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IEU GWAS information

Trait: Percent emphysema.

name	value
id	ieu-a-1021
pmid	24383474
year	2014
mr	1
note	NULL
trait	Percent emphysema
category	Risk factor
subcategory	Lung disease
population	Chinese
sex	Males and females
ncase	NULL
ncontrol	NULL
sample_size	702
nsnp	2011196
sd	0.697
priority	5
author	Manichaikul A
group_name	public
access	public
build	HG19/GRCh37

Report information

name	value
gwas_id	ieu-a-1021
bcf_file	ieu-a-1021.vcf.gz
qc_metrics_file	qc_metrics.json
metadata	metadata.json
refdata	1kg_v3_nomult.bcf
compile_time	2020-05-10 08:06 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

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-1021/ieu-a-1021.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-1021/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 10:56:10 2020
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-1021/ieu-a-1021.vcf.gz ...
Read summary statistics for 2005933 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, 999865 SNPs remain.
After merging with regression SNP LD, 999865 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: -0.145 (0.1592)
Lambda GC: 1.0162
Mean Chi^2: 1.0079
Intercept: 1.0153 (0.0072)
Ratio: 1.9522 (0.9206)
Analysis finished at Wed Feb  5 10:56:37 2020
Total time elapsed: 26.69s

QC metrics

Metrics

{
    "af_correlation": 0.8703,
    "inflation_factor": 1.0161,
    "mean_EFFECT": 0.0004,
    "n": 2469,
    "n_snps": 2005933,
    "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": 0,
    "n_miss_AF_reference": 14768,
    "n_est": 2449.3377,
    "ratio_se_n": 0.996,
    "mean_diff": -0,
    "ratio_diff": 8.7405,
    "sd_y_est1": 1.0965,
    "sd_y_est2": 1.0922,
    "r2_sum1": 0,
    "r2_sum2": 0,
    "r2_sum3": 0,
    "r2_sum4": 0,
    "ldsc_nsnp_merge_refpanel_ld": 999865,
    "ldsc_nsnp_merge_regression_ld": 999865,
    "ldsc_observed_scale_h2_beta": "NA",
    "ldsc_observed_scale_h2_se": "NA",
    "ldsc_intercept_beta": 1.0153,
    "ldsc_intercept_se": 0.0072,
    "ldsc_lambda_gc": 1.0162,
    "ldsc_mean_chisq": 1.0079,
    "ldsc_ratio": 1.9367
}

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	2005933	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	8.508659e+00	5.624844e+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	7.942183e+07	5.565525e+07	6.6890e+03	3.329494e+07	7.085136e+07	1.149588e+08	2.492086e+08	▇▇▅▂▁
numeric	EFFECT	0	1.0000000	NA	NA	NA	NA	NA	4.171000e-04	5.097840e-02	-6.2097e-01	-2.759600e-02	3.662000e-04	2.805300e-02	5.509400e-01	▁▁▇▁▁
numeric	SE	0	1.0000000	NA	NA	NA	NA	NA	4.596860e-02	2.184260e-02	2.6525e-02	3.253900e-02	3.708900e-02	4.960800e-02	2.173600e-01	▇▁▁▁▁
numeric	PVAL	0	1.0000000	NA	NA	NA	NA	NA	4.982668e-01	2.886842e-01	9.0000e-07	2.479602e-01	4.965797e-01	7.481902e-01	1.000000e+00	▇▇▇▇▇
numeric	PVAL_ztest	0	1.0000000	NA	NA	NA	NA	NA	4.982667e-01	2.886842e-01	9.0000e-07	2.479636e-01	4.965824e-01	7.481832e-01	1.000000e+00	▇▇▇▇▇
numeric	AF	0	1.0000000	NA	NA	NA	NA	NA	3.880711e-01	2.765616e-01	1.0001e-02	1.469300e-01	3.348900e-01	5.988900e-01	9.899990e-01	▇▆▅▃▃
numeric	AF_reference	14768	0.9926378	NA	NA	NA	NA	NA	3.746055e-01	2.393242e-01	1.9970e-04	1.737220e-01	3.250800e-01	5.503190e-01	9.984030e-01	▇▇▅▃▂
numeric	N	0	1.0000000	NA	NA	NA	NA	NA	2.469000e+03	0.000000e+00	2.4690e+03	2.469000e+03	2.469000e+03	2.469000e+03	2.469000e+03	▁▁▇▁▁

Head and tail

CHROM	POS	ID	REF	ALT	EFFECT	SE	PVAL	PVAL_ztest	AF	AF_reference	N
1	721290	rs12565286	G	C	-0.0372520	0.100060	0.7096693	0.7096720	0.024964	0.0371406	2469
1	740857	rs12082473	G	A	-0.0386910	0.103030	0.7072696	0.7072653	0.023504	0.0585064	2469
1	752566	rs3094315	G	A	0.0212100	0.052761	0.6876794	0.6876829	0.907407	0.7182510	2469
1	761732	rs2286139	C	T	0.0341260	0.040360	0.3978002	0.3978093	0.790300	0.6257990	2469
1	777122	rs2980319	A	T	0.0498550	0.056094	0.3741304	0.3741235	0.911681	0.7472040	2469
1	779322	rs4040617	A	G	-0.0509380	0.056716	0.3691204	0.3691195	0.087522	0.2264380	2469
1	785050	rs2905062	G	A	0.0087003	0.036631	0.8122601	0.8122597	0.742220	0.6269970	2469
1	785989	rs2980300	T	C	0.0098980	0.035763	0.7819608	0.7819594	0.740660	0.6269970	2469
1	798959	rs11240777	G	A	-0.0015443	0.032307	0.9618800	0.9618750	0.362270	0.4099440	2469
1	888659	rs3748597	T	C	0.0103300	0.058767	0.8604699	0.8604676	0.919401	0.9227240	2469

CHROM	POS	ID	REF	ALT	EFFECT	SE	PVAL	PVAL_ztest	AF	AF_reference	N
22	51162059	rs10451	G	A	-0.0530160	0.032078	0.0983830	0.0983876	0.398100	0.3865810	2469
22	51163138	rs715586	C	T	0.0678730	0.047336	0.1516202	0.1516134	0.113250	0.0902556	2469
22	51165664	rs8137951	G	A	-0.0413820	0.030776	0.1787500	0.1787482	0.428060	0.4063500	2469
22	51175626	rs3810648	A	G	0.0364550	0.074268	0.6235295	0.6235273	0.044160	0.1084270	2469
22	51186228	rs3865766	C	T	0.0148030	0.030811	0.6309094	0.6309108	0.405000	0.4532750	2469
22	51212875	rs2238837	A	C	0.0122100	0.031501	0.6982999	0.6983071	0.371060	0.3724040	2469
22	51213613	rs34726907	C	T	-0.0037858	0.057168	0.9472000	0.9472008	0.077372	0.1727240	2469
22	51219006	rs28729663	G	A	0.0220910	0.049019	0.6522303	0.6522332	0.116430	0.2052720	2469
23	51666786	rs14115	A	G	0.0300890	0.055228	0.5858899	0.5858813	0.087607	NA	2469
23	118495837	rs12882977	G	A	-0.0608730	0.082322	0.4596402	0.4596338	0.038127	0.2307280	2469

bcf preview

1   721290  rs12565286  G   C   .   PASS    AF=0.024964 ES:SE:LP:AF:SS:ID   -0.037252:0.10006:0.148944:0.024964:2469:rs12565286
1   740857  rs12082473  G   A   .   PASS    AF=0.023504 ES:SE:LP:AF:SS:ID   -0.038691:0.10303:0.150415:0.023504:2469:rs12082473
1   752566  rs3094315   G   A   .   PASS    AF=0.907407 ES:SE:LP:AF:SS:ID   0.02121:0.052761:0.162614:0.907407:2469:rs3094315
1   761732  rs2286139   C   T   .   PASS    AF=0.7903   ES:SE:LP:AF:SS:ID   0.034126:0.04036:0.400335:0.7903:2469:rs2286139
1   777122  rs2980319   A   T   .   PASS    AF=0.911681 ES:SE:LP:AF:SS:ID   0.049855:0.056094:0.426977:0.911681:2469:rs2980319
1   779322  rs4040617   A   G   .   PASS    AF=0.087522 ES:SE:LP:AF:SS:ID   -0.050938:0.056716:0.432832:0.087522:2469:rs4040617
1   785050  rs2905062   G   A   .   PASS    AF=0.74222  ES:SE:LP:AF:SS:ID   0.0087003:0.036631:0.0903049:0.74222:2469:rs2905062
1   785989  rs2980300   T   C   .   PASS    AF=0.74066  ES:SE:LP:AF:SS:ID   0.009898:0.035763:0.106815:0.74066:2469:rs2980300
1   798959  rs11240777  G   A   .   PASS    AF=0.36227  ES:SE:LP:AF:SS:ID   -0.0015443:0.032307:0.0168791:0.36227:2469:rs11240777
1   888659  rs3748597   T   C   .   PASS    AF=0.919401 ES:SE:LP:AF:SS:ID   0.01033:0.058767:0.0652643:0.919401:2469:rs3748597
1   918573  rs2341354   A   G   .   PASS    AF=0.82123  ES:SE:LP:AF:SS:ID   0.0022275:0.040527:0.0194649:0.82123:2469:rs2341354
1   926431  rs4970403   A   T   .   PASS    AF=0.957917 ES:SE:LP:AF:SS:ID   0.061385:0.078645:0.361441:0.957917:2469:rs4970403
1   947034  rs2465126   G   A   .   PASS    AF=0.934473 ES:SE:LP:AF:SS:ID   0.030202:0.064622:0.193657:0.934473:2469:rs2465126
1   949608  rs1921  G   A   .   PASS    AF=0.19231  ES:SE:LP:AF:SS:ID   0.024558:0.038941:0.277144:0.19231:2469:rs1921
1   990417  rs2465136   T   C   .   PASS    AF=0.16738  ES:SE:LP:AF:SS:ID   0.010976:0.040822:0.103457:0.16738:2469:rs2465136
1   990839  rs13129 C   T   .   PASS    AF=0.026429 ES:SE:LP:AF:SS:ID   -0.034518:0.097499:0.14067:0.026429:2469:rs13129
1   1003629 rs4075116   C   T   .   PASS    AF=0.912072 ES:SE:LP:AF:SS:ID   -0.060041:0.056992:0.534439:0.912072:2469:rs4075116
1   1017170 rs3766193   C   G   .   PASS    AF=0.7815   ES:SE:LP:AF:SS:ID   -0.036165:0.041388:0.417687:0.7815:2469:rs3766193
1   1017197 rs3766192   C   T   .   PASS    AF=0.78218  ES:SE:LP:AF:SS:ID   -0.042394:0.041576:0.511604:0.78218:2469:rs3766192
1   1018562 rs9442371   C   T   .   PASS    AF=0.78524  ES:SE:LP:AF:SS:ID   -0.038561:0.040332:0.469762:0.78524:2469:rs9442371
1   1018704 rs9442372   A   G   .   PASS    AF=0.80535  ES:SE:LP:AF:SS:ID   -0.04437:0.041132:0.551758:0.80535:2469:rs9442372
1   1022037 rs6701114   C   T   .   PASS    AF=0.7862   ES:SE:LP:AF:SS:ID   -0.032344:0.041281:0.363181:0.7862:2469:rs6701114
1   1036959 rs11579015  T   C   .   PASS    AF=0.17655  ES:SE:LP:AF:SS:ID   0.009857:0.043309:0.0862073:0.17655:2469:rs11579015
1   1041700 rs6604968   A   G   .   PASS    AF=0.18091  ES:SE:LP:AF:SS:ID   0.0256:0.039124:0.289976:0.18091:2469:rs6604968
1   1048955 rs4970405   A   G   .   PASS    AF=0.14672  ES:SE:LP:AF:SS:ID   -0.00063614:0.042647:0.0051991:0.14672:2469:rs4970405
1   1097335 rs9442385   T   G   .   PASS    AF=0.59559  ES:SE:LP:AF:SS:ID   -0.023567:0.031224:0.346421:0.59559:2469:rs9442385
1   1099342 rs9660710   A   C   .   PASS    AF=0.58159  ES:SE:LP:AF:SS:ID   -0.022434:0.032413:0.310807:0.58159:2469:rs9660710
1   1121014 rs3813204   G   A   .   PASS    AF=0.53962  ES:SE:LP:AF:SS:ID   0.025214:0.034326:0.334766:0.53962:2469:rs3813204
1   1121794 rs11260549  G   A   .   PASS    AF=0.56149  ES:SE:LP:AF:SS:ID   0.025566:0.032843:0.360205:0.56149:2469:rs11260549
1   1125553 rs10907174  A   T   .   PASS    AF=0.7491   ES:SE:LP:AF:SS:ID   -0.0055108:0.035927:0.056461:0.7491:2469:rs10907174
1   1129672 rs11260554  G   T   .   PASS    AF=0.58226  ES:SE:LP:AF:SS:ID   0.025156:0.031194:0.376751:0.58226:2469:rs11260554
1   1130727 rs10907175  A   C   .   PASS    AF=0.17023  ES:SE:LP:AF:SS:ID   -0.049062:0.040893:0.637838:0.17023:2469:rs10907175
1   1156131 rs2887286   T   C   .   PASS    AF=0.83832  ES:SE:LP:AF:SS:ID   0.022785:0.042411:0.228332:0.83832:2469:rs2887286
1   1158277 rs3813199   G   A   .   PASS    AF=0.19017  ES:SE:LP:AF:SS:ID   -0.016735:0.039734:0.171579:0.19017:2469:rs3813199
1   1162435 rs3766186   C   A   .   PASS    AF=0.18837  ES:SE:LP:AF:SS:ID   -0.014705:0.040401:0.145166:0.18837:2469:rs3766186
1   1163804 rs7515488   C   T   .   PASS    AF=0.19659  ES:SE:LP:AF:SS:ID   -0.0084638:0.040212:0.0791986:0.19659:2469:rs7515488
1   1165310 rs11260562  G   A   .   PASS    AF=0.015692 ES:SE:LP:AF:SS:ID   0.041459:0.11972:0.137201:0.015692:2469:rs11260562
1   1176597 rs6675798   T   C   .   PASS    AF=0.18598  ES:SE:LP:AF:SS:ID   -0.000636:0.043604:0.00508484:0.18598:2469:rs6675798
1   1195690 rs11260568  G   C   .   PASS    AF=0.081909 ES:SE:LP:AF:SS:ID   0.090001:0.056077:0.96457:0.081909:2469:rs11260568
1   1198618 rs12563338  T   A   .   PASS    AF=0.60256  ES:SE:LP:AF:SS:ID   0.0021624:0.032377:0.0237647:0.60256:2469:rs12563338
1   1203938 rs4018608   T   C   .   PASS    AF=0.60076  ES:SE:LP:AF:SS:ID   0.0017351:0.032481:0.0189066:0.60076:2469:rs4018608
1   1211292 rs6685064   C   T   .   PASS    AF=0.59117  ES:SE:LP:AF:SS:ID   -0.0036382:0.032067:0.0411161:0.59117:2469:rs6685064
1   1217058 rs3753340   G   A   .   PASS    AF=0.01361  ES:SE:LP:AF:SS:ID   0.19465:0.12774:0.894217:0.01361:2469:rs3753340
1   1218086 rs6603788   C   T   .   PASS    AF=0.60328  ES:SE:LP:AF:SS:ID   0.015195:0.032552:0.193372:0.60328:2469:rs6603788
1   1242468 rs2274264   G   A   .   PASS    AF=0.57929  ES:SE:LP:AF:SS:ID   -0.034489:0.031938:0.552547:0.57929:2469:rs2274264
1   1268847 rs307378    T   G   .   PASS    AF=0.914956 ES:SE:LP:AF:SS:ID   -0.074016:0.0572:0.708476:0.914956:2469:rs307378
1   1297065 rs2765023   C   T   .   PASS    AF=0.79986  ES:SE:LP:AF:SS:ID   -0.01302:0.03856:0.133341:0.79986:2469:rs2765023
1   1297422 rs2765021   C   T   .   PASS    AF=0.81125  ES:SE:LP:AF:SS:ID   -0.032281:0.039046:0.388925:0.81125:2469:rs2765021
1   1311716 rs2649589   G   A   .   PASS    AF=0.88993  ES:SE:LP:AF:SS:ID   -0.068729:0.051043:0.749214:0.88993:2469:rs2649589
1   1421531 rs819976    C   A   .   PASS    AF=0.62717  ES:SE:LP:AF:SS:ID   0.0058259:0.032475:0.0667:0.62717:2469:rs819976