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IEU GWAS information

Trait: Diseases of the skin and subcutaneous tissue.

name	value
id	ukb-d-XII_SKIN_SUBCUTAN
trait	Diseases of the skin and subcutaneous tissue
category	Binary
ncase	27074
ncontrol	334120
sample_size	361194
sex	Males and females
population	European
group_name	public
access	public
build	HG19/GRCh37
author	Neale lab
year	2018
mr	1
nsnp	13586589

Report information

name	value
gwas_id	ukb-d-XII_SKIN_SUBCUTAN
bcf_file	ukb-d-XII_SKIN_SUBCUTAN.vcf.gz
qc_metrics_file	qc_metrics.json
metadata	metadata.json
refdata	1kg_v3_nomult.bcf
compile_time	2020-05-09 17:34 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-XII_SKIN_SUBCUTAN/ukb-d-XII_SKIN_SUBCUTAN.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-XII_SKIN_SUBCUTAN/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 14:51:21 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-XII_SKIN_SUBCUTAN/ukb-d-XII_SKIN_SUBCUTAN.vcf.gz ...
Read summary statistics for 13586588 SNPs.
Dropped 12710 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: 0.0054 (0.0015)
Lambda GC: 1.0464
Mean Chi^2: 1.051
Intercept: 1.0126 (0.0069)
Ratio: 0.2465 (0.1354)
Analysis finished at Mon Nov 25 14:53:47 2019
Total time elapsed: 2.0m:26.39s

QC metrics

Metrics

{
    "af_correlation": 0.9521,
    "inflation_factor": 1.0332,
    "mean_EFFECT": -4.5188e-06,
    "n": 361194,
    "n_snps": 13586588,
    "n_clumped_hits": 2,
    "n_p_sig": 177,
    "n_mono": 0,
    "n_ns": 1251809,
    "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": 569299,
    "n_est": 362574.814,
    "ratio_se_n": 1.0019,
    "mean_diff": -0,
    "ratio_diff": 50.9363,
    "sd_y_est1": 0.264,
    "sd_y_est2": 0.2646,
    "r2_sum1": 0.0001,
    "r2_sum2": 0.0012,
    "r2_sum3": 0.0012,
    "r2_sum4": 0.0012,
    "ldsc_nsnp_merge_refpanel_ld": 1283504,
    "ldsc_nsnp_merge_regression_ld": 1283504,
    "ldsc_observed_scale_h2_beta": 0.0054,
    "ldsc_observed_scale_h2_se": 0.0015,
    "ldsc_intercept_beta": 1.0126,
    "ldsc_intercept_se": 0.0069,
    "ldsc_lambda_gc": 1.0464,
    "ldsc_mean_chisq": 1.051,
    "ldsc_ratio": 0.2471
}

Flags

name	value
af_correlation	FALSE
inflation_factor	FALSE
n	FALSE
is_snpid_non_unique	TRUE
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

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	13574542	0	NA	NA	NA	NA	NA	NA	NA	NA
character	REF	0	1.0000000	1	100	0	57083	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	9.051333e+00	6.184971e+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	7.902505e+07	5.591478e+07	3.02000e+02	3.293100e+07	7.013845e+07	1.148590e+08	2.492309e+08	▇▆▅▂▁
numeric	EFFECT	0	1.0000000	NA	NA	NA	NA	NA	-4.500000e-06	3.648400e-03	-4.19255e-02	-9.850000e-04	-5.700000e-06	9.636000e-04	4.770830e-02	▁▁▇▁▁
numeric	SE	0	1.0000000	NA	NA	NA	NA	NA	2.610800e-03	2.518500e-03	5.10800e-04	7.433000e-04	1.369700e-03	3.752000e-03	1.267050e-02	▇▂▁▁▁
numeric	PVAL	0	1.0000000	NA	NA	NA	NA	NA	4.949141e-01	2.901022e-01	0.00000e+00	2.422942e-01	4.929615e-01	7.464986e-01	1.000000e+00	▇▇▇▇▇
numeric	PVAL_ztest	0	1.0000000	NA	NA	NA	NA	NA	4.949136e-01	2.901025e-01	0.00000e+00	2.422937e-01	4.929610e-01	7.464985e-01	9.999997e-01	▇▇▇▇▇
numeric	AF	0	1.0000000	NA	NA	NA	NA	NA	1.908016e-01	2.544020e-01	1.00000e-03	7.429000e-03	6.002940e-02	2.953060e-01	9.989990e-01	▇▂▁▁▁
numeric	AF_reference	569299	0.9580985	NA	NA	NA	NA	NA	1.963330e-01	2.471005e-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	3.611940e+05	0.000000e+00	3.61194e+05	3.611940e+05	3.611940e+05	3.611940e+05	3.611940e+05	▁▁▇▁▁

Head and tail

CHROM	POS	ID	REF	ALT	EFFECT	SE	PVAL	PVAL_ztest	AF	AF_reference	N
1	692794	rs530212009	CA	C	0.0000656	0.0010880	0.9519201	0.9519203	0.1106400	0.1894970	361194
1	693731	rs12238997	A	G	-0.0002782	0.0010281	0.7867197	0.7867197	0.1158300	0.1417730	361194
1	707522	rs371890604	G	C	-0.0003556	0.0011558	0.7583313	0.7583312	0.0973034	0.1293930	361194
1	717587	rs144155419	G	A	0.0020308	0.0027579	0.4615067	0.4615066	0.0156880	0.0045926	361194
1	723329	rs189787166	A	T	-0.0051656	0.0081369	0.5255354	0.5255352	0.0017336	0.0003994	361194
1	730087	rs148120343	T	C	-0.0008216	0.0014322	0.5661832	0.5661839	0.0564602	0.0127796	361194
1	731718	rs142557973	T	C	-0.0002790	0.0009750	0.7747918	0.7747916	0.1217380	0.1543530	361194
1	732032	rs61770163	A	C	0.0002926	0.0010400	0.7784182	0.7784200	0.1211710	0.1555510	361194
1	734349	rs141242758	T	C	-0.0002893	0.0009755	0.7667945	0.7667949	0.1209650	0.1525560	361194
1	740284	rs61770167	C	T	-0.0046577	0.0044631	0.2966709	0.2966705	0.0057851	0.0023962	361194

CHROM	POS	ID	REF	ALT	EFFECT	SE	PVAL	PVAL_ztest	AF	AF_reference	N
23	154923311	rs141127553	C	T	0.0020502	0.0011264	0.0687337	0.0687331	0.0561667	0.0309934	361194
23	154923374	rs111332691	T	A	-0.0015538	0.0012379	0.2094059	0.2094061	0.0447862	0.0116556	361194
23	154925045	rs509981	C	T	-0.0013270	0.0005956	0.0258941	0.0258929	0.2456060	0.3634440	361194
23	154925895	rs538470	C	T	-0.0012725	0.0006093	0.0367519	0.0367517	0.2419150	0.3634440	361194
23	154927581	rs644138	G	A	-0.0006550	0.0005602	0.2423042	0.2423032	0.3021620	0.4635760	361194
23	154929412	rs557132	C	T	-0.0013258	0.0005958	0.0260633	0.0260624	0.2454590	0.3568210	361194
23	154929637	rs35185538	CT	C	-0.0011444	0.0006218	0.0657158	0.0657145	0.2296970	0.3011920	361194
23	154929952	rs4012982	CAA	C	-0.0014456	0.0006266	0.0210630	0.0210624	0.2394250	0.3165560	361194
23	154930230	rs781880	A	G	-0.0012759	0.0005957	0.0322055	0.0322044	0.2458690	0.3618540	361194
23	154930487	rs781879	T	A	-0.0037664	0.0020436	0.0653266	0.0653250	0.0195623	0.1263580	361194

bcf preview

1   692794  rs530212009 CA  C   .   PASS    AF=0.11064  ES:SE:LP:AF:SS:ID   6.56033e-05:0.00108803:0.0213995:0.11064:361194:1_692794_CA_C
1   693731  rs12238997  A   G   .   PASS    AF=0.11583  ES:SE:LP:AF:SS:ID   -0.000278165:0.00102806:0.10418:0.11583:361194:rs12238997
1   707522  rs371890604 G   C   .   PASS    AF=0.0973034    ES:SE:LP:AF:SS:ID   -0.000355593:0.00115575:0.120141:0.0973034:361194:rs371890604
1   717587  rs144155419 G   A   .   PASS    AF=0.015688 ES:SE:LP:AF:SS:ID   0.00203083:0.0027579:0.335822:0.015688:361194:rs144155419
1   723329  rs189787166 A   T   .   PASS    AF=0.00173363   ES:SE:LP:AF:SS:ID   -0.00516558:0.00813687:0.279398:0.00173363:361194:rs189787166
1   730087  rs148120343 T   C   .   PASS    AF=0.0564602    ES:SE:LP:AF:SS:ID   -0.000821637:0.00143222:0.247043:0.0564602:361194:rs148120343
1   731718  rs58276399  T   C   .   PASS    AF=0.121738 ES:SE:LP:AF:SS:ID   -0.000278963:0.00097501:0.110815:0.121738:361194:rs58276399
1   732032  rs61770163  A   C   .   PASS    AF=0.121171 ES:SE:LP:AF:SS:ID   0.000292645:0.00104004:0.108787:0.121171:361194:rs61770163
1   734349  rs141242758 T   C   .   PASS    AF=0.120965 ES:SE:LP:AF:SS:ID   -0.000289314:0.000975534:0.115321:0.120965:361194:rs141242758
1   740284  rs61770167  C   T   .   PASS    AF=0.00578512   ES:SE:LP:AF:SS:ID   -0.00465767:0.00446308:0.527725:0.00578512:361194:rs61770167
1   742813  rs112573343 C   T   .   PASS    AF=0.00187787   ES:SE:LP:AF:SS:ID   0.00252806:0.00842898:0.116773:0.00187787:361194:rs112573343
1   749963  rs529266287 T   TAA .   PASS    AF=0.869742 ES:SE:LP:AF:SS:ID   0.000281037:0.000961722:0.113443:0.869742:361194:rs529266287
1   750230  rs190826124 G   C   .   PASS    AF=0.00153021   ES:SE:LP:AF:SS:ID   -0.00285146:0.00870643:0.128847:0.00153021:361194:rs190826124
1   751343  rs28544273  T   A   .   PASS    AF=0.122916 ES:SE:LP:AF:SS:ID   -0.00050535:0.000952459:0.224962:0.122916:361194:rs28544273
1   751488  rs200141114 G   GA  .   PASS    AF=0.142712 ES:SE:LP:AF:SS:ID   -0.000325954:0.000941454:0.137168:0.142712:361194:rs200141114
1   751756  rs28527770  T   C   .   PASS    AF=0.123031 ES:SE:LP:AF:SS:ID   -0.000533575:0.000951133:0.240479:0.123031:361194:rs28527770
1   753405  rs3115860   C   A   .   PASS    AF=0.87089  ES:SE:LP:AF:SS:ID   0.000680337:0.000926848:0.334486:0.87089:361194:rs3115860
1   753425  rs3131970   T   C   .   PASS    AF=0.875472 ES:SE:LP:AF:SS:ID   0.000618968:0.000942207:0.291389:0.875472:361194:rs3131970
1   753541  rs2073813   G   A   .   PASS    AF=0.128631 ES:SE:LP:AF:SS:ID   -0.000640462:0.000929172:0.309232:0.128631:361194:rs2073813
1   754105  rs12184325  C   T   .   PASS    AF=0.0363613    ES:SE:LP:AF:SS:ID   0.000575206:0.00168573:0.134933:0.0363613:361194:rs12184325
1   754182  rs3131969   A   G   .   PASS    AF=0.870484 ES:SE:LP:AF:SS:ID   0.000635472:0.000925884:0.307596:0.870484:361194:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.870589 ES:SE:LP:AF:SS:ID   0.00069221:0.000926307:0.342089:0.870589:361194:rs3131968
1   754334  rs3131967   T   C   .   PASS    AF=0.870481 ES:SE:LP:AF:SS:ID   0.00062084:0.00092585:0.298864:0.870481:361194:rs3131967
1   754433  rs150578204 G   A   .   PASS    AF=0.00504367   ES:SE:LP:AF:SS:ID   -0.00699878:0.00475314:0.851092:0.00504367:361194:rs150578204
1   754458  rs142682604 G   T   .   PASS    AF=0.00501064   ES:SE:LP:AF:SS:ID   -0.00707385:0.00476586:0.860949:0.00501064:361194:rs142682604
1   755435  rs184270342 T   G   .   PASS    AF=0.00558665   ES:SE:LP:AF:SS:ID   0.000903037:0.00460354:0.0734086:0.00558665:361194:rs184270342
1   755890  rs3115858   A   T   .   PASS    AF=0.870563 ES:SE:LP:AF:SS:ID   0.000660209:0.00092422:0.323292:0.870563:361194:rs3115858
1   756434  rs61768170  G   C   .   PASS    AF=0.125985 ES:SE:LP:AF:SS:ID   -0.000637053:0.000943044:0.301603:0.125985:361194:rs61768170
1   756604  rs3131962   A   G   .   PASS    AF=0.870127 ES:SE:LP:AF:SS:ID   0.000633594:0.000921996:0.308071:0.870127:361194:rs3131962
1   757640  rs3115853   G   A   .   PASS    AF=0.869414 ES:SE:LP:AF:SS:ID   0.00057085:0.000921156:0.271282:0.869414:361194:rs3115853
1   757734  rs4951929   C   T   .   PASS    AF=0.870281 ES:SE:LP:AF:SS:ID   0.000640066:0.00092279:0.311651:0.870281:361194:rs4951929
1   757936  rs4951862   C   A   .   PASS    AF=0.870287 ES:SE:LP:AF:SS:ID   0.000640982:0.000922855:0.312178:0.870287:361194:rs4951862
1   758144  rs3131956   A   G   .   PASS    AF=0.870295 ES:SE:LP:AF:SS:ID   0.000641296:0.000922884:0.312356:0.870295:361194:rs3131956
1   758626  rs3131954   C   T   .   PASS    AF=0.870739 ES:SE:LP:AF:SS:ID   0.000659537:0.000925234:0.32244:0.870739:361194:rs3131954
1   759293  rs10157329  T   A   .   PASS    AF=0.0988442    ES:SE:LP:AF:SS:ID   -0.0005986:0.00107518:0.238296:0.0988442:361194:rs10157329
1   759600  rs545998451 AGT A   .   PASS    AF=0.00647588   ES:SE:LP:AF:SS:ID   0.00118101:0.00415885:0.109898:0.00647588:361194:1_759600_AGT_A
1   759837  rs3115851   T   A   .   PASS    AF=0.874635 ES:SE:LP:AF:SS:ID   0.000620296:0.000939023:0.29338:0.874635:361194:rs3115851
1   761732  rs2286139   C   T   .   PASS    AF=0.864027 ES:SE:LP:AF:SS:ID   0.000492817:0.000920852:0.22729:0.864027:361194:rs2286139
1   761752  rs1057213   C   T   .   PASS    AF=0.869425 ES:SE:LP:AF:SS:ID   0.000743347:0.000929792:0.372619:0.869425:361194:rs1057213
1   762273  rs3115849   G   A   .   PASS    AF=0.866371 ES:SE:LP:AF:SS:ID   0.000751761:0.00092998:0.377908:0.866371:361194:rs3115849
1   762485  rs12095200  C   A   .   PASS    AF=0.0987831    ES:SE:LP:AF:SS:ID   -0.000411224:0.00111336:0.147603:0.0987831:361194:rs12095200
1   762589  rs3115848   G   C   .   PASS    AF=0.871556 ES:SE:LP:AF:SS:ID   0.000779616:0.000940575:0.390217:0.871556:361194:rs3115848
1   762592  rs3131950   C   G   .   PASS    AF=0.871556 ES:SE:LP:AF:SS:ID   0.000779704:0.000940575:0.390272:0.871556:361194:rs3131950
1   762601  rs3131949   T   C   .   PASS    AF=0.871555 ES:SE:LP:AF:SS:ID   0.00077854:0.000940593:0.389517:0.871555:361194:rs3131949
1   762632  rs3131948   T   A   .   PASS    AF=0.871929 ES:SE:LP:AF:SS:ID   0.000741212:0.00094113:0.365578:0.871929:361194:rs3131948
1   764191  rs7515915   T   G   .   PASS    AF=0.125562 ES:SE:LP:AF:SS:ID   -0.000629539:0.000941872:0.297669:0.125562:361194:rs7515915
1   766007  rs61768174  A   C   .   PASS    AF=0.105428 ES:SE:LP:AF:SS:ID   -0.000538385:0.00102536:0.222186:0.105428:361194:rs61768174
1   766105  rs2519015   T   A   .   PASS    AF=0.855376 ES:SE:LP:AF:SS:ID   0.000942883:0.000920506:0.514719:0.855376:361194:rs2519015
1   767393  rs538667473 A   C   .   PASS    AF=0.00165444   ES:SE:LP:AF:SS:ID   -0.00740292:0.00815436:0.438948:0.00165444:361194:rs538667473
1   768116  rs376645387 A   AGTTTT  .   PASS    AF=0.838358 ES:SE:LP:AF:SS:ID   -0.00103879:0.000906863:0.598582:0.838358:361194:rs376645387