IEU GWAS QC Report

name	value
id	ieu-a-1007
pmid	27089181
year	2016
mr	1
note	NULL
trait	Neuroticism
category	Risk factor
subcategory	Personality
population	European
sex	Males and females
ncase	NULL
ncontrol	NULL
sample_size	170911
nsnp	6524433
sd	NULL
priority	1
author	Okbay
group_name	public
access	public
build	HG19/GRCh37

name	value
gwas_id	ieu-a-1007
bcf_file	ieu-a-1007.vcf.gz
qc_metrics_file	qc_metrics.json
metadata	metadata.json
refdata	1kg_v3_nomult.bcf
compile_time	2020-05-10 11:21 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-1007/ieu-a-1007.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-1007/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 08:24:05 2020
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-1007/ieu-a-1007.vcf.gz ...
Read summary statistics for 6412174 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, 1223918 SNPs remain.
After merging with regression SNP LD, 1223918 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0905 (0.0069)
Lambda GC: 1.2365
Mean Chi^2: 1.3137
Intercept: 0.9902 (0.0101)
Ratio < 0 (usually indicates GC correction).
Analysis finished at Wed Feb  5 08:25:13 2020
Total time elapsed: 1.0m:8.11s

{
    "af_correlation": 0.9262,
    "inflation_factor": 1.222,
    "mean_EFFECT": 0,
    "n": 170911,
    "n_snps": 6412174,
    "n_clumped_hits": 10,
    "n_p_sig": 2188,
    "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": 39877,
    "n_est": 229818.8392,
    "ratio_se_n": 1.1596,
    "mean_diff": -7.7331e-07,
    "ratio_diff": 1.1251,
    "sd_y_est1": 0.9075,
    "sd_y_est2": 1.0523,
    "r2_sum1": 0.0023,
    "r2_sum2": 0.0028,
    "r2_sum3": 0.0021,
    "r2_sum4": 0.0022,
    "ldsc_nsnp_merge_refpanel_ld": 1223918,
    "ldsc_nsnp_merge_regression_ld": 1223918,
    "ldsc_observed_scale_h2_beta": 0.0905,
    "ldsc_observed_scale_h2_se": 0.0069,
    "ldsc_intercept_beta": 0.9902,
    "ldsc_intercept_se": 0.0101,
    "ldsc_lambda_gc": 1.2365,
    "ldsc_mean_chisq": 1.3137,
    "ldsc_ratio": -0.0312
}

name	value
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

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	1.000000	3	57	0	6412174	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	8.697242e+00	5.777413e+00	1.00000e+00	4.000000e+00	8.000000e+00	1.300000e+01	2.300000e+01	▇▅▅▂▂
numeric	POS	0	1.000000	NA	NA	NA	NA	NA	7.860856e+07	5.661204e+07	8.28000e+02	3.198241e+07	6.909664e+07	1.146070e+08	2.492205e+08	▇▆▅▂▁
numeric	EFFECT	0	1.000000	NA	NA	NA	NA	NA	2.940000e-05	6.514800e-03	-6.30000e-02	-4.000000e-03	0.000000e+00	4.000000e-03	8.500000e-02	▁▃▇▁▁
numeric	SE	0	1.000000	NA	NA	NA	NA	NA	5.480600e-03	2.431700e-03	3.00000e-03	4.000000e-03	4.000000e-03	6.000000e-03	2.100000e-02	▇▂▁▁▁
numeric	PVAL	0	1.000000	NA	NA	NA	NA	NA	4.669281e-01	2.977737e-01	0.00000e+00	2.004001e-01	4.559004e-01	7.245994e-01	1.000000e+00	▇▆▆▆▆
numeric	PVAL_ztest	0	1.000000	NA	NA	NA	NA	NA	4.701350e-01	3.020695e-01	0.00000e+00	2.112995e-01	4.532547e-01	7.388827e-01	1.000000e+00	▇▆▆▆▇
numeric	AF	0	1.000000	NA	NA	NA	NA	NA	3.052619e-01	2.541503e-01	1.11900e-02	9.142000e-02	2.220000e-01	4.701000e-01	9.888100e-01	▇▃▂▂▁
numeric	AF_reference	39877	0.993781	NA	NA	NA	NA	NA	3.043005e-01	2.479503e-01	1.99700e-04	1.002400e-01	2.322280e-01	4.644570e-01	1.000000e+00	▇▅▂▂▁
numeric	N	0	1.000000	NA	NA	NA	NA	NA	1.709110e+05	0.000000e+00	1.70911e+05	1.709110e+05	1.709110e+05	1.709110e+05	1.709110e+05	▁▁▇▁▁

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	662622	rs61769339	G	A	0.005	0.007	0.4862001	0.4750505	0.09515	0.1475640	170911
1	704637	rs142559957	G	A	-0.004	0.010	0.7120000	0.6891565	0.04851	0.0473243	170911
1	705882	rs72631875	G	A	-0.004	0.008	0.5761002	0.6170751	0.08209	0.0315495	170911
1	714019	rs114983708	A	G	-0.009	0.010	0.3730001	0.3681203	0.04664	0.1383790	170911
1	714427	rs12028261	G	A	0.009	0.018	0.6211007	0.6170751	0.98507	0.7727640	170911
1	715367	rs12184277	A	G	-0.006	0.010	0.5605005	0.5485062	0.04664	0.0281550	170911
1	719914	rs187772768	C	G	-0.006	0.010	0.5350003	0.5485062	0.04851	0.0277556	170911
1	720381	rs116801199	G	T	-0.007	0.011	0.5018998	0.5245394	0.04291	0.0359425	170911
1	721290	rs12565286	G	C	-0.006	0.010	0.5619996	0.5485062	0.04664	0.0371406	170911
1	721757	rs189147642	T	A	-0.007	0.010	0.5143006	0.4839273	0.04851	0.0281550	170911

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
22	51219387	rs9616832	T	C	0.005	0.008	0.5184000	0.5319711	0.07463	0.0654952	170911
22	51219704	rs147475742	G	A	0.007	0.010	0.4763005	0.4839273	0.04851	0.0473243	170911
22	51221731	rs115055839	T	C	0.006	0.008	0.4431003	0.4532547	0.07836	0.0625000	170911
22	51222052	rs2879915	G	A	0.003	0.005	0.5064004	0.5485062	0.21640	0.2194490	170911
22	51224600	rs187908482	G	A	0.000	0.007	0.9458000	1.0000000	0.09515	0.0387380	170911
22	51227891	rs6010091	G	A	0.004	0.004	0.2817001	0.3173105	0.34700	0.4039540	170911
22	51229805	rs9616985	T	C	0.002	0.008	0.8245999	0.8025873	0.07836	0.0730831	170911
22	51229855	rs144549712	G	A	-0.006	0.006	0.2791997	0.3173105	0.13250	0.1160140	170911
22	51237063	rs3896457	T	C	0.005	0.005	0.2703000	0.3173105	0.23320	0.2050720	170911
23	100784211	rs188350543	C	A	-0.005	0.004	0.2263002	0.2112995	0.72200	0.6498010	170911

1   662622  rs61769339  G   A   .   PASS    AF=0.09515  ES:SE:LP:AF:SS:ID   0.005:0.007:0.313185:0.09515:170911:rs61769339
1   704637  rs142559957 G   A   .   PASS    AF=0.04851  ES:SE:LP:AF:SS:ID   -0.004:0.01:0.14752:0.04851:170911:rs142559957
1   705882  rs72631875  G   A   .   PASS    AF=0.08209  ES:SE:LP:AF:SS:ID   -0.004:0.008:0.239502:0.08209:170911:rs72631875
1   714019  rs114983708 A   G   .   PASS    AF=0.04664  ES:SE:LP:AF:SS:ID   -0.009:0.01:0.428291:0.04664:170911:rs114983708
1   714427  rs12028261  G   A   .   PASS    AF=0.98507  ES:SE:LP:AF:SS:ID   0.009:0.018:0.206838:0.98507:170911:rs12028261
1   715367  rs12184277  A   G   .   PASS    AF=0.04664  ES:SE:LP:AF:SS:ID   -0.006:0.01:0.251424:0.04664:170911:rs12184277
1   719914  rs187772768 C   G   .   PASS    AF=0.04851  ES:SE:LP:AF:SS:ID   -0.006:0.01:0.271646:0.04851:170911:rs187772768
1   720381  rs116801199 G   T   .   PASS    AF=0.04291  ES:SE:LP:AF:SS:ID   -0.007:0.011:0.299383:0.04291:170911:rs116801199
1   721290  rs12565286  G   C   .   PASS    AF=0.04664  ES:SE:LP:AF:SS:ID   -0.006:0.01:0.250264:0.04664:170911:rs12565286
1   721757  rs189147642 T   A   .   PASS    AF=0.04851  ES:SE:LP:AF:SS:ID   -0.007:0.01:0.288783:0.04851:170911:rs189147642
1   722670  rs116030099 T   C   .   PASS    AF=0.1082   ES:SE:LP:AF:SS:ID   0.005:0.007:0.313096:0.1082:170911:rs116030099
1   723307  rs28659788  C   G   .   PASS    AF=0.04104  ES:SE:LP:AF:SS:ID   -0.007:0.011:0.299383:0.04104:170911:rs28659788
1   723742  rs28375378  T   C   .   PASS    AF=0.03918  ES:SE:LP:AF:SS:ID   -0.008:0.011:0.339324:0.03918:170911:rs28375378
1   723819  rs11804171  T   A   .   PASS    AF=0.04851  ES:SE:LP:AF:SS:ID   -0.005:0.01:0.19071:0.04851:170911:rs11804171
1   723891  rs2977670   G   C   .   PASS    AF=0.9459   ES:SE:LP:AF:SS:ID   0.005:0.009:0.221559:0.9459:170911:rs2977670
1   726794  rs28454925  C   G   .   PASS    AF=0.04851  ES:SE:LP:AF:SS:ID   -0.007:0.01:0.334888:0.04851:170911:rs28454925
1   727841  rs116587930 G   A   .   PASS    AF=0.06157  ES:SE:LP:AF:SS:ID   0.009:0.009:0.4642:0.06157:170911:rs116587930
1   729679  rs4951859   C   G   .   PASS    AF=0.8489   ES:SE:LP:AF:SS:ID   0.001:0.006:0.0614302:0.8489:170911:rs4951859
1   730087  rs148120343 T   C   .   PASS    AF=0.06157  ES:SE:LP:AF:SS:ID   0.008:0.009:0.438779:0.06157:170911:rs148120343
1   732809  rs12131618  T   C   .   PASS    AF=0.05224  ES:SE:LP:AF:SS:ID   -0.007:0.01:0.327995:0.05224:170911:rs12131618
1   734349  rs141242758 T   C   .   PASS    AF=0.1045   ES:SE:LP:AF:SS:ID   0.002:0.007:0.105075:0.1045:170911:rs141242758
1   735985  rs12405651  G   A   .   PASS    AF=0.03358  ES:SE:LP:AF:SS:ID   -0.005:0.012:0.157953:0.03358:170911:rs12405651
1   736289  rs79010578  T   A   .   PASS    AF=0.1269   ES:SE:LP:AF:SS:ID   -0.003:0.006:0.223662:0.1269:170911:rs79010578
1   736736  rs10454457  A   G   .   PASS    AF=0.03918  ES:SE:LP:AF:SS:ID   -0.007:0.011:0.284414:0.03918:170911:rs10454457
1   739528  rs3094317   G   A   .   PASS    AF=0.91791  ES:SE:LP:AF:SS:ID   0.005:0.008:0.267606:0.91791:170911:rs3094317
1   746727  rs144595511 G   A   .   PASS    AF=0.04478  ES:SE:LP:AF:SS:ID   -0.007:0.01:0.30777:0.04478:170911:rs144595511
1   748141  rs2427893   G   A   .   PASS    AF=0.01679  ES:SE:LP:AF:SS:ID   -0.007:0.017:0.183494:0.01679:170911:rs2427893
1   752478  rs146277091 G   A   .   PASS    AF=0.04104  ES:SE:LP:AF:SS:ID   -0.004:0.011:0.140561:0.04104:170911:rs146277091
1   752566  rs3094315   G   A   .   PASS    AF=0.8451   ES:SE:LP:AF:SS:ID   0.002:0.005:0.137392:0.8451:170911:rs3094315
1   752617  rs149886465 C   A   .   PASS    AF=0.04478  ES:SE:LP:AF:SS:ID   -0.005:0.01:0.204537:0.04478:170911:rs149886465
1   752721  rs3131972   A   G   .   PASS    AF=0.8414   ES:SE:LP:AF:SS:ID   0.002:0.005:0.188358:0.8414:170911:rs3131972
1   752894  rs3131971   T   C   .   PASS    AF=0.8228   ES:SE:LP:AF:SS:ID   0.001:0.005:0.0479344:0.8228:170911:rs3131971
1   753474  rs2073814   C   G   .   PASS    AF=0.8358   ES:SE:LP:AF:SS:ID   0:0.005:0.0180003:0.8358:170911:rs2073814
1   753541  rs2073813   G   A   .   PASS    AF=0.1213   ES:SE:LP:AF:SS:ID   0.001:0.007:0.045661:0.1213:170911:rs2073813
1   754063  rs12184312  G   T   .   PASS    AF=0.05037  ES:SE:LP:AF:SS:ID   -0.005:0.01:0.189364:0.05037:170911:rs12184312
1   754105  rs12184325  C   T   .   PASS    AF=0.05037  ES:SE:LP:AF:SS:ID   0:0.01:0.0169152:0.05037:170911:rs12184325
1   754182  rs3131969   A   G   .   PASS    AF=0.8787   ES:SE:LP:AF:SS:ID   -0.001:0.006:0.0397195:0.8787:170911:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.8787   ES:SE:LP:AF:SS:ID   -0.001:0.006:0.0316105:0.8787:170911:rs3131968
1   754334  rs3131967   T   C   .   PASS    AF=0.8638   ES:SE:LP:AF:SS:ID   -0.001:0.006:0.0387213:0.8638:170911:rs3131967
1   754503  rs3115859   G   A   .   PASS    AF=0.8414   ES:SE:LP:AF:SS:ID   0.001:0.005:0.0478374:0.8414:170911:rs3115859
1   754964  rs3131966   C   T   .   PASS    AF=0.8302   ES:SE:LP:AF:SS:ID   0:0.005:0.0198602:0.8302:170911:rs3131966
1   755890  rs3115858   A   T   .   PASS    AF=0.8713   ES:SE:LP:AF:SS:ID   -0.001:0.006:0.0656026:0.8713:170911:rs3115858
1   756604  rs3131962   A   G   .   PASS    AF=0.8451   ES:SE:LP:AF:SS:ID   -0.001:0.005:0.0344691:0.8451:170911:rs3131962
1   756912  rs6699990   A   G   .   PASS    AF=0.02612  ES:SE:LP:AF:SS:ID   -0.009:0.014:0.286678:0.02612:170911:rs6699990
1   757640  rs3115853   G   A   .   PASS    AF=0.8787   ES:SE:LP:AF:SS:ID   0:0.006:0.0177288:0.8787:170911:rs3115853
1   757734  rs4951929   C   T   .   PASS    AF=0.8787   ES:SE:LP:AF:SS:ID   -0.001:0.006:0.0457092:0.8787:170911:rs4951929
1   757936  rs4951862   C   A   .   PASS    AF=0.8769   ES:SE:LP:AF:SS:ID   -0.001:0.006:0.0474982:0.8769:170911:rs4951862
1   758048  rs3131957   A   G   .   PASS    AF=0.1343   ES:SE:LP:AF:SS:ID   -0.005:0.006:0.370794:0.1343:170911:rs3131957
1   758144  rs3131956   A   G   .   PASS    AF=0.8489   ES:SE:LP:AF:SS:ID   0:0.005:0.0283995:0.8489:170911:rs3131956
1   758626  rs3131954   C   T   .   PASS    AF=0.8731   ES:SE:LP:AF:SS:ID   -0.001:0.006:0.0441199:0.8731:170911:rs3131954

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