IEU GWAS QC Report

name	value
id	ieu-a-2
pmid	25673413
year	2015
mr	1
note	NULL
trait	Body mass index
category	Risk factor
subcategory	Anthropometric
population	Mixed
sex	Males and females
ncase	NULL
ncontrol	NULL
sample_size	339224
nsnp	2555511
sd	4.77
priority	1
author	Locke AE
group_name	public
access	public
build	HG19/GRCh37

name	value
gwas_id	ieu-a-2
bcf_file	ieu-a-2.vcf.gz
qc_metrics_file	qc_metrics.json
metadata	metadata.json
refdata	1kg_v3_nomult.bcf
compile_time	2020-05-06 23:03 BST
build_version	run_igd-0675b08-2020-05-06

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-2/ieu-a-2.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-2/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 10:58:37 2020
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-2/ieu-a-2.vcf.gz ...
Read summary statistics for 2554285 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, 1177013 SNPs remain.
After merging with regression SNP LD, 1177013 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.1344 (0.0054)
Lambda GC: 1.1148
Mean Chi^2: 1.3108
Intercept: 0.7046 (0.007)
Ratio < 0 (usually indicates GC correction).
Analysis finished at Wed Feb  5 10:59:07 2020
Total time elapsed: 29.92s

{
    "af_correlation": 0.9183,
    "inflation_factor": 1.1116,
    "mean_EFFECT": 0.0001,
    "n": 339224,
    "n_snps": 2554285,
    "n_clumped_hits": 79,
    "n_p_sig": 2041,
    "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": 54864,
    "n_miss_AF_reference": 23058,
    "n_est": 328183.7264,
    "ratio_se_n": 0.9836,
    "mean_diff": -0,
    "ratio_diff": 7.5485,
    "sd_y_est1": 1.5387,
    "sd_y_est2": 1.5134,
    "r2_sum1": 0.0236,
    "r2_sum2": 0.01,
    "r2_sum3": 0.0103,
    "r2_sum4": 0.0153,
    "ldsc_nsnp_merge_refpanel_ld": 1177013,
    "ldsc_nsnp_merge_regression_ld": 1177013,
    "ldsc_observed_scale_h2_beta": 0.1344,
    "ldsc_observed_scale_h2_se": 0.0054,
    "ldsc_intercept_beta": 0.7046,
    "ldsc_intercept_se": 0.007,
    "ldsc_lambda_gc": 1.1148,
    "ldsc_mean_chisq": 1.3108,
    "ldsc_ratio": -0.9505
}

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	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	1.0000000	3	42	0	2554285	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	8.599732e+00	5.665262e+00	1.0000	4.000000e+00	8.000000e+00	1.200000e+01	2.30000e+01	<U+2587><U+2585><U+2585><U+2582><U+2582>
numeric	POS	0	1.0000000	NA	NA	NA	NA	NA	7.878794e+07	5.567688e+07	11523.0000	3.262390e+07	7.016154e+07	1.142167e+08	2.49219e+08	<U+2587><U+2586><U+2585><U+2582><U+2581>
numeric	EFFECT	0	1.0000000	NA	NA	NA	NA	NA	1.082000e-04	8.249100e-03	-0.2540	-3.700000e-03	1.000000e-04	3.800000e-03	2.49900e-01	<U+2581><U+2581><U+2587><U+2581><U+2581>
numeric	SE	0	1.0000000	NA	NA	NA	NA	NA	6.470100e-03	5.872400e-03	0.0029	3.900000e-03	4.600000e-03	6.500000e-03	2.39200e-01	<U+2587><U+2581><U+2581><U+2581><U+2581>
numeric	PVAL	0	1.0000000	NA	NA	NA	NA	NA	4.805441e-01	2.966777e-01	0.0000	2.206002e-01	4.769996e-01	7.389006e-01	1.00000e+00	<U+2587><U+2587><U+2587><U+2586><U+2586>
numeric	PVAL_ztest	0	1.0000000	NA	NA	NA	NA	NA	4.805442e-01	2.966802e-01	0.0000	2.205752e-01	4.770154e-01	7.388827e-01	1.00000e+00	<U+2587><U+2587><U+2587><U+2586><U+2586>
numeric	AF	54864	0.9785208	NA	NA	NA	NA	NA	3.543042e-01	2.770664e-01	0.0083	1.167000e-01	2.833000e-01	5.583000e-01	9.91700e-01	<U+2587><U+2585><U+2583><U+2582><U+2582>
numeric	AF_reference	23058	0.9909728	NA	NA	NA	NA	NA	3.592546e-01	2.580299e-01	0.0000	1.421730e-01	2.957270e-01	5.449280e-01	1.00000e+00	<U+2587><U+2586><U+2583><U+2583><U+2582>
numeric	N	0	1.0000000	NA	NA	NA	NA	NA	2.269688e+05	3.630437e+04	50002.0000	2.244090e+05	2.356780e+05	2.361130e+05	3.39224e+05	<U+2581><U+2581><U+2582><U+2587><U+2581>

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	721290	rs12565286	G	C	0.0067	0.0145	0.6412007	0.6440319	0.06780	0.0371406	109823.0
1	723819	rs11804171	T	A	0.0146	0.0175	0.4041001	0.4041200	0.03704	0.1345850	84828.0
1	723891	rs2977670	G	C	-0.0044	0.0184	0.8110001	0.8110044	0.92857	0.7799520	68458.9
1	750235	rs12138618	G	A	0.0045	0.0202	0.8237001	0.8237127	0.05833	NA	59954.0
1	752566	rs3094315	G	A	-0.0060	0.0065	0.3560000	0.3559671	0.84480	0.7182510	131544.0
1	753541	rs2073813	G	A	-0.0035	0.0102	0.7314994	0.7314952	NA	0.3019170	64351.3
1	754192	rs3131968	A	G	-0.0077	0.0089	0.3869002	0.3869463	0.87500	0.6785140	98348.7
1	768448	rs12562034	G	A	0.0027	0.0108	0.8026001	0.8025873	0.09167	0.1918930	87508.9
1	775659	rs2905035	A	G	-0.0029	0.0073	0.6912004	0.6911755	0.87500	0.7450080	140187.0
1	777122	rs2980319	A	T	-0.0031	0.0072	0.6668006	0.6667916	0.87500	0.7472040	143053.0

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	51217134	rs117417021	A	G	0.0114	0.0066	0.0841201	0.0841187	0.441700	0.2671730	131080.0
22	51222100	rs114553188	G	T	-0.0111	0.0105	0.2904003	0.2904464	0.066700	0.0880591	190892.0
22	51223637	rs375798137	G	A	-0.0124	0.0106	0.2421001	0.2420769	0.066700	0.0788738	189615.0
22	51229805	rs9616985	T	C	0.0151	0.0126	0.2308001	0.2307564	0.091700	0.0730831	129801.0
23	35921591	rs2204667	C	G	-0.0006	0.0049	0.9025000	0.9025435	0.166700	NA	236057.0
23	51666786	rs14115	A	G	0.0157	0.0082	0.0555405	0.0555392	0.025000	NA	223708.0
23	70163799	rs1626496	A	C	-0.0080	0.0071	0.2597999	0.2598437	0.075000	NA	235854.0
23	74963352	rs1053838	T	G	-0.0295	0.0489	0.5462997	0.5463278	0.991379	NA	97215.8
23	91415872	rs6562597	G	A	-0.0029	0.0136	0.8311000	0.8311434	0.008300	0.0021192	210254.0
23	118495837	rs12882977	G	A	0.0007	0.0036	0.8458000	0.8458279	0.516700	0.2307280	236143.0

1   721290  rs12565286  G   C   .   PASS    AF=0.0678   ES:SE:LP:AF:SS:ID   0.0067:0.0145:0.193006:0.0678:109823:rs12565286
1   723819  rs11804171  T   A   .   PASS    AF=0.03704  ES:SE:LP:AF:SS:ID   0.0146:0.0175:0.393511:0.03704:84828:rs11804171
1   723891  rs2977670   G   C   .   PASS    AF=0.92857  ES:SE:LP:AF:SS:ID   -0.0044:0.0184:0.0909791:0.92857:68458.9:rs2977670
1   750235  rs12138618  G   A   .   PASS    AF=0.05833  ES:SE:LP:AF:SS:ID   0.0045:0.0202:0.0842309:0.05833:59954:rs12138618
1   752566  rs3094315   G   A   .   PASS    AF=0.8448   ES:SE:LP:AF:SS:ID   -0.006:0.0065:0.44855:0.8448:131544:rs3094315
1   753541  rs2073813   G   A   .   PASS    .   ES:SE:LP:SS:ID  -0.0035:0.0102:0.135786:64351.3:rs2073813
1   754192  rs3131968   A   G   .   PASS    AF=0.875    ES:SE:LP:AF:SS:ID   -0.0077:0.0089:0.412401:0.875:98348.7:rs3131968
1   768448  rs12562034  G   A   .   PASS    AF=0.09167  ES:SE:LP:AF:SS:ID   0.0027:0.0108:0.0955008:0.09167:87508.9:rs12562034
1   775659  rs2905035   A   G   .   PASS    AF=0.875    ES:SE:LP:AF:SS:ID   -0.0029:0.0073:0.160396:0.875:140187:rs2905035
1   777122  rs2980319   A   T   .   PASS    AF=0.875    ES:SE:LP:AF:SS:ID   -0.0031:0.0072:0.176004:0.875:143053:rs2980319
1   779322  rs4040617   A   G   .   PASS    AF=0.125    ES:SE:LP:AF:SS:ID   0.0062:0.0077:0.376027:0.125:131198:rs4040617
1   780785  rs2977612   T   A   .   PASS    AF=0.8661   ES:SE:LP:AF:SS:ID   -0.0058:0.0078:0.339989:0.8661:128446:rs2977612
1   785050  rs2905062   G   A   .   PASS    .   ES:SE:LP:SS:ID  -0.0046:0.006:0.353989:187047:rs2905062
1   785989  rs2980300   T   C   .   PASS    AF=0.8729   ES:SE:LP:AF:SS:ID   -0.0055:0.0076:0.328549:0.8729:131206:rs2980300
1   798026  rs4951864   C   T   .   PASS    AF=0.9  ES:SE:LP:AF:SS:ID   -0.0044:0.0126:0.138525:0.9:83845.5:rs4951864
1   798801  rs12132517  G   A   .   PASS    AF=0.1083   ES:SE:LP:AF:SS:ID   0.0047:0.0129:0.14533:0.1083:79908.8:rs12132517
1   798959  rs11240777  G   A   .   PASS    AF=0.1667   ES:SE:LP:AF:SS:ID   0.0003:0.008:0.0131835:0.1667:107014:rs11240777
1   962210  rs3128126   A   G   .   PASS    AF=0.425    ES:SE:LP:AF:SS:ID   0.0028:0.0081:0.136915:0.425:92745:rs3128126
1   990380  rs3121561   C   T   .   PASS    AF=0.2667   ES:SE:LP:AF:SS:ID   0.0034:0.0064:0.225337:0.2667:168169:rs3121561
1   998501  rs3813193   G   C   .   PASS    AF=0.15 ES:SE:LP:AF:SS:ID   0.0101:0.0064:0.941195:0.15:166940:rs3813193
1   1003629 rs4075116   C   T   .   PASS    AF=0.7373   ES:SE:LP:AF:SS:ID   0.0059:0.0047:0.679023:0.7373:224000:rs4075116
1   1005806 rs3934834   C   T   .   PASS    AF=0.1167   ES:SE:LP:AF:SS:ID   0.011:0.006:1.17555:0.1167:178981:rs3934834
1   1017170 rs3766193   C   G   .   PASS    AF=0.5667   ES:SE:LP:AF:SS:ID   0:0.0045:-0:0.5667:220327:rs3766193
1   1017197 rs3766192   C   T   .   PASS    AF=0.5763   ES:SE:LP:AF:SS:ID   0.0003:0.0042:0.0254423:0.5763:222155:rs3766192
1   1017587 rs3766191   C   T   .   PASS    AF=0.09649  ES:SE:LP:AF:SS:ID   0.0122:0.0061:1.34199:0.09649:182119:rs3766191
1   1018562 rs9442371   C   T   .   PASS    AF=0.5917   ES:SE:LP:AF:SS:ID   -0.0006:0.0041:0.0536951:0.5917:226488:rs9442371
1   1018704 rs9442372   A   G   .   PASS    AF=0.6017   ES:SE:LP:AF:SS:ID   -0.0006:0.0041:0.0536951:0.6017:226440:rs9442372
1   1021346 rs10907177  A   G   .   PASS    AF=0.1271   ES:SE:LP:AF:SS:ID   0.0115:0.0063:1.16787:0.1271:181924:rs10907177
1   1021415 rs3737728   A   G   .   PASS    AF=0.7167   ES:SE:LP:AF:SS:ID   0.004:0.0043:0.453087:0.7167:229068:rs3737728
1   1021583 rs10907178  A   C   .   PASS    .   ES:SE:LP:SS:ID  0.0119:0.0063:1.22981:178910:rs10907178
1   1021695 rs9442398   A   G   .   PASS    AF=0.725    ES:SE:LP:AF:SS:ID   0.0041:0.0046:0.428524:0.725:228012:rs9442398
1   1022037 rs6701114   C   T   .   PASS    AF=0.5667   ES:SE:LP:AF:SS:ID   -0.002:0.0045:0.182633:0.5667:206365:rs6701114
1   1025301 rs9442400   T   C   .   PASS    AF=0.94737  ES:SE:LP:AF:SS:ID   -0.0017:0.0179:0.034187:0.94737:83573.5:rs9442400
1   1026707 rs4074137   C   A   .   PASS    AF=0.6  ES:SE:LP:AF:SS:ID   -0.0078:0.0047:1.01323:0.6:178166:rs4074137
1   1030565 rs6687776   C   T   .   PASS    AF=0.08333  ES:SE:LP:AF:SS:ID   0.0094:0.0057:1.00384:0.08333:186003:rs6687776
1   1030633 rs6678318   G   A   .   PASS    AF=0.08621  ES:SE:LP:AF:SS:ID   0.0096:0.0063:0.894149:0.08621:165051:rs6678318
1   1031540 rs9651273   A   G   .   PASS    AF=0.6583   ES:SE:LP:AF:SS:ID   -0.0029:0.0048:0.263046:0.6583:177137:rs9651273
1   1036959 rs11579015  T   C   .   PASS    AF=0.05 ES:SE:LP:AF:SS:ID   0.0153:0.0067:1.64975:0.05:205974:rs11579015
1   1040026 rs6671356   T   C   .   PASS    AF=0.075    ES:SE:LP:AF:SS:ID   0.0096:0.0061:0.937418:0.075:194944:rs6671356
1   1046164 rs6666280   C   T   .   PASS    AF=0.06667  ES:SE:LP:AF:SS:ID   0.0093:0.0063:0.854182:0.06667:201254:rs6666280
1   1048955 rs4970405   A   G   .   PASS    AF=0.05172  ES:SE:LP:AF:SS:ID   0.0137:0.0067:1.38849:0.05172:206868:rs4970405
1   1049950 rs12726255  A   G   .   PASS    AF=0.06667  ES:SE:LP:AF:SS:ID   0.0087:0.0061:0.813044:0.06667:201301:rs12726255
1   1053452 rs4970409   G   A   .   PASS    AF=0.05 ES:SE:LP:AF:SS:ID   0.0139:0.007:1.32726:0.05:200958:rs4970409
1   1060174 rs7548798   C   T   .   PASS    AF=0.3981   ES:SE:LP:AF:SS:ID   -0.0017:0.0058:0.113848:0.3981:140678:rs7548798
1   1060235 rs7540009   G   A   .   PASS    AF=0.01667  ES:SE:LP:AF:SS:ID   -0.0126:0.0133:0.464073:0.01667:166242:rs7540009
1   1060608 rs17160824  G   A   .   PASS    AF=0.05833  ES:SE:LP:AF:SS:ID   0.0142:0.007:1.37161:0.05833:205753:rs17160824
1   1061115 rs17160826  T   C   .   PASS    AF=0.05455  ES:SE:LP:AF:SS:ID   0.0145:0.007:1.41657:0.05455:205789:rs17160826
1   1061152 rs12748370  T   C   .   PASS    .   ES:SE:LP:SS:ID  0.0151:0.0071:1.47573:200804:rs12748370
1   1061166 rs11807848  T   C   .   PASS    AF=0.4123   ES:SE:LP:AF:SS:ID   0.0044:0.0048:0.444543:0.4123:170135:rs11807848
1   1062015 rs9659914   C   T   .   PASS    AF=0.01667  ES:SE:LP:AF:SS:ID   -0.0116:0.0143:0.379552:0.01667:153801:rs9659914

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