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IEU GWAS information

Trait: Mean sphered cell volume.

name	value
id	ukb-d-30270_irnt
trait	Mean sphered cell volume
category	Continuous
sample_size	344729
sex	Males and females
population	European
group_name	public
access	public
build	HG19/GRCh37
author	Neale lab
year	2018
mr	1
nsnp	13586218

Report information

name	value
gwas_id	ukb-d-30270_irnt
bcf_file	ukb-d-30270_irnt.vcf.gz
qc_metrics_file	qc_metrics.json
metadata	metadata.json
refdata	1kg_v3_nomult.bcf
compile_time	2020-05-10 03:57 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/ukb-d-import/processed/ukb-d-30270_irnt/ukb-d-30270_irnt.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/ukb-d-import/processed/ukb-d-30270_irnt/ldsc.txt \
--w-ld-chr /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/reference/eur_w_ld_chr/ 

Beginning analysis at Mon Nov 25 14:54:38 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-30270_irnt/ukb-d-30270_irnt.vcf.gz ...
Read summary statistics for 13586217 SNPs.
Dropped 12711 SNPs with duplicated rs numbers.
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, 1283504 SNPs remain.
After merging with regression SNP LD, 1283504 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.181 (0.0175)
Lambda GC: 1.5158
Mean Chi^2: 2.4341
Intercept: 1.184 (0.0196)
Ratio: 0.1283 (0.0137)
Analysis finished at Mon Nov 25 14:56:55 2019
Total time elapsed: 2.0m:17.36s

QC metrics

Metrics

{
    "af_correlation": 0.9521,
    "inflation_factor": 1.3378,
    "mean_EFFECT": -0,
    "n": 344729,
    "n_snps": 13586217,
    "n_clumped_hits": 337,
    "n_p_sig": 75970,
    "n_mono": 0,
    "n_ns": 1251786,
    "n_mac": 0,
    "is_snpid_unique": false,
    "n_miss_EFFECT": 0,
    "n_miss_SE": 0,
    "n_miss_PVAL": 0,
    "n_miss_AF": 0,
    "n_miss_AF_reference": 569217,
    "n_est": 346034.3048,
    "ratio_se_n": 1.0019,
    "mean_diff": -7.1728e-07,
    "ratio_diff": 1.0054,
    "sd_y_est1": 0.9978,
    "sd_y_est2": 0.9997,
    "r2_sum1": 0.1231,
    "r2_sum2": 0.1236,
    "r2_sum3": 0.1232,
    "r2_sum4": 0.1232,
    "ldsc_nsnp_merge_refpanel_ld": 1283504,
    "ldsc_nsnp_merge_regression_ld": 1283504,
    "ldsc_observed_scale_h2_beta": 0.181,
    "ldsc_observed_scale_h2_se": 0.0175,
    "ldsc_intercept_beta": 1.184,
    "ldsc_intercept_se": 0.0196,
    "ldsc_lambda_gc": 1.5158,
    "ldsc_mean_chisq": 2.4341,
    "ldsc_ratio": 0.1283
}

Flags

name	value
af_correlation	FALSE
inflation_factor	TRUE
n	FALSE
is_snpid_non_unique	TRUE
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

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	94	0	13574170	0	NA	NA	NA	NA	NA	NA	NA	NA
character	REF	0	1.0000000	1	100	0	57082	0	NA	NA	NA	NA	NA	NA	NA	NA
character	ALT	0	1.0000000	1	342	0	33337	0	NA	NA	NA	NA	NA	NA	NA	NA
numeric	CHROM	0	1.0000000	NA	NA	NA	NA	NA	9.051358e+00	6.184962e+00	1.00000e+00	4.000000e+00	8.000000e+00	1.300000e+01	2.300000e+01	▇▅▅▂▂
numeric	POS	0	1.0000000	NA	NA	NA	NA	NA	7.902498e+07	5.591474e+07	3.02000e+02	3.293100e+07	7.013848e+07	1.148588e+08	2.492309e+08	▇▆▅▂▁
numeric	EFFECT	0	1.0000000	NA	NA	NA	NA	NA	-1.180000e-05	1.513430e-02	-4.09398e-01	-4.489300e-03	6.900000e-06	4.510400e-03	4.300360e-01	▁▁▇▁▁
numeric	SE	0	1.0000000	NA	NA	NA	NA	NA	1.009790e-02	9.740900e-03	1.97500e-03	2.874800e-03	5.297800e-03	1.451070e-02	4.954070e-02	▇▂▁▁▁
numeric	PVAL	0	1.0000000	NA	NA	NA	NA	NA	4.508988e-01	3.033980e-01	0.00000e+00	1.754519e-01	4.353124e-01	7.137925e-01	1.000000e+00	▇▆▅▅▅
numeric	PVAL_ztest	0	1.0000000	NA	NA	NA	NA	NA	4.508983e-01	3.033983e-01	0.00000e+00	1.754514e-01	4.353108e-01	7.137919e-01	9.999999e-01	▇▆▅▅▅
numeric	AF	0	1.0000000	NA	NA	NA	NA	NA	1.908069e-01	2.544041e-01	1.00000e-03	7.430400e-03	6.003420e-02	2.953250e-01	9.989990e-01	▇▂▁▁▁
numeric	AF_reference	569217	0.9581033	NA	NA	NA	NA	NA	1.963367e-01	2.471015e-01	0.00000e+00	5.591000e-03	8.426520e-02	3.081070e-01	1.000000e+00	▇▂▁▁▁
numeric	N	0	1.0000000	NA	NA	NA	NA	NA	3.447290e+05	0.000000e+00	3.44729e+05	3.447290e+05	3.447290e+05	3.447290e+05	3.447290e+05	▁▁▇▁▁

Head and tail

CHROM	POS	ID	REF	ALT	EFFECT	SE	PVAL	PVAL_ztest	AF	AF_reference	N
1	692794	rs530212009	CA	C	-0.0027350	0.0042083	0.5157426	0.5157432	0.1106300	0.1894970	344729
1	693731	rs12238997	A	G	-0.0035935	0.0039764	0.3661500	0.3661495	0.1158130	0.1417730	344729
1	707522	rs371890604	G	C	-0.0021973	0.0044724	0.6232123	0.6232119	0.0972243	0.1293930	344729
1	717587	rs144155419	G	A	-0.0135033	0.0106495	0.2048071	0.2048069	0.0157292	0.0045926	344729
1	723329	rs189787166	A	T	-0.0080058	0.0316402	0.8002471	0.8002472	0.0017197	0.0003994	344729
1	730087	rs148120343	T	C	-0.0023654	0.0055354	0.6691477	0.6691463	0.0564849	0.0127796	344729
1	731718	rs142557973	T	C	-0.0027443	0.0037711	0.4667937	0.4667935	0.1217300	0.1543530	344729
1	732032	rs61770163	A	C	-0.0025598	0.0040233	0.5246226	0.5246225	0.1211220	0.1555510	344729
1	734349	rs141242758	T	C	-0.0028451	0.0037731	0.4508250	0.4508249	0.1209620	0.1525560	344729
1	740284	rs61770167	C	T	-0.0096655	0.0172757	0.5758296	0.5758294	0.0057743	0.0023962	344729

CHROM	POS	ID	REF	ALT	EFFECT	SE	PVAL	PVAL_ztest	AF	AF_reference	N
23	154923311	rs141127553	C	T	-0.0009763	0.0043542	0.8225869	0.8225864	0.0561570	0.0309934	344729
23	154923374	rs111332691	T	A	0.0025917	0.0047852	0.5880943	0.5880955	0.0447961	0.0116556	344729
23	154925045	rs509981	C	T	0.0025913	0.0023028	0.2604792	0.2604768	0.2456220	0.3634440	344729
23	154925895	rs538470	C	T	0.0025912	0.0023555	0.2713008	0.2712983	0.2419530	0.3634440	344729
23	154927581	rs644138	G	A	0.0020616	0.0021657	0.3411112	0.3411106	0.3021780	0.4635760	344729
23	154929412	rs557132	C	T	0.0026638	0.0023035	0.2475067	0.2475059	0.2454760	0.3568210	344729
23	154929637	rs35185538	CT	C	0.0027374	0.0024041	0.2548537	0.2548531	0.2297040	0.3011920	344729
23	154929952	rs4012982	CAA	C	0.0033756	0.0024228	0.1635502	0.1635497	0.2394410	0.3165560	344729
23	154930230	rs781880	A	G	0.0025914	0.0023031	0.2605140	0.2605122	0.2458870	0.3618540	344729
23	154930487	rs781879	T	A	-0.0040360	0.0079058	0.6096983	0.6096973	0.0195262	0.1263580	344729

bcf preview

1   692794  rs530212009 CA  C   .   PASS    AF=0.11063  ES:SE:LP:AF:SS:ID   -0.00273505:0.00420828:0.287567:0.11063:344729:1_692794_CA_C
1   693731  rs12238997  A   G   .   PASS    AF=0.115813 ES:SE:LP:AF:SS:ID   -0.00359351:0.0039764:0.436341:0.115813:344729:rs12238997
1   707522  rs371890604 G   C   .   PASS    AF=0.0972243    ES:SE:LP:AF:SS:ID   -0.00219733:0.00447245:0.205364:0.0972243:344729:rs371890604
1   717587  rs144155419 G   A   .   PASS    AF=0.0157292    ES:SE:LP:AF:SS:ID   -0.0135033:0.0106495:0.688655:0.0157292:344729:rs144155419
1   723329  rs189787166 A   T   .   PASS    AF=0.00171967   ES:SE:LP:AF:SS:ID   -0.00800583:0.0316402:0.0967759:0.00171967:344729:rs189787166
1   730087  rs148120343 T   C   .   PASS    AF=0.0564849    ES:SE:LP:AF:SS:ID   -0.00236537:0.00553536:0.174478:0.0564849:344729:rs148120343
1   731718  rs58276399  T   C   .   PASS    AF=0.12173  ES:SE:LP:AF:SS:ID   -0.00274426:0.00377111:0.330875:0.12173:344729:rs58276399
1   732032  rs61770163  A   C   .   PASS    AF=0.121122 ES:SE:LP:AF:SS:ID   -0.00255975:0.00402327:0.280153:0.121122:344729:rs61770163
1   734349  rs141242758 T   C   .   PASS    AF=0.120962 ES:SE:LP:AF:SS:ID   -0.00284507:0.0037731:0.345992:0.120962:344729:rs141242758
1   740284  rs61770167  C   T   .   PASS    AF=0.00577432   ES:SE:LP:AF:SS:ID   -0.00966553:0.0172757:0.239706:0.00577432:344729:rs61770167
1   742813  rs112573343 C   T   .   PASS    AF=0.0018795    ES:SE:LP:AF:SS:ID   -0.0434687:0.0326271:0.738102:0.0018795:344729:rs112573343
1   749963  rs529266287 T   TAA .   PASS    AF=0.869782 ES:SE:LP:AF:SS:ID   0.00223405:0.00372016:0.261095:0.869782:344729:rs529266287
1   750230  rs190826124 G   C   .   PASS    AF=0.00153601   ES:SE:LP:AF:SS:ID   -0.0349627:0.033606:0.525537:0.00153601:344729:rs190826124
1   751343  rs28544273  T   A   .   PASS    AF=0.122886 ES:SE:LP:AF:SS:ID   -0.00073826:0.00368378:0.0751209:0.122886:344729:rs28544273
1   751488  rs200141114 G   GA  .   PASS    AF=0.142712 ES:SE:LP:AF:SS:ID   0.000232159:0.00364122:0.0226592:0.142712:344729:rs200141114
1   751756  rs28527770  T   C   .   PASS    AF=0.123004 ES:SE:LP:AF:SS:ID   -0.000862362:0.00367863:0.0890263:0.123004:344729:rs28527770
1   753405  rs3115860   C   A   .   PASS    AF=0.870907 ES:SE:LP:AF:SS:ID   0.00205864:0.00358489:0.247341:0.870907:344729:rs3115860
1   753425  rs3131970   T   C   .   PASS    AF=0.875493 ES:SE:LP:AF:SS:ID   0.00140947:0.00364412:0.155572:0.875493:344729:rs3131970
1   753541  rs2073813   G   A   .   PASS    AF=0.128617 ES:SE:LP:AF:SS:ID   -0.00162331:0.00359379:0.186095:0.128617:344729:rs2073813
1   754105  rs12184325  C   T   .   PASS    AF=0.0363561    ES:SE:LP:AF:SS:ID   0.00783482:0.00652109:0.639077:0.0363561:344729:rs12184325
1   754182  rs3131969   A   G   .   PASS    AF=0.8705   ES:SE:LP:AF:SS:ID   0.0022534:0.00358111:0.276391:0.8705:344729:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.870603 ES:SE:LP:AF:SS:ID   0.00201891:0.0035827:0.241782:0.870603:344729:rs3131968
1   754334  rs3131967   T   C   .   PASS    AF=0.870495 ES:SE:LP:AF:SS:ID   0.00227176:0.00358096:0.279163:0.870495:344729:rs3131967
1   754433  rs150578204 G   A   .   PASS    AF=0.00505869   ES:SE:LP:AF:SS:ID   0.000263928:0.0183536:0.00501146:0.00505869:344729:rs150578204
1   754458  rs142682604 G   T   .   PASS    AF=0.00502542   ES:SE:LP:AF:SS:ID   -1.62553e-05:0.0184028:0.000306286:0.00502542:344729:rs142682604
1   755435  rs184270342 T   G   .   PASS    AF=0.00558651   ES:SE:LP:AF:SS:ID   -0.00821141:0.0177995:0.190734:0.00558651:344729:rs184270342
1   755890  rs3115858   A   T   .   PASS    AF=0.870579 ES:SE:LP:AF:SS:ID   0.00236235:0.00357467:0.293536:0.870579:344729:rs3115858
1   756434  rs61768170  G   C   .   PASS    AF=0.125958 ES:SE:LP:AF:SS:ID   -0.00160939:0.00364769:0.181073:0.125958:344729:rs61768170
1   756604  rs3131962   A   G   .   PASS    AF=0.870143 ES:SE:LP:AF:SS:ID   0.00231582:0.00356604:0.287288:0.870143:344729:rs3131962
1   757640  rs3115853   G   A   .   PASS    AF=0.869424 ES:SE:LP:AF:SS:ID   0.00239342:0.00356272:0.299544:0.869424:344729:rs3115853
1   757734  rs4951929   C   T   .   PASS    AF=0.870297 ES:SE:LP:AF:SS:ID   0.00230925:0.00356914:0.285981:0.870297:344729:rs4951929
1   757936  rs4951862   C   A   .   PASS    AF=0.870303 ES:SE:LP:AF:SS:ID   0.0023075:0.0035694:0.28569:0.870303:344729:rs4951862
1   758144  rs3131956   A   G   .   PASS    AF=0.870312 ES:SE:LP:AF:SS:ID   0.00234326:0.00356951:0.291133:0.870312:344729:rs3131956
1   758626  rs3131954   C   T   .   PASS    AF=0.870753 ES:SE:LP:AF:SS:ID   0.00233173:0.0035786:0.288468:0.870753:344729:rs3131954
1   759293  rs10157329  T   A   .   PASS    AF=0.0987463    ES:SE:LP:AF:SS:ID   0.000988655:0.00416048:0.0903541:0.0987463:344729:rs10157329
1   759600  rs545998451 AGT A   .   PASS    AF=0.00648112   ES:SE:LP:AF:SS:ID   -0.0103499:0.0160765:0.284236:0.00648112:344729:1_759600_AGT_A
1   759837  rs3115851   T   A   .   PASS    AF=0.874658 ES:SE:LP:AF:SS:ID   0.00162525:0.00363193:0.184075:0.874658:344729:rs3115851
1   761732  rs2286139   C   T   .   PASS    AF=0.864055 ES:SE:LP:AF:SS:ID   0.00274827:0.0035617:0.35621:0.864055:344729:rs2286139
1   761752  rs1057213   C   T   .   PASS    AF=0.869438 ES:SE:LP:AF:SS:ID   0.00259642:0.00359624:0.327619:0.869438:344729:rs1057213
1   762273  rs3115849   G   A   .   PASS    AF=0.866397 ES:SE:LP:AF:SS:ID   0.0015003:0.00359719:0.169653:0.866397:344729:rs3115849
1   762485  rs12095200  C   A   .   PASS    AF=0.0987143    ES:SE:LP:AF:SS:ID   -0.000756146:0.00430765:0.0651689:0.0987143:344729:rs12095200
1   762589  rs3115848   G   C   .   PASS    AF=0.871574 ES:SE:LP:AF:SS:ID   0.00168163:0.003638:0.191175:0.871574:344729:rs3115848
1   762592  rs3131950   C   G   .   PASS    AF=0.871574 ES:SE:LP:AF:SS:ID   0.00168172:0.003638:0.191187:0.871574:344729:rs3131950
1   762601  rs3131949   T   C   .   PASS    AF=0.871574 ES:SE:LP:AF:SS:ID   0.00164511:0.00363808:0.186332:0.871574:344729:rs3131949
1   762632  rs3131948   T   A   .   PASS    AF=0.871945 ES:SE:LP:AF:SS:ID   0.00170731:0.00364015:0.194462:0.871945:344729:rs3131948
1   764191  rs7515915   T   G   .   PASS    AF=0.125545 ES:SE:LP:AF:SS:ID   -0.00115777:0.00364291:0.124576:0.125545:344729:rs7515915
1   766007  rs61768174  A   C   .   PASS    AF=0.105343 ES:SE:LP:AF:SS:ID   0.000214382:0.00396704:0.0191321:0.105343:344729:rs61768174
1   766105  rs2519015   T   A   .   PASS    AF=0.855408 ES:SE:LP:AF:SS:ID   0.00136778:0.00356088:0.154347:0.855408:344729:rs2519015
1   767393  rs538667473 A   C   .   PASS    AF=0.00164172   ES:SE:LP:AF:SS:ID   0.00181753:0.0316963:0.0203274:0.00164172:344729:rs538667473
1   768116  rs376645387 A   AGTTTT  .   PASS    AF=0.838258 ES:SE:LP:AF:SS:ID   0.0010296:0.00350539:0.114089:0.838258:344729:rs376645387