IEU GWAS QC Report

name	value
id	ieu-a-71
pmid	25673412
year	2015
mr	1
note	Adjusted for BMI
trait	Waist circumference
category	Risk factor
subcategory	Anthropometric
population	European
sex	Males
ncase	NULL
ncontrol	NULL
sample_size	104079
nsnp	2294966
sd	12.52
priority	14
author	Shungin D
group_name	public
access	public
build	HG19/GRCh37

name	value
gwas_id	ieu-a-71
bcf_file	ieu-a-71.vcf.gz
qc_metrics_file	qc_metrics.json
metadata	metadata.json
refdata	1kg_v3_nomult.bcf
compile_time	2020-05-10 09:29 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-71/ieu-a-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/ieu-a-import/processed/ieu-a-71/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 11:28:43 2020
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-71/ieu-a-71.vcf.gz ...
Read summary statistics for 2294034 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, 1091705 SNPs remain.
After merging with regression SNP LD, 1091705 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.1661 (0.0108)
Lambda GC: 1.0336
Mean Chi^2: 1.0858
Intercept: 0.8844 (0.0075)
Ratio < 0 (usually indicates GC correction).
Analysis finished at Wed Feb  5 11:29:12 2020
Total time elapsed: 28.63s

{
    "af_correlation": 0.9116,
    "inflation_factor": 1.0475,
    "mean_EFFECT": -0.0001,
    "n": 104079,
    "n_snps": 2294034,
    "n_clumped_hits": 27,
    "n_p_sig": 274,
    "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": 8331,
    "n_miss_AF_reference": 18210,
    "n_est": 102116.3359,
    "ratio_se_n": 0.9905,
    "mean_diff": 0,
    "ratio_diff": 4.4399,
    "sd_y_est1": 1.467,
    "sd_y_est2": 1.4531,
    "r2_sum1": 0.0134,
    "r2_sum2": 0.0062,
    "r2_sum3": 0.0063,
    "r2_sum4": 0.0114,
    "ldsc_nsnp_merge_refpanel_ld": 1091705,
    "ldsc_nsnp_merge_regression_ld": 1091705,
    "ldsc_observed_scale_h2_beta": 0.1661,
    "ldsc_observed_scale_h2_se": 0.0108,
    "ldsc_intercept_beta": 0.8844,
    "ldsc_intercept_se": 0.0075,
    "ldsc_lambda_gc": 1.0336,
    "ldsc_mean_chisq": 1.0858,
    "ldsc_ratio": -1.3473
}

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	42	0	2294034	0	NA	NA	NA	NA	NA	NA	NA	NA
character	REF	0	1.0000000	1	1	0	4	0	NA	NA	NA	NA	NA	NA	NA	NA
character	ALT	0	1.0000000	1	1	0	4	0	NA	NA	NA	NA	NA	NA	NA	NA
numeric	CHROM	0	1.0000000	NA	NA	NA	NA	NA	8.539775e+00	5.626728e+00	1.0000e+00	4.000000e+00	8.000000e+00	1.200000e+01	2.300000e+01	▇▅▅▂▂
numeric	POS	0	1.0000000	NA	NA	NA	NA	NA	7.894138e+07	5.547247e+07	1.3034e+04	3.295368e+07	7.043194e+07	1.142237e+08	2.491808e+08	▇▇▅▂▁
numeric	EFFECT	0	1.0000000	NA	NA	NA	NA	NA	-1.429000e-04	1.026040e-02	-1.4000e-01	-5.900000e-03	-1.000000e-04	5.700000e-03	1.400000e-01	▁▁▇▁▁
numeric	SE	0	1.0000000	NA	NA	NA	NA	NA	9.305900e-03	4.141900e-03	4.7000e-03	6.700000e-03	7.700000e-03	1.000000e-02	4.500000e-01	▇▁▁▁▁
numeric	PVAL	0	1.0000000	NA	NA	NA	NA	NA	4.936477e-01	2.917258e-01	0.0000e+00	2.399999e-01	4.899999e-01	7.499995e-01	1.000000e+00	▇▇▇▇▇
numeric	PVAL_ztest	0	1.0000000	NA	NA	NA	NA	NA	4.934969e-01	2.915171e-01	0.0000e+00	2.399947e-01	4.923555e-01	7.459807e-01	1.000000e+00	▇▇▇▇▇
numeric	AF	8331	0.9963684	NA	NA	NA	NA	NA	3.661063e-01	2.691460e-01	8.3000e-03	1.333000e-01	3.083000e-01	5.667000e-01	9.917000e-01	▇▅▃▃▂
numeric	AF_reference	18210	0.9920620	NA	NA	NA	NA	NA	3.683053e-01	2.512988e-01	1.9970e-04	1.567490e-01	3.095050e-01	5.509190e-01	1.000000e+00	▇▇▅▃▂
numeric	N	0	1.0000000	NA	NA	NA	NA	NA	6.141796e+04	8.227166e+03	5.0000e+04	6.016400e+04	6.107500e+04	6.146100e+04	1.040790e+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	785050	rs2905062	G	A	-0.0048	0.0089	0.5900000	0.5896620	NA	0.626997	64267
1	1003629	rs4075116	C	T	0.0015	0.0080	0.8499999	0.8512686	0.7373	0.720647	58568
1	1017170	rs3766193	C	G	0.0055	0.0075	0.4600002	0.4633551	0.5667	0.575479	59110
1	1017197	rs3766192	C	T	0.0071	0.0072	0.3200000	0.3240786	0.5763	0.511182	58855
1	1018562	rs9442371	C	T	0.0058	0.0071	0.4100001	0.4139848	0.5917	0.530152	59436
1	1018704	rs9442372	A	G	0.0053	0.0072	0.4600002	0.4616631	0.6017	0.611022	58906
1	1021415	rs3737728	A	G	0.0076	0.0077	0.3200000	0.3236363	0.7167	0.812700	58766
1	1021695	rs9442398	A	G	0.0082	0.0079	0.2999998	0.2992818	0.7250	0.727236	59056
1	1022037	rs6701114	C	T	0.0090	0.0079	0.2500000	0.2546029	0.5667	0.586661	53280
1	1036959	rs11579015	T	C	0.0024	0.0130	0.8499999	0.8535307	0.0500	0.156949	50183

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	51163138	rs715586	C	T	-0.0039	0.0073	0.5900000	0.5931709	0.1500	0.0902556	94615
22	51165664	rs8137951	G	A	0.0047	0.0053	0.3800004	0.3751907	0.2750	0.4063500	101606
22	51175626	rs3810648	A	G	-0.0073	0.0150	0.6200004	0.6264946	0.0667	0.1084270	51179
22	51178090	rs2285395	G	A	0.0130	0.0100	0.2200002	0.1936010	0.0667	0.0666933	96455
22	51196164	rs8136603	A	T	-0.0047	0.0180	0.8000000	0.7940068	0.0750	0.1427720	50214
23	35921591	rs2204667	C	G	0.0130	0.0087	0.1499999	0.1351095	0.1667	NA	61429
23	51666786	rs14115	A	G	-0.0058	0.0150	0.6899999	0.6990030	0.0250	NA	55140
23	70163799	rs1626496	A	C	-0.0002	0.0130	0.9900000	0.9877253	0.0750	NA	61441
23	91415872	rs6562597	G	A	-0.0240	0.0250	0.3300000	0.3370552	0.0083	0.0021192	52407
23	118495837	rs12882977	G	A	0.0043	0.0063	0.4899999	0.4948978	0.5167	0.2307280	61362

1   785050  rs2905062   G   A   .   PASS    .   ES:SE:LP:SS:ID  -0.0048:0.0089:0.229148:64267:rs2905062
1   1003629 rs4075116   C   T   .   PASS    AF=0.7373   ES:SE:LP:AF:SS:ID   0.0015:0.008:0.0705811:0.7373:58568:rs4075116
1   1017170 rs3766193   C   G   .   PASS    AF=0.5667   ES:SE:LP:AF:SS:ID   0.0055:0.0075:0.337242:0.5667:59110:rs3766193
1   1017197 rs3766192   C   T   .   PASS    AF=0.5763   ES:SE:LP:AF:SS:ID   0.0071:0.0072:0.49485:0.5763:58855:rs3766192
1   1018562 rs9442371   C   T   .   PASS    AF=0.5917   ES:SE:LP:AF:SS:ID   0.0058:0.0071:0.387216:0.5917:59436:rs9442371
1   1018704 rs9442372   A   G   .   PASS    AF=0.6017   ES:SE:LP:AF:SS:ID   0.0053:0.0072:0.337242:0.6017:58906:rs9442372
1   1021415 rs3737728   A   G   .   PASS    AF=0.7167   ES:SE:LP:AF:SS:ID   0.0076:0.0077:0.49485:0.7167:58766:rs3737728
1   1021695 rs9442398   A   G   .   PASS    AF=0.725    ES:SE:LP:AF:SS:ID   0.0082:0.0079:0.522879:0.725:59056:rs9442398
1   1022037 rs6701114   C   T   .   PASS    AF=0.5667   ES:SE:LP:AF:SS:ID   0.009:0.0079:0.60206:0.5667:53280:rs6701114
1   1036959 rs11579015  T   C   .   PASS    AF=0.05 ES:SE:LP:AF:SS:ID   0.0024:0.013:0.0705811:0.05:50183:rs11579015
1   1053452 rs4970409   G   A   .   PASS    AF=0.05 ES:SE:LP:AF:SS:ID   0.0053:0.013:0.161151:0.05:50706:rs4970409
1   1060608 rs17160824  G   A   .   PASS    AF=0.0583   ES:SE:LP:AF:SS:ID   0.0045:0.013:0.130768:0.0583:50671:rs17160824
1   1061115 rs17160826  T   C   .   PASS    AF=0.0546   ES:SE:LP:AF:SS:ID   0.0077:0.013:0.251812:0.0546:50675:rs17160826
1   1061152 rs12748370  T   C   .   PASS    .   ES:SE:LP:SS:ID  0.0074:0.013:0.236572:50673:rs12748370
1   1077064 rs4970357   C   A   .   PASS    AF=0.9237   ES:SE:LP:AF:SS:ID   -0.01:0.015:0.29243:0.9237:51038:rs4970357
1   1087683 rs9442380   T   C   .   PASS    AF=0.9123   ES:SE:LP:AF:SS:ID   -0.0083:0.013:0.267606:0.9123:53234:rs9442380
1   1089262 rs4970358   A   G   .   PASS    AF=0.9661   ES:SE:LP:AF:SS:ID   -0.018:0.017:0.508638:0.9661:54732:rs4970358
1   1097335 rs9442385   T   G   .   PASS    AF=0.9417   ES:SE:LP:AF:SS:ID   -0.012:0.013:0.431798:0.9417:56034:rs9442385
1   1099342 rs9660710   A   C   .   PASS    AF=0.9407   ES:SE:LP:AF:SS:ID   -0.0063:0.013:0.207608:0.9407:58303:rs9660710
1   1100217 rs1891905   C   T   .   PASS    AF=0.9583   ES:SE:LP:AF:SS:ID   0.011:0.018:0.275724:0.9583:58482:rs1891905
1   1124663 rs6684820   G   A   .   PASS    AF=0.2667   ES:SE:LP:AF:SS:ID   -0.001:0.0083:0.0457575:0.2667:58800:rs6684820
1   1125553 rs10907174  A   T   .   PASS    AF=0.225    ES:SE:LP:AF:SS:ID   0.0032:0.0087:0.148742:0.225:58697:rs10907174
1   1130727 rs10907175  A   C   .   PASS    AF=0.1  ES:SE:LP:AF:SS:ID   0.0004:0.012:0.0132283:0.1:59277:rs10907175
1   1135242 rs9729550   A   C   .   PASS    AF=0.275    ES:SE:LP:AF:SS:ID   0.0011:0.008:0.05061:0.275:58324:rs9729550
1   1138913 rs3819001   T   C   .   PASS    AF=0.0431   ES:SE:LP:AF:SS:ID   -0.017:0.018:0.468521:0.0431:54432:rs3819001
1   1140435 rs1815606   G   T   .   PASS    AF=0.3103   ES:SE:LP:AF:SS:ID   -0.014:0.006:1.72125:0.3103:82299:rs1815606
1   1143657 rs3753348   C   G   .   PASS    AF=0.0333   ES:SE:LP:AF:SS:ID   -0.017:0.02:0.408935:0.0333:55900:rs3753348
1   1152631 rs11721 C   A   .   PASS    AF=0.0833   ES:SE:LP:AF:SS:ID   0.011:0.013:0.420216:0.0833:57598:rs11721
1   1158277 rs3813199   G   A   .   PASS    AF=0.1  ES:SE:LP:AF:SS:ID   0.0026:0.012:0.0861861:0.1:58770:rs3813199
1   1162435 rs3766186   C   A   .   PASS    AF=0.1  ES:SE:LP:AF:SS:ID   0.004:0.012:0.136677:0.1:59298:rs3766186
1   1163804 rs7515488   C   T   .   PASS    AF=0.15 ES:SE:LP:AF:SS:ID   -0.005:0.01:0.207608:0.15:58725:rs7515488
1   1165310 rs11260562  G   A   .   PASS    AF=0.0517   ES:SE:LP:AF:SS:ID   -0.015:0.016:0.468521:0.0517:54065:rs11260562
1   1176597 rs6675798   T   C   .   PASS    AF=0.1083   ES:SE:LP:AF:SS:ID   0.0023:0.013:0.0705811:0.1083:56002:rs6675798
1   1181751 rs6603783   T   C   .   PASS    AF=0.1  ES:SE:LP:AF:SS:ID   0.0025:0.012:0.0757207:0.1:58026:rs6603783
1   1192515 rs7524470   A   G   .   PASS    AF=0.0583   ES:SE:LP:AF:SS:ID   -0.014:0.019:0.337242:0.0583:54576:rs7524470
1   1194804 rs11804831  T   C   .   PASS    AF=0.2083   ES:SE:LP:AF:SS:ID   -0.0087:0.0091:0.468521:0.2083:59187:rs11804831
1   1198618 rs12563338  T   A   .   PASS    AF=0.0417   ES:SE:LP:AF:SS:ID   -0.024:0.019:0.721246:0.0417:58256:rs12563338
1   1206343 rs6667923   C   A   .   PASS    AF=0.0583   ES:SE:LP:AF:SS:ID   -0.017:0.018:0.468521:0.0583:59416:rs6667923
1   1206619 rs6668223   C   A   .   PASS    AF=0.0339   ES:SE:LP:AF:SS:ID   -0.012:0.021:0.251812:0.0339:59203:rs6668223
1   1211292 rs6685064   C   T   .   PASS    AF=0.1  ES:SE:LP:AF:SS:ID   -0.016:0.013:0.69897:0.1:57319:rs6685064
1   1232319 rs604618    G   A   .   PASS    AF=0.0917   ES:SE:LP:AF:SS:ID   -0.019:0.016:0.638272:0.0917:50414:rs604618
1   1474304 rs1571150   C   A   .   PASS    AF=0.3  ES:SE:LP:AF:SS:ID   0.0081:0.007:0.60206:0.3:61254:rs1571150
1   1478153 rs3766180   T   C   .   PASS    AF=0.2417   ES:SE:LP:AF:SS:ID   0.0097:0.0072:0.744727:0.2417:60823:rs3766180
1   1478180 rs3766178   T   C   .   PASS    AF=0.2667   ES:SE:LP:AF:SS:ID   0.0095:0.0072:0.721246:0.2667:60821:rs3766178
1   1481348 rs3766177   T   C   .   PASS    .   ES:SE:LP:SS:ID  0.012:0.0077:0.886057:60578:rs3766177
1   1483010 rs7517401   G   A   .   PASS    AF=0.2833   ES:SE:LP:AF:SS:ID   0.0076:0.0072:0.537602:0.2833:60803:rs7517401
1   1486834 rs3128342   C   A   .   PASS    AF=0.3333   ES:SE:LP:AF:SS:ID   0.0043:0.0074:0.251812:0.3333:55339:rs3128342
1   1489670 rs7531530   C   T   .   PASS    AF=0.25 ES:SE:LP:AF:SS:ID   0.012:0.0075:0.920819:0.25:60322:rs7531530
1   1489928 rs7366884   T   C   .   PASS    AF=0.25 ES:SE:LP:AF:SS:ID   0.011:0.0076:0.79588:0.25:60855:rs7366884
1   1497201 rs3766169   A   C   .   PASS    AF=0.2458   ES:SE:LP:AF:SS:ID   0.0096:0.0072:0.744727:0.2458:61404:rs3766169

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