IEU GWAS QC Report

name	value
id	ieu-a-1089
pmid	26961502
year	2016
mr	0
note	Dominance model? If so then not necessarily of value for MR; Results from interim Biobank release enriched for smokers; could lead to bias through collider issues in MR
trait	Body mass index
category	Risk factor
subcategory	Anthropometric
population	European
sex	Males and females
ncase	NULL
ncontrol	NULL
sample_size	120286
nsnp	8654252
sd	NULL
priority	1
author	Wood
group_name	public
access	public
build	HG19/GRCh37

name	value
gwas_id	ieu-a-1089
bcf_file	ieu-a-1089.vcf.gz
qc_metrics_file	qc_metrics.json
metadata	metadata.json
refdata	1kg_v3_nomult.bcf
compile_time	2020-05-10 11:44 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-1089/ieu-a-1089.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-1089/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 09:21:13 2020
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-1089/ieu-a-1089.vcf.gz ...
Read summary statistics for 8234065 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, 1244038 SNPs remain.
After merging with regression SNP LD, 1244038 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0029 (0.0029)
Lambda GC: 1.0036
Mean Chi^2: 1.0051
Intercept: 0.9983 (0.0051)
Ratio < 0 (usually indicates GC correction).
Analysis finished at Wed Feb  5 09:22:35 2020
Total time elapsed: 1.0m:21.55s

{
    "af_correlation": 0.9391,
    "inflation_factor": 1,
    "mean_EFFECT": -0.0002,
    "n": 119688,
    "n_snps": 8234065,
    "n_clumped_hits": 1,
    "n_p_sig": 1,
    "n_mono": 0,
    "n_ns": 529643,
    "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": 125910,
    "n_est": 121787.288,
    "ratio_se_n": 1.0087,
    "mean_diff": 0.0002,
    "ratio_diff": 2.8163,
    "sd_y_est1": 2.0493,
    "sd_y_est2": 2.0672,
    "r2_sum1": 0.0006,
    "r2_sum2": 0.0001,
    "r2_sum3": 0.0001,
    "r2_sum4": 0.0003,
    "ldsc_nsnp_merge_refpanel_ld": 1244038,
    "ldsc_nsnp_merge_regression_ld": 1244038,
    "ldsc_observed_scale_h2_beta": 0.0029,
    "ldsc_observed_scale_h2_se": 0.0029,
    "ldsc_intercept_beta": 0.9983,
    "ldsc_intercept_se": 0.0051,
    "ldsc_lambda_gc": 1.0036,
    "ldsc_mean_chisq": 1.0051,
    "ldsc_ratio": -0.3333
}

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	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

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	58	0	8234065	0	NA	NA	NA	NA	NA	NA	NA	NA
character	REF	0	1.0000000	1	51	0	29514	0	NA	NA	NA	NA	NA	NA	NA	NA
character	ALT	0	1.0000000	1	51	0	15745	0	NA	NA	NA	NA	NA	NA	NA	NA
numeric	CHROM	0	1.0000000	NA	NA	NA	NA	NA	8.622937e+00	5.748526e+00	1.0000	4.000000e+00	8.000000e+00	1.300000e+01	2.200000e+01	▇▅▃▂▂
numeric	POS	0	1.0000000	NA	NA	NA	NA	NA	7.896169e+07	5.638206e+07	302.0000	3.244396e+07	6.962347e+07	1.146657e+08	2.492297e+08	▇▆▅▂▁
numeric	EFFECT	0	1.0000000	NA	NA	NA	NA	NA	-1.924000e-04	4.298960e-02	-0.7900	-8.900000e-03	-7.500000e-05	8.700000e-03	7.100000e-01	▁▁▇▁▁
numeric	SE	0	1.0000000	NA	NA	NA	NA	NA	2.756080e-02	3.319250e-02	0.0058	7.000000e-03	1.200000e-02	3.300000e-02	2.500000e-01	▇▁▁▁▁
numeric	PVAL	0	1.0000000	NA	NA	NA	NA	NA	4.998262e-01	2.886531e-01	0.0000	2.500000e-01	5.000000e-01	7.499995e-01	1.000000e+00	▇▇▇▇▇
numeric	PVAL_ztest	0	1.0000000	NA	NA	NA	NA	NA	4.998840e-01	2.886056e-01	0.0000	2.493627e-01	5.011208e-01	7.493895e-01	9.999997e-01	▇▇▇▇▇
numeric	AF	0	1.0000000	NA	NA	NA	NA	NA	2.700384e-01	2.643581e-01	0.0050	5.000000e-02	1.700000e-01	4.290000e-01	9.950000e-01	▇▃▂▁▁
numeric	AF_reference	125910	0.9847086	NA	NA	NA	NA	NA	2.666407e-01	2.523943e-01	0.0000	5.910540e-02	1.811100e-01	4.165340e-01	1.000000e+00	▇▃▂▁▁
numeric	N	0	1.0000000	NA	NA	NA	NA	NA	1.181701e+05	2.423412e+03	84747.0000	1.179120e+05	1.189950e+05	1.194740e+05	1.196880e+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	751343	rs28544273	T	A	-3.5e-05	0.014	1.0000000	0.9980053	0.126	0.242612	118061
1	751488	rs200141114	GA	G	-1.3e-03	0.014	0.9299999	0.9260171	0.855	NA	108511
1	753405	rs3115860	C	A	-3.3e-03	0.013	0.8000000	0.7996144	0.872	0.751797	118301
1	753425	rs3131970	T	C	-3.3e-03	0.013	0.8000000	0.7996144	0.872	0.749002	118293
1	753541	rs2073813	G	A	4.0e-03	0.013	0.7700005	0.7583165	0.127	0.301917	118494
1	754182	rs3131969	A	G	-7.5e-03	0.013	0.5700002	0.5639914	0.871	0.678514	118771
1	754192	rs3131968	A	G	-7.6e-03	0.013	0.5700002	0.5588064	0.871	0.678514	118768
1	754334	rs3131967	T	C	-8.2e-03	0.013	0.5400003	0.5281914	0.871	0.684305	118745
1	755890	rs3115858	A	T	-5.2e-03	0.013	0.6899999	0.6891565	0.871	0.751398	118960
1	756434	rs61768170	G	C	4.3e-03	0.013	0.7400005	0.7408188	0.128	0.188498	118969

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	51216051	rs376488897	A	G	-0.0097	0.016	0.5300002	0.5443488	0.127	0.1365810	110698
22	51216149	rs373165495	C	A	-0.0110	0.016	0.5000000	0.4917677	0.127	0.1361820	110718
22	51216564	rs9616970	T	C	-0.0110	0.016	0.4700002	0.4917677	0.127	0.1563500	110609
22	51217954	rs9616974	G	A	-0.0067	0.028	0.8100000	0.8108840	0.072	0.0621006	114572
22	51218224	rs9616975	C	A	-0.0066	0.028	0.8100000	0.8136544	0.072	0.0619010	114574
22	51218377	rs2519461	G	C	0.0061	0.027	0.8200001	0.8212590	0.073	0.0826677	114510
22	51218615	rs9616976	T	A	0.0063	0.027	0.8200001	0.8155026	0.073	0.0858626	114446
22	51219387	rs9616832	T	C	0.0100	0.027	0.7099994	0.7111065	0.073	0.0654952	114125
22	51220249	rs9616977	A	T	0.0210	0.029	0.4600002	0.4689811	0.072	0.0595048	113707
22	51220319	rs9616978	C	G	0.0240	0.032	0.4500005	0.4532547	0.069	0.0397364	113600

1   751343  rs28544273  T   A   .   PASS    AF=0.126    ES:SE:LP:AF:SS:ID   -3.5e-05:0.014:-0:0.126:118061:rs28544273
1   751488  rs200141114 GA  G   .   PASS    AF=0.855    ES:SE:LP:AF:SS:ID   -0.0013:0.014:0.0315171:0.855:108511:rs200141114
1   753405  rs3115860   C   A   .   PASS    AF=0.872    ES:SE:LP:AF:SS:ID   -0.0033:0.013:0.09691:0.872:118301:rs3115860
1   753425  rs3131970   T   C   .   PASS    AF=0.872    ES:SE:LP:AF:SS:ID   -0.0033:0.013:0.09691:0.872:118293:rs3131970
1   753541  rs2073813   G   A   .   PASS    AF=0.127    ES:SE:LP:AF:SS:ID   0.004:0.013:0.113509:0.127:118494:rs2073813
1   754182  rs3131969   A   G   .   PASS    AF=0.871    ES:SE:LP:AF:SS:ID   -0.0075:0.013:0.244125:0.871:118771:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.871    ES:SE:LP:AF:SS:ID   -0.0076:0.013:0.244125:0.871:118768:rs3131968
1   754334  rs3131967   T   C   .   PASS    AF=0.871    ES:SE:LP:AF:SS:ID   -0.0082:0.013:0.267606:0.871:118745:rs3131967
1   755890  rs3115858   A   T   .   PASS    AF=0.871    ES:SE:LP:AF:SS:ID   -0.0052:0.013:0.161151:0.871:118960:rs3115858
1   756434  rs61768170  G   C   .   PASS    AF=0.128    ES:SE:LP:AF:SS:ID   0.0043:0.013:0.130768:0.128:118969:rs61768170
1   756604  rs3131962   A   G   .   PASS    AF=0.87 ES:SE:LP:AF:SS:ID   -0.0069:0.013:0.221849:0.87:119688:rs3131962
1   757640  rs3115853   G   A   .   PASS    AF=0.869    ES:SE:LP:AF:SS:ID   -0.0074:0.013:0.244125:0.869:119270:rs3115853
1   757734  rs4951929   C   T   .   PASS    AF=0.87 ES:SE:LP:AF:SS:ID   -0.0081:0.013:0.275724:0.87:119538:rs4951929
1   757936  rs4951862   C   A   .   PASS    AF=0.87 ES:SE:LP:AF:SS:ID   -0.0076:0.013:0.251812:0.87:119540:rs4951862
1   758144  rs3131956   A   G   .   PASS    AF=0.869    ES:SE:LP:AF:SS:ID   -0.0072:0.013:0.236572:0.869:118906:rs3131956
1   758626  rs3131954   C   T   .   PASS    AF=0.871    ES:SE:LP:AF:SS:ID   -0.0091:0.013:0.309804:0.871:119185:rs3131954
1   759293  rs10157329  T   A   .   PASS    AF=0.102    ES:SE:LP:AF:SS:ID   0.012:0.018:0.29243:0.102:114987:rs10157329
1   761732  rs2286139   C   T   .   PASS    AF=0.863    ES:SE:LP:AF:SS:ID   -0.0095:0.013:0.337242:0.863:116334:rs2286139
1   761752  rs1057213   C   T   .   PASS    AF=0.868    ES:SE:LP:AF:SS:ID   -0.0076:0.013:0.251812:0.868:118131:rs1057213
1   762273  rs3115849   G   A   .   PASS    AF=0.865    ES:SE:LP:AF:SS:ID   -0.0066:0.013:0.21467:0.865:116946:rs3115849
1   762632  rs3131948   T   A   .   PASS    AF=0.869    ES:SE:LP:AF:SS:ID   -0.0073:0.013:0.236572:0.869:117471:rs3131948
1   764191  rs7515915   T   G   .   PASS    AF=0.129    ES:SE:LP:AF:SS:ID   0.0062:0.013:0.19382:0.129:119063:rs7515915
1   766007  rs61768174  A   C   .   PASS    AF=0.099    ES:SE:LP:AF:SS:ID   0.0031:0.019:0.0604807:0.099:113646:rs61768174
1   768253  rs2977608   A   C   .   PASS    AF=0.764    ES:SE:LP:AF:SS:ID   -0.016:0.0081:1.34679:0.764:119167:rs2977608
1   768448  rs12562034  G   A   .   PASS    AF=0.105    ES:SE:LP:AF:SS:ID   0.0013:0.015:0.0268721:0.105:119688:rs12562034
1   769138  rs59306077  CAT C   .   PASS    AF=0.129    ES:SE:LP:AF:SS:ID   0.0067:0.013:0.21467:0.129:119061:rs59306077
1   769223  rs60320384  C   G   .   PASS    AF=0.129    ES:SE:LP:AF:SS:ID   0.0065:0.013:0.207608:0.129:119333:rs60320384
1   769963  rs7518545   G   A   .   PASS    AF=0.105    ES:SE:LP:AF:SS:ID   -0.00063:0.016:0.0132283:0.105:119405:rs7518545
1   770886  rs371458725 G   A   .   PASS    AF=0.104    ES:SE:LP:AF:SS:ID   0.0054:0.016:0.130768:0.104:118743:rs371458725
1   771823  rs2977605   T   C   .   PASS    AF=0.87 ES:SE:LP:AF:SS:ID   -0.0064:0.013:0.207608:0.87:119269:rs2977605
1   771967  rs59066358  G   A   .   PASS    AF=0.129    ES:SE:LP:AF:SS:ID   0.005:0.013:0.154902:0.129:119266:rs59066358
1   772755  rs2905039   A   C   .   PASS    AF=0.871    ES:SE:LP:AF:SS:ID   -0.0067:0.013:0.21467:0.871:119244:rs2905039
1   774874  rs28810152  A   C   .   PASS    AF=0.87 ES:SE:LP:AF:SS:ID   -0.0081:0.013:0.267606:0.87:118519:rs28810152
1   775181  rs61768182  A   G   .   PASS    AF=0.129    ES:SE:LP:AF:SS:ID   0.0076:0.013:0.251812:0.129:119274:rs61768182
1   775659  rs2905035   A   G   .   PASS    AF=0.87 ES:SE:LP:AF:SS:ID   -0.0071:0.013:0.229148:0.87:119300:rs2905035
1   777122  rs2980319   A   T   .   PASS    AF=0.871    ES:SE:LP:AF:SS:ID   -0.0061:0.013:0.19382:0.871:119317:rs2980319
1   777232  rs112618790 C   T   .   PASS    AF=0.096    ES:SE:LP:AF:SS:ID   0.0052:0.018:0.107905:0.096:116781:rs112618790
1   778745  rs1055606   A   G   .   PASS    AF=0.128    ES:SE:LP:AF:SS:ID   0.0049:0.013:0.148742:0.128:119423:rs1055606
1   779322  rs4040617   A   G   .   PASS    AF=0.128    ES:SE:LP:AF:SS:ID   0.0054:0.013:0.167491:0.128:119688:rs4040617
1   780785  rs2977612   T   A   .   PASS    AF=0.87 ES:SE:LP:AF:SS:ID   -0.0061:0.013:0.19382:0.87:118775:rs2977612
1   781845  rs61768199  A   G   .   PASS    AF=0.095    ES:SE:LP:AF:SS:ID   -0.0016:0.02:0.0268721:0.095:113333:rs61768199
1   782981  rs6594026   C   T   .   PASS    AF=0.128    ES:SE:LP:AF:SS:ID   0.0042:0.013:0.124939:0.128:118966:rs6594026
1   783318  rs6686696   A   G   .   PASS    AF=0.127    ES:SE:LP:AF:SS:ID   0.0053:0.013:0.161151:0.127:119380:rs6686696
1   785050  rs2905062   G   A   .   PASS    AF=0.87 ES:SE:LP:AF:SS:ID   -0.0039:0.013:0.119186:0.87:118692:rs2905062
1   785989  rs2980300   T   C   .   PASS    AF=0.87 ES:SE:LP:AF:SS:ID   -0.0039:0.013:0.119186:0.87:118775:rs2980300
1   786995  rs61768202  G   A   .   PASS    AF=0.127    ES:SE:LP:AF:SS:ID   0.0027:0.013:0.0757207:0.127:119260:rs61768202
1   787399  rs2905055   G   T   .   PASS    AF=0.863    ES:SE:LP:AF:SS:ID   -0.007:0.013:0.229148:0.863:113287:rs2905055
1   787606  rs3863622   G   T   .   PASS    AF=0.127    ES:SE:LP:AF:SS:ID   0.0086:0.014:0.283997:0.127:118012:rs3863622
1   787685  rs2905054   G   T   .   PASS    AF=0.868    ES:SE:LP:AF:SS:ID   -0.0065:0.013:0.207608:0.868:116098:rs2905054
1   787844  rs2905053   C   T   .   PASS    AF=0.87 ES:SE:LP:AF:SS:ID   -0.0089:0.013:0.29243:0.87:116958:rs2905053

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