum2": 0.0088,
    "r2_sum3": 0.0091,
    "r2_sum4": 0.0095,
    "ldsc_nsnp_merge_refpanel_ld": 1282601,
    "ldsc_nsnp_merge_regression_ld": 1282601,
    "ldsc_observed_scale_h2_beta": 0.127,
    "ldsc_observed_scale_h2_se": 0.0041,
    "ldsc_intercept_beta": 0.9282,
    "ldsc_intercept_se": 0.0086,
    "ldsc_lambda_gc": 1.2365,
    "ldsc_mean_chisq": 1.6581,
    "ldsc_ratio": -0.1091
}

Flags

name	value
af_correlation	FALSE
inflation_factor	TRUE
n	FALSE
is_snpid_non_unique	FALSE
mean_EFFECT_nonfinite	FALSE
mean_EFFECT_05	FALSE
mean_EFFECT_01	FALSE
mean_chisq	TRUE
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	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	1.000000	3	58	0	8018494	0	NA	NA	NA	NA	NA	NA	NA	NA
character	REF	0	1.000000	1	1	0	4	0	NA	NA	NA	NA	NA	NA	NA	NA
character	ALT	0	1.000000	1	1	0	4	0	NA	NA	NA	NA	NA	NA	NA	NA
numeric	CHROM	0	1.000000	NA	NA	NA	NA	NA	8.676981e+00	5.774335e+00	1.00000	4.000000e+00	8.000000e+00	1.300000e+01	2.300000e+01	▇▅▅▂▂
numeric	POS	0	1.000000	NA	NA	NA	NA	NA	7.877419e+07	5.651374e+07	828.00000	3.230283e+07	6.933748e+07	1.146926e+08	2.492297e+08	▇▆▅▂▁
numeric	EFFECT	0	1.000000	NA	NA	NA	NA	NA	-3.970000e-05	6.968900e-03	-0.10600	-3.000000e-03	0.000000e+00	3.000000e-03	1.180000e-01	▁▁▇▁▁
numeric	SE	0	1.000000	NA	NA	NA	NA	NA	5.407700e-03	3.810800e-03	0.00200	3.000000e-03	4.000000e-03	7.000000e-03	4.400000e-02	▇▁▁▁▁
numeric	PVAL	0	1.000000	NA	NA	NA	NA	NA	4.506842e-01	3.023239e-01	0.00000	1.766001e-01	4.326005e-01	7.124001e-01	1.000000e+00	▇▆▅▅▅
numeric	PVAL_ztest	0	1.000000	NA	NA	NA	NA	NA	4.564407e-01	3.084625e-01	0.00000	1.824224e-01	4.532547e-01	7.388827e-01	1.000000e+00	▇▅▅▆▅
numeric	AF	0	1.000000	NA	NA	NA	NA	NA	2.560224e-01	2.600529e-01	0.01119	4.291000e-02	1.530000e-01	4.049000e-01	9.888100e-01	▇▂▂▁▁
numeric	AF_reference	111882	0.986047	NA	NA	NA	NA	NA	2.567407e-01	2.533053e-01	0.00000	4.792330e-02	1.677320e-01	4.027560e-01	1.000000e+00	▇▃▂▁▁
numeric	N	0	1.000000	NA	NA	NA	NA	NA	2.937230e+05	0.000000e+00	293723.00000	2.937230e+05	2.937230e+05	2.937230e+05	2.937230e+05	▁▁▇▁▁

Head and tail

CHROM	POS	ID	REF	ALT	EFFECT	SE	PVAL	PVAL_ztest	AF	AF_reference	N
1	662622	rs61769339	G	A	0.009	0.007	0.1693998	0.1985428	0.09515	0.1475640	293723
1	714019	rs114983708	A	G	0.010	0.012	0.4058000	0.4046568	0.04664	0.1383790	293723
1	715265	rs12184267	C	T	0.009	0.011	0.4320003	0.4132534	0.05037	0.0275559	293723
1	715367	rs12184277	A	G	0.010	0.012	0.3984997	0.4046568	0.04664	0.0281550	293723
1	717587	rs144155419	G	A	-0.014	0.015	0.3386998	0.3506479	0.01119	0.0045926	293723
1	719914	rs187772768	C	G	0.007	0.011	0.4995006	0.5245394	0.04851	0.0277556	293723
1	720381	rs116801199	G	T	0.010	0.011	0.3915002	0.3633021	0.04291	0.0359425	293723
1	721290	rs12565286	G	C	0.010	0.011	0.3692003	0.3633021	0.04664	0.0371406	293723
1	721757	rs189147642	T	A	0.008	0.011	0.4838002	0.4670589	0.04851	0.0281550	293723
1	723307	rs28659788	C	G	0.011	0.011	0.3310999	0.3173105	0.04104	0.0357428	293723

CHROM	POS	ID	REF	ALT	EFFECT	SE	PVAL	PVAL_ztest	AF	AF_reference	N
22	51219704	rs147475742	G	A	-0.018	0.010	0.0807793	0.0718606	0.04851	0.0473243	293723
22	51221731	rs115055839	T	C	-0.010	0.008	0.2013998	0.2112995	0.07836	0.0625000	293723
22	51222052	rs2879915	G	A	0.003	0.004	0.5002994	0.4532547	0.21640	0.2194490	293723
22	51224600	rs187908482	G	A	0.003	0.007	0.7006998	0.6682351	0.09515	0.0387380	293723
22	51227891	rs6010091	G	A	-0.002	0.004	0.6274007	0.6170751	0.34700	0.4039540	293723
22	51229805	rs9616985	T	C	-0.009	0.008	0.2424002	0.2605890	0.07836	0.0730831	293723
22	51229855	rs144549712	G	A	-0.004	0.006	0.5392995	0.5049851	0.13250	0.1160140	293723
22	51234799	rs191117135	G	A	-0.017	0.017	0.3298998	0.3173105	0.01119	0.0059904	293723
22	51237063	rs3896457	T	C	0.003	0.004	0.5543002	0.4532547	0.23320	0.2050720	293723
23	100784211	rs188350543	C	A	0.002	0.003	0.5462004	0.5049851	0.72200	0.6498010	293723

bcf preview

1   662622  rs61769339  G   A   .   PASS    AF=0.09515  ES:SE:LP:AF:SS:ID   0.009:0.007:0.771087:0.09515:293723:rs61769339
1   714019  rs114983708 A   G   .   PASS    AF=0.04664  ES:SE:LP:AF:SS:ID   0.01:0.012:0.391688:0.04664:293723:rs114983708
1   715265  rs12184267  C   T   .   PASS    AF=0.05037  ES:SE:LP:AF:SS:ID   0.009:0.011:0.364516:0.05037:293723:rs12184267
1   715367  rs12184277  A   G   .   PASS    AF=0.04664  ES:SE:LP:AF:SS:ID   0.01:0.012:0.399572:0.04664:293723:rs12184277
1   717587  rs144155419 G   A   .   PASS    AF=0.01119  ES:SE:LP:AF:SS:ID   -0.014:0.015:0.470185:0.01119:293723:rs144155419
1   719914  rs187772768 C   G   .   PASS    AF=0.04851  ES:SE:LP:AF:SS:ID   0.007:0.011:0.301464:0.04851:293723:rs187772768
1   720381  rs116801199 G   T   .   PASS    AF=0.04291  ES:SE:LP:AF:SS:ID   0.01:0.011:0.407268:0.04291:293723:rs116801199
1   721290  rs12565286  G   C   .   PASS    AF=0.04664  ES:SE:LP:AF:SS:ID   0.01:0.011:0.432738:0.04664:293723:rs12565286
1   721757  rs189147642 T   A   .   PASS    AF=0.04851  ES:SE:LP:AF:SS:ID   0.008:0.011:0.315334:0.04851:293723:rs189147642
1   723307  rs28659788  C   G   .   PASS    AF=0.04104  ES:SE:LP:AF:SS:ID   0.011:0.011:0.480041:0.04104:293723:rs28659788
1   723742  rs28375378  T   C   .   PASS    AF=0.03918  ES:SE:LP:AF:SS:ID   0.01:0.011:0.450997:0.03918:293723:rs28375378
1   723819  rs11804171  T   A   .   PASS    AF=0.04851  ES:SE:LP:AF:SS:ID   0.006:0.011:0.242073:0.04851:293723:rs11804171
1   723891  rs2977670   G   C   .   PASS    AF=0.9459   ES:SE:LP:AF:SS:ID   -0.002:0.011:0.0799811:0.9459:293723:rs2977670
1   726794  rs28454925  C   G   .   PASS    AF=0.04851  ES:SE:LP:AF:SS:ID   0.014:0.011:0.664743:0.04851:293723:rs28454925
1   727841  rs116587930 G   A   .   PASS    AF=0.06157  ES:SE:LP:AF:SS:ID   0.008:0.009:0.414314:0.06157:293723:rs116587930
1   729632  rs116720794 C   T   .   PASS    AF=0.05037  ES:SE:LP:AF:SS:ID   0.007:0.012:0.287182:0.05037:293723:rs116720794
1   729679  rs4951859   C   G   .   PASS    AF=0.8489   ES:SE:LP:AF:SS:ID   -0.006:0.005:0.623788:0.8489:293723:rs4951859
1   730087  rs148120343 T   C   .   PASS    AF=0.06157  ES:SE:LP:AF:SS:ID   0.009:0.009:0.489723:0.06157:293723:rs148120343
1   734349  rs141242758 T   C   .   PASS    AF=0.1045   ES:SE:LP:AF:SS:ID   0.007:0.006:0.631899:0.1045:293723:rs141242758
1   735985  rs12405651  G   A   .   PASS    AF=0.03358  ES:SE:LP:AF:SS:ID   0.011:0.012:0.463442:0.03358:293723:rs12405651
1   736289  rs79010578  T   A   .   PASS    AF=0.1269   ES:SE:LP:AF:SS:ID   0.01:0.005:1.18303:0.1269:293723:rs79010578
1   736736  rs10454457  A   G   .   PASS    AF=0.03918  ES:SE:LP:AF:SS:ID   0.005:0.011:0.199489:0.03918:293723:rs10454457
1   739528  rs3094317   G   A   .   PASS    AF=0.91791  ES:SE:LP:AF:SS:ID   -0.007:0.012:0.280503:0.91791:293723:rs3094317
1   740285  rs193160839 G   A   .   PASS    AF=0.04291  ES:SE:LP:AF:SS:ID   0.006:0.012:0.199902:0.04291:293723:rs193160839
1   746727  rs144595511 G   A   .   PASS    AF=0.04478  ES:SE:LP:AF:SS:ID   0.009:0.011:0.365019:0.04478:293723:rs144595511
1   748141  rs2427893   G   A   .   PASS    AF=0.01679  ES:SE:LP:AF:SS:ID   0.007:0.01:0.283746:0.01679:293723:rs2427893
1   752478  rs146277091 G   A   .   PASS    AF=0.04104  ES:SE:LP:AF:SS:ID   0.005:0.011:0.200659:0.04104:293723:rs146277091
1   752566  rs3094315   G   A   .   PASS    AF=0.8451   ES:SE:LP:AF:SS:ID   0:0.004:0.0290491:0.8451:293723:rs3094315
1   752617  rs149886465 C   A   .   PASS    AF=0.04478  ES:SE:LP:AF:SS:ID   0.008:0.011:0.349887:0.04478:293723:rs149886465
1   752721  rs3131972   A   G   .   PASS    AF=0.8414   ES:SE:LP:AF:SS:ID   -0.001:0.004:0.10007:0.8414:293723:rs3131972
1   752894  rs3131971   T   C   .   PASS    AF=0.8228   ES:SE:LP:AF:SS:ID   -0.003:0.005:0.301986:0.8228:293723:rs3131971
1   753474  rs2073814   C   G   .   PASS    AF=0.8358   ES:SE:LP:AF:SS:ID   -0.001:0.004:0.056456:0.8358:293723:rs2073814
1   753541  rs2073813   G   A   .   PASS    AF=0.1213   ES:SE:LP:AF:SS:ID   0:0.005:0.0298857:0.1213:293723:rs2073813
1   754063  rs12184312  G   T   .   PASS    AF=0.05037  ES:SE:LP:AF:SS:ID   0.007:0.011:0.279427:0.05037:293723:rs12184312
1   754105  rs12184325  C   T   .   PASS    AF=0.05037  ES:SE:LP:AF:SS:ID   0.006:0.01:0.272296:0.05037:293723:rs12184325
1   754182  rs3131969   A   G   .   PASS    AF=0.8787   ES:SE:LP:AF:SS:ID   0:0.005:0.00541892:0.8787:293723:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.8787   ES:SE:LP:AF:SS:ID   0:0.005:0.00432094:0.8787:293723:rs3131968
1   754211  rs12184313  G   A   .   PASS    AF=0.05037  ES:SE:LP:AF:SS:ID   0.004:0.012:0.152181:0.05037:293723:rs12184313
1   754334  rs3131967   T   C   .   PASS    AF=0.8638   ES:SE:LP:AF:SS:ID   -0.002:0.005:0.136083:0.8638:293723:rs3131967
1   754503  rs3115859   G   A   .   PASS    AF=0.8414   ES:SE:LP:AF:SS:ID   -0.001:0.004:0.0638886:0.8414:293723:rs3115859
1   754629  rs10454459  A   G   .   PASS    AF=0.05037  ES:SE:LP:AF:SS:ID   0.008:0.011:0.332921:0.05037:293723:rs10454459
1   754964  rs3131966   C   T   .   PASS    AF=0.8302   ES:SE:LP:AF:SS:ID   -0.002:0.005:0.233215:0.8302:293723:rs3131966
1   755240  rs181660517 T   G   .   PASS    AF=0.01119  ES:SE:LP:AF:SS:ID   -0.004:0.017:0.0966387:0.01119:293723:rs181660517
1   755890  rs3115858   A   T   .   PASS    AF=0.8713   ES:SE:LP:AF:SS:ID   -0.002:0.005:0.1897:0.8713:293723:rs3115858
1   756604  rs3131962   A   G   .   PASS    AF=0.8451   ES:SE:LP:AF:SS:ID   -0.001:0.005:0.0429197:0.8451:293723:rs3131962
1   756912  rs6699990   A   G   .   PASS    AF=0.02612  ES:SE:LP:AF:SS:ID   -0.017:0.011:0.888066:0.02612:293723:rs6699990
1   757640  rs3115853   G   A   .   PASS    AF=0.8787   ES:SE:LP:AF:SS:ID   0:0.005:0.0169604:0.8787:293723:rs3115853
1   757734  rs4951929   C   T   .   PASS    AF=0.8787   ES:SE:LP:AF:SS:ID   0:0.005:0.0184079:0.8787:293723:rs4951929
1   757936  rs4951862   C   A   .   PASS    AF=0.8769   ES:SE:LP:AF:SS:ID   0:0.005:0.0268259:0.8769:293723:rs4951862
1   758144  rs3131956   A   G   .   PASS    AF=0.8489   ES:SE:LP:AF:SS:ID   0:0.005:0.0151128:0.8489:293723:rs3131956