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IEU GWAS information

Trait: Urinary albumin-to-creatinine ratio.

name	value
id	ieu-a-1100
pmid	26631737
year	2015
mr	1
note	In subjects with diabetes mellitus
trait	Urinary albumin-to-creatinine ratio
category	Risk factor
subcategory	Kidney
population	European
sex	Males and females
ncase	NULL
ncontrol	NULL
sample_size	5825
nsnp	2191488
sd	0.96
priority	3
author	Teumer
group_name	public
access	public
build	HG19/GRCh37

Report information

name	value
gwas_id	ieu-a-1100
bcf_file	ieu-a-1100.vcf.gz
qc_metrics_file	qc_metrics.json
metadata	metadata.json
refdata	1kg_v3_nomult.bcf
compile_time	2020-05-10 04:56 BST
build_version	run_igd-8f4f4c9-2020-05-09

Summary

Summary {data-width=650}

Manhattan plot

manhattan_plot

QQ plot

qq_plot

AF plot

$af_plot$

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-1100/ieu-a-1100.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-1100/ldsc.txt \
--w-ld-chr /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/reference/eur_w_ld_chr/ 

Beginning analysis at Tue Feb  4 19:46:49 2020
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-1100/ieu-a-1100.vcf.gz ...
Read summary statistics for 2189141 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, 1067474 SNPs remain.
After merging with regression SNP LD, 1067474 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: -0.1061 (0.064)
Lambda GC: 1.0088
Mean Chi^2: 1.0083
Intercept: 1.0208 (0.0058)
Ratio: 2.5133 (0.7014)
Analysis finished at Tue Feb  4 19:47:17 2020
Total time elapsed: 27.59s

QC metrics

Metrics

{
    "af_correlation": 0.9011,
    "inflation_factor": 1,
    "mean_EFFECT": -0.0003,
    "n": 5826,
    "n_snps": 2189141,
    "n_clumped_hits": 0,
    "n_p_sig": 0,
    "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": 686,
    "n_miss_AF_reference": 18366,
    "n_est": 5488.632,
    "ratio_se_n": 0.9706,
    "mean_diff": 0.0001,
    "ratio_diff": 4.3879,
    "sd_y_est1": 1.5719,
    "sd_y_est2": 1.5257,
    "r2_sum1": 0,
    "r2_sum2": 0,
    "r2_sum3": 0,
    "r2_sum4": 0,
    "ldsc_nsnp_merge_refpanel_ld": 1067474,
    "ldsc_nsnp_merge_regression_ld": 1067474,
    "ldsc_observed_scale_h2_beta": "NA",
    "ldsc_observed_scale_h2_se": "NA",
    "ldsc_intercept_beta": 1.0208,
    "ldsc_intercept_se": 0.0058,
    "ldsc_lambda_gc": 1.0088,
    "ldsc_mean_chisq": 1.0083,
    "ldsc_ratio": 2.506
}

Flags

name	value
af_correlation	FALSE
inflation_factor	FALSE
n	TRUE
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	TRUE
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	1.0000000	3	42	0	2189141	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	8.599715e+00	5.663765e+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	7.873459e+07	5.573775e+07	1.1523e+04	3.245190e+07	7.008414e+07	1.143625e+08	2.491808e+08	▇▆▅▂▁
numeric	EFFECT	0	1.0000000	NA	NA	NA	NA	NA	-3.337000e-04	4.030890e-02	-6.5000e-01	-2.500000e-02	-3.000000e-04	2.400000e-02	9.400000e-01	▁▅▇▁▁
numeric	SE	0	1.0000000	NA	NA	NA	NA	NA	3.818760e-02	1.240550e-02	2.7000e-02	3.000000e-02	3.400000e-02	4.300000e-02	5.100000e-01	▇▁▁▁▁
numeric	PVAL	0	1.0000000	NA	NA	NA	NA	NA	4.986148e-01	2.889840e-01	5.0000e-07	2.500000e-01	5.000000e-01	7.499995e-01	1.000000e+00	▇▇▇▇▇
numeric	PVAL_ztest	0	1.0000000	NA	NA	NA	NA	NA	4.987292e-01	2.889638e-01	3.0000e-07	2.480198e-01	4.981399e-01	7.494575e-01	1.000000e+00	▇▇▇▇▇
numeric	AF	686	0.9996866	NA	NA	NA	NA	NA	3.811686e-01	2.565483e-01	4.0000e-03	1.590000e-01	3.260000e-01	5.750000e-01	9.960000e-01	▇▆▅▃▂
numeric	AF_reference	18366	0.9916104	NA	NA	NA	NA	NA	3.809003e-01	2.427606e-01	1.9970e-04	1.775160e-01	3.294730e-01	5.597040e-01	1.000000e+00	▇▇▅▃▂
numeric	N	0	1.0000000	NA	NA	NA	NA	NA	5.731109e+03	3.934484e+02	9.9300e+02	5.823000e+03	5.824000e+03	5.825000e+03	5.826000e+03	▁▁▁▁▇

Head and tail

CHROM	POS	ID	REF	ALT	EFFECT	SE	PVAL	PVAL_ztest	AF	AF_reference	N
1	723891	rs2977670	G	C	0.0360	0.110	0.7400005	0.7434616	0.934	0.7799520	2485
1	752566	rs3094315	G	A	0.0290	0.056	0.5999997	0.6045579	0.835	0.7182510	3444
1	754192	rs3131968	A	G	-0.0088	0.063	0.8900000	0.8889108	0.885	0.6785140	3048
1	768448	rs12562034	G	A	0.1600	0.120	0.1800002	0.1824224	0.102	0.1918930	2979
1	775659	rs2905035	A	G	0.0032	0.057	0.9500000	0.9552300	0.885	0.7450080	3622
1	776546	rs12124819	A	G	-0.0096	0.092	0.9199999	0.9168933	0.288	0.0756789	3472
1	777122	rs2980319	A	T	0.0370	0.044	0.4000000	0.4003989	0.866	0.7472040	5825
1	779322	rs4040617	A	G	-0.0360	0.063	0.5700002	0.5677092	0.133	0.2264380	3311
1	780785	rs2977612	T	A	0.0350	0.063	0.5700002	0.5785147	0.877	0.6693290	3446
1	785050	rs2905062	G	A	0.0310	0.063	0.6300007	0.6226745	0.868	0.6269970	3446

CHROM	POS	ID	REF	ALT	EFFECT	SE	PVAL	PVAL_ztest	AF	AF_reference	N
22	51212875	rs2238837	A	C	0.043	0.035	0.2200002	0.2192325	0.385	0.3724040	5509
22	51216564	rs9616970	T	C	0.029	0.057	0.6100002	0.6109121	0.146	0.1563500	5143
22	51217134	rs117417021	A	G	0.012	0.052	0.8200001	0.8174941	0.415	0.2671730	2940
22	51222100	rs114553188	G	T	-0.024	0.100	0.8200001	0.8103303	0.062	0.0880591	2940
22	51223637	rs375798137	G	A	-0.023	0.100	0.8200001	0.8180918	0.062	0.0788738	2940
22	51229805	rs9616985	T	C	-0.071	0.100	0.4899999	0.4777041	0.092	0.0730831	3173
23	35921591	rs2204667	C	G	0.031	0.039	0.4199997	0.4266881	0.162	NA	5825
23	51666786	rs14115	A	G	0.066	0.064	0.2999998	0.3024236	0.027	NA	5508
23	70163799	rs1626496	A	C	0.045	0.054	0.4100001	0.4046568	0.069	NA	5825
23	118495837	rs12882977	G	A	0.045	0.034	0.1800002	0.1856594	0.508	0.2307280	3622

bcf preview

1   723891  rs2977670   G   C   .   PASS    AF=0.934    ES:SE:LP:AF:SS:ID   0.036:0.11:0.130768:0.934:2485:rs2977670
1   752566  rs3094315   G   A   .   PASS    AF=0.835    ES:SE:LP:AF:SS:ID   0.029:0.056:0.221849:0.835:3444:rs3094315
1   754192  rs3131968   A   G   .   PASS    AF=0.885    ES:SE:LP:AF:SS:ID   -0.0088:0.063:0.05061:0.885:3048:rs3131968
1   768448  rs12562034  G   A   .   PASS    AF=0.102    ES:SE:LP:AF:SS:ID   0.16:0.12:0.744727:0.102:2979:rs12562034
1   775659  rs2905035   A   G   .   PASS    AF=0.885    ES:SE:LP:AF:SS:ID   0.0032:0.057:0.0222764:0.885:3622:rs2905035
1   776546  rs12124819  A   G   .   PASS    AF=0.288    ES:SE:LP:AF:SS:ID   -0.0096:0.092:0.0362122:0.288:3472:rs12124819
1   777122  rs2980319   A   T   .   PASS    AF=0.866    ES:SE:LP:AF:SS:ID   0.037:0.044:0.39794:0.866:5825:rs2980319
1   779322  rs4040617   A   G   .   PASS    AF=0.133    ES:SE:LP:AF:SS:ID   -0.036:0.063:0.244125:0.133:3311:rs4040617
1   780785  rs2977612   T   A   .   PASS    AF=0.877    ES:SE:LP:AF:SS:ID   0.035:0.063:0.244125:0.877:3446:rs2977612
1   785050  rs2905062   G   A   .   PASS    AF=0.868    ES:SE:LP:AF:SS:ID   0.031:0.063:0.200659:0.868:3446:rs2905062
1   785989  rs2980300   T   C   .   PASS    AF=0.868    ES:SE:LP:AF:SS:ID   0.02:0.044:0.187087:0.868:5647:rs2980300
1   798026  rs4951864   C   T   .   PASS    AF=0.9  ES:SE:LP:AF:SS:ID   -0.11:0.12:0.443698:0.9:2979:rs4951864
1   798801  rs12132517  G   A   .   PASS    AF=0.108    ES:SE:LP:AF:SS:ID   0.11:0.12:0.468521:0.108:2979:rs12132517
1   798959  rs11240777  G   A   .   PASS    AF=0.219    ES:SE:LP:AF:SS:ID   0.025:0.043:0.251812:0.219:5825:rs11240777
1   846864  rs950122    G   C   .   PASS    AF=0.138    ES:SE:LP:AF:SS:ID   0.0048:0.11:0.0132283:0.138:2563:rs950122
1   882033  rs2272756   G   A   .   PASS    AF=0.23 ES:SE:LP:AF:SS:ID   -0.0028:0.076:0.0132283:0.23:3550:rs2272756
1   962210  rs3128126   A   G   .   PASS    AF=0.415    ES:SE:LP:AF:SS:ID   -0.049:0.07:0.309804:0.415:3410:rs3128126
1   990380  rs3121561   C   T   .   PASS    AF=0.254    ES:SE:LP:AF:SS:ID   -0.1:0.043:1.69897:0.254:5752:rs3121561
1   998501  rs3813193   G   C   .   PASS    AF=0.146    ES:SE:LP:AF:SS:ID   -0.021:0.08:0.102373:0.146:3550:rs3813193
1   1003629 rs4075116   C   T   .   PASS    AF=0.734    ES:SE:LP:AF:SS:ID   -0.024:0.034:0.318759:0.734:5753:rs4075116
1   1005806 rs3934834   C   T   .   PASS    AF=0.124    ES:SE:LP:AF:SS:ID   -0.076:0.055:0.769551:0.124:5753:rs3934834
1   1017170 rs3766193   C   G   .   PASS    AF=0.587    ES:SE:LP:AF:SS:ID   -0.02:0.032:0.275724:0.587:5825:rs3766193
1   1017197 rs3766192   C   T   .   PASS    AF=0.571    ES:SE:LP:AF:SS:ID   -0.019:0.031:0.267606:0.571:5825:rs3766192
1   1017587 rs3766191   C   T   .   PASS    AF=0.124    ES:SE:LP:AF:SS:ID   -0.091:0.056:1:0.124:5753:rs3766191
1   1018562 rs9442371   C   T   .   PASS    AF=0.608    ES:SE:LP:AF:SS:ID   -0.015:0.03:0.21467:0.608:5825:rs9442371
1   1018704 rs9442372   A   G   .   PASS    AF=0.588    ES:SE:LP:AF:SS:ID   -0.015:0.03:0.207608:0.588:5825:rs9442372
1   1021346 rs10907177  A   G   .   PASS    AF=0.137    ES:SE:LP:AF:SS:ID   -0.085:0.055:0.920819:0.137:5753:rs10907177
1   1021415 rs3737728   A   G   .   PASS    AF=0.735    ES:SE:LP:AF:SS:ID   -0.026:0.036:0.327902:0.735:5753:rs3737728
1   1021583 rs10907178  A   C   .   PASS    AF=0.112    ES:SE:LP:AF:SS:ID   -0.06:0.068:0.420216:0.112:3550:rs10907178
1   1021695 rs9442398   A   G   .   PASS    AF=0.726    ES:SE:LP:AF:SS:ID   -0.026:0.037:0.318759:0.726:5753:rs9442398
1   1022037 rs6701114   C   T   .   PASS    AF=0.585    ES:SE:LP:AF:SS:ID   -0.022:0.034:0.283997:0.585:5825:rs6701114
1   1025301 rs9442400   T   C   .   PASS    AF=0.952    ES:SE:LP:AF:SS:ID   -0.14:0.23:0.267606:0.952:1915:rs9442400
1   1026707 rs4074137   C   A   .   PASS    AF=0.623    ES:SE:LP:AF:SS:ID   0.029:0.053:0.236572:0.623:3550:rs4074137
1   1030565 rs6687776   C   T   .   PASS    AF=0.133    ES:SE:LP:AF:SS:ID   -0.062:0.052:0.638272:0.133:5753:rs6687776
1   1030633 rs6678318   G   A   .   PASS    AF=0.134    ES:SE:LP:AF:SS:ID   -0.1:0.055:1.18046:0.134:5251:rs6678318
1   1031540 rs9651273   A   G   .   PASS    AF=0.717    ES:SE:LP:AF:SS:ID   -0.0084:0.041:0.0757207:0.717:5825:rs9651273
1   1036959 rs11579015  T   C   .   PASS    AF=0.046    ES:SE:LP:AF:SS:ID   -0.083:0.056:0.853872:0.046:5753:rs11579015
1   1040026 rs6671356   T   C   .   PASS    AF=0.115    ES:SE:LP:AF:SS:ID   -0.058:0.052:0.568636:0.115:5753:rs6671356
1   1046164 rs6666280   C   T   .   PASS    AF=0.062    ES:SE:LP:AF:SS:ID   -0.065:0.058:0.585027:0.062:5752:rs6666280
1   1048955 rs4970405   A   G   .   PASS    AF=0.088    ES:SE:LP:AF:SS:ID   -0.072:0.057:0.69897:0.088:5753:rs4970405
1   1049950 rs12726255  A   G   .   PASS    AF=0.115    ES:SE:LP:AF:SS:ID   -0.06:0.056:0.537602:0.115:5753:rs12726255
1   1053452 rs4970409   G   A   .   PASS    AF=0.093    ES:SE:LP:AF:SS:ID   -0.086:0.06:0.79588:0.093:5753:rs4970409
1   1060174 rs7548798   C   T   .   PASS    AF=0.314    ES:SE:LP:AF:SS:ID   0.071:0.071:0.49485:0.314:2916:rs7548798
1   1060608 rs17160824  G   A   .   PASS    AF=0.097    ES:SE:LP:AF:SS:ID   -0.094:0.061:0.920819:0.097:5753:rs17160824
1   1061115 rs17160826  T   C   .   PASS    AF=0.051    ES:SE:LP:AF:SS:ID   -0.1:0.063:0.958607:0.051:5753:rs17160826
1   1061152 rs12748370  T   C   .   PASS    AF=0.055    ES:SE:LP:AF:SS:ID   -0.098:0.064:0.920819:0.055:5753:rs12748370
1   1061166 rs11807848  T   C   .   PASS    AF=0.389    ES:SE:LP:AF:SS:ID   0.0051:0.043:0.0409586:0.389:5753:rs11807848
1   1062638 rs9442373   C   A   .   PASS    AF=0.575    ES:SE:LP:AF:SS:ID   -0.018:0.043:0.173925:0.575:5825:rs9442373
1   1064535 rs6682475   G   C   .   PASS    AF=0.766    ES:SE:LP:AF:SS:ID   0.041:0.075:0.229148:0.766:3622:rs6682475
1   1064979 rs2298217   C   T   .   PASS    AF=0.115    ES:SE:LP:AF:SS:ID   -0.094:0.061:0.920819:0.115:5753:rs2298217