IEU GWAS QC Report

name	value
id	ieu-a-1082
pmid	23894154
year	2013
mr	1
note	NULL
trait	Thyroid cancer
category	Disease
subcategory	Cancer
population	European
sex	Males and females
ncase	649
ncontrol	431
sample_size	1080
nsnp	572028
sd	NULL
priority	1
author	Kohler A
group_name	public
access	public
build	HG19/GRCh37

name	value
gwas_id	ieu-a-1082
bcf_file	ieu-a-1082.vcf.gz
qc_metrics_file	qc_metrics.json
metadata	metadata.json
refdata	1kg_v3_nomult.bcf
compile_time	2020-05-09 21:46 BST
build_version	run_igd-8f4f4c9-2020-05-09

manhattan_plot

qq_plot

af_plot

pz_plot

beta_std_plot

{
    "fileformat": "VCFv4.2",
    "FILTER": "<ID=PASS,Description=\"All filters passed\">",
    "INFO": "<ID=AF,Number=A,Type=Float,Description=\"Allele Frequency\">",
    "FORMAT": "<ID=ES,Number=A,Type=Float,Description=\"Effect size estimate relative to the alternative allele\">",
    "FORMAT.1": "<ID=SE,Number=A,Type=Float,Description=\"Standard error of effect size estimate\">",
    "FORMAT.2": "<ID=LP,Number=A,Type=Float,Description=\"-log10 p-value for effect estimate\">",
    "FORMAT.3": "<ID=AF,Number=A,Type=Float,Description=\"Alternate allele frequency in the association study\">",
    "FORMAT.4": "<ID=SS,Number=A,Type=Float,Description=\"Sample size used to estimate genetic effect\">",
    "FORMAT.5": "<ID=EZ,Number=A,Type=Float,Description=\"Z-score provided if it was used to derive the EFFECT and SE fields\">",
    "FORMAT.6": "<ID=SI,Number=A,Type=Float,Description=\"Accuracy score of summary data imputation\">",
    "FORMAT.7": "<ID=NC,Number=A,Type=Float,Description=\"Number of cases used to estimate genetic effect\">",
    "FORMAT.8": "<ID=ID,Number=1,Type=String,Description=\"Study variant identifier\">",
    "META": "<ID=TotalVariants,Number=1,Type=Integer,Description=\"Total number of variants in input\">",
    "META.1": "<ID=VariantsNotRead,Number=1,Type=Integer,Description=\"Number of variants that could not be read\">",
    "META.2": "<ID=HarmonisedVariants,Number=1,Type=Integer,Description=\"Total number of harmonised variants\">",
    "META.3": "<ID=VariantsNotHarmonised,Number=1,Type=Integer,Description=\"Total number of variants that could not be harmonised\">",
    "META.4": "<ID=SwitchedAlleles,Number=1,Type=Integer,Description=\"Total number of variants strand switched\">",
    "META.5": "<ID=TotalControls,Number=1,Type=Integer,Description=\"Total number of controls in the association study\">",
    "META.6": "<ID=TotalCases,Number=1,Type=Integer,Description=\"Total number of cases in the association study\">",
    "META.7": "<ID=StudyType,Number=1,Type=String,Description=\"Type of GWAS study [Continuous or CaseControl]\">",
    "SAMPLE": "<ID=ieu-a-1082,TotalVariants=571227,VariantsNotRead=0,HarmonisedVariants=571078,VariantsNotHarmonised=149,SwitchedAlleles=0,StudyType=Continuous>",
    "contig": "<ID=1,length=249250621,assembly=HG19/GRCh37>",
    "contig.1": "<ID=2,length=243199373,assembly=HG19/GRCh37>",
    "contig.2": "<ID=3,length=198022430,assembly=HG19/GRCh37>",
    "contig.3": "<ID=4,length=191154276,assembly=HG19/GRCh37>",
    "contig.4": "<ID=5,length=180915260,assembly=HG19/GRCh37>",
    "contig.5": "<ID=6,length=171115067,assembly=HG19/GRCh37>",
    "contig.6": "<ID=7,length=159138663,assembly=HG19/GRCh37>",
    "contig.7": "<ID=8,length=146364022,assembly=HG19/GRCh37>",
    "contig.8": "<ID=9,length=141213431,assembly=HG19/GRCh37>",
    "contig.9": "<ID=10,length=135534747,assembly=HG19/GRCh37>",
    "contig.10": "<ID=11,length=135006516,assembly=HG19/GRCh37>",
    "contig.11": "<ID=12,length=133851895,assembly=HG19/GRCh37>",
    "contig.12": "<ID=13,length=115169878,assembly=HG19/GRCh37>",
    "contig.13": "<ID=14,length=107349540,assembly=HG19/GRCh37>",
    "contig.14": "<ID=15,length=102531392,assembly=HG19/GRCh37>",
    "contig.15": "<ID=16,length=90354753,assembly=HG19/GRCh37>",
    "contig.16": "<ID=17,length=81195210,assembly=HG19/GRCh37>",
    "contig.17": "<ID=18,length=78077248,assembly=HG19/GRCh37>",
    "contig.18": "<ID=19,length=59128983,assembly=HG19/GRCh37>",
    "contig.19": "<ID=20,length=63025520,assembly=HG19/GRCh37>",
    "contig.20": "<ID=21,length=48129895,assembly=HG19/GRCh37>",
    "contig.21": "<ID=22,length=51304566,assembly=HG19/GRCh37>",
    "contig.22": "<ID=X,length=155270560,assembly=HG19/GRCh37>",
    "contig.23": "<ID=Y,length=59373566,assembly=HG19/GRCh37>",
    "contig.24": "<ID=MT,length=16569,assembly=HG19/GRCh37>",
    "contig.25": "<ID=GL000207.1,length=4262,assembly=HG19/GRCh37>",
    "contig.26": "<ID=GL000226.1,length=15008,assembly=HG19/GRCh37>",
    "contig.27": "<ID=GL000229.1,length=19913,assembly=HG19/GRCh37>",
    "contig.28": "<ID=GL000231.1,length=27386,assembly=HG19/GRCh37>",
    "contig.29": "<ID=GL000210.1,length=27682,assembly=HG19/GRCh37>",
    "contig.30": "<ID=GL000239.1,length=33824,assembly=HG19/GRCh37>",
    "contig.31": "<ID=GL000235.1,length=34474,assembly=HG19/GRCh37>",
    "contig.32": "<ID=GL000201.1,length=36148,assembly=HG19/GRCh37>",
    "contig.33": "<ID=GL000247.1,length=36422,assembly=HG19/GRCh37>",
    "contig.34": "<ID=GL000245.1,length=36651,assembly=HG19/GRCh37>",
    "contig.35": "<ID=GL000197.1,length=37175,assembly=HG19/GRCh37>",
    "contig.36": "<ID=GL000203.1,length=37498,assembly=HG19/GRCh37>",
    "contig.37": "<ID=GL000246.1,length=38154,assembly=HG19/GRCh37>",
    "contig.38": "<ID=GL000249.1,length=38502,assembly=HG19/GRCh37>",
    "contig.39": "<ID=GL000196.1,length=38914,assembly=HG19/GRCh37>",
    "contig.40": "<ID=GL000248.1,length=39786,assembly=HG19/GRCh37>",
    "contig.41": "<ID=GL000244.1,length=39929,assembly=HG19/GRCh37>",
    "contig.42": "<ID=GL000238.1,length=39939,assembly=HG19/GRCh37>",
    "contig.43": "<ID=GL000202.1,length=40103,assembly=HG19/GRCh37>",
    "contig.44": "<ID=GL000234.1,length=40531,assembly=HG19/GRCh37>",
    "contig.45": "<ID=GL000232.1,length=40652,assembly=HG19/GRCh37>",
    "contig.46": "<ID=GL000206.1,length=41001,assembly=HG19/GRCh37>",
    "contig.47": "<ID=GL000240.1,length=41933,assembly=HG19/GRCh37>",
    "contig.48": "<ID=GL000236.1,length=41934,assembly=HG19/GRCh37>",
    "contig.49": "<ID=GL000241.1,length=42152,assembly=HG19/GRCh37>",
    "contig.50": "<ID=GL000243.1,length=43341,assembly=HG19/GRCh37>",
    "contig.51": "<ID=GL000242.1,length=43523,assembly=HG19/GRCh37>",
    "contig.52": "<ID=GL000230.1,length=43691,assembly=HG19/GRCh37>",
    "contig.53": "<ID=GL000237.1,length=45867,assembly=HG19/GRCh37>",
    "contig.54": "<ID=GL000233.1,length=45941,assembly=HG19/GRCh37>",
    "contig.55": "<ID=GL000204.1,length=81310,assembly=HG19/GRCh37>",
    "contig.56": "<ID=GL000198.1,length=90085,assembly=HG19/GRCh37>",
    "contig.57": "<ID=GL000208.1,length=92689,assembly=HG19/GRCh37>",
    "contig.58": "<ID=GL000191.1,length=106433,assembly=HG19/GRCh37>",
    "contig.59": "<ID=GL000227.1,length=128374,assembly=HG19/GRCh37>",
    "contig.60": "<ID=GL000228.1,length=129120,assembly=HG19/GRCh37>",
    "contig.61": "<ID=GL000214.1,length=137718,assembly=HG19/GRCh37>",
    "contig.62": "<ID=GL000221.1,length=155397,assembly=HG19/GRCh37>",
    "contig.63": "<ID=GL000209.1,length=159169,assembly=HG19/GRCh37>",
    "contig.64": "<ID=GL000218.1,length=161147,assembly=HG19/GRCh37>",
    "contig.65": "<ID=GL000220.1,length=161802,assembly=HG19/GRCh37>",
    "contig.66": "<ID=GL000213.1,length=164239,assembly=HG19/GRCh37>",
    "contig.67": "<ID=GL000211.1,length=166566,assembly=HG19/GRCh37>",
    "contig.68": "<ID=GL000199.1,length=169874,assembly=HG19/GRCh37>",
    "contig.69": "<ID=GL000217.1,length=172149,assembly=HG19/GRCh37>",
    "contig.70": "<ID=GL000216.1,length=172294,assembly=HG19/GRCh37>",
    "contig.71": "<ID=GL000215.1,length=172545,assembly=HG19/GRCh37>",
    "contig.72": "<ID=GL000205.1,length=174588,assembly=HG19/GRCh37>",
    "contig.73": "<ID=GL000219.1,length=179198,assembly=HG19/GRCh37>",
    "contig.74": "<ID=GL000224.1,length=179693,assembly=HG19/GRCh37>",
    "contig.75": "<ID=GL000223.1,length=180455,assembly=HG19/GRCh37>",
    "contig.76": "<ID=GL000195.1,length=182896,assembly=HG19/GRCh37>",
    "contig.77": "<ID=GL000212.1,length=186858,assembly=HG19/GRCh37>",
    "contig.78": "<ID=GL000222.1,length=186861,assembly=HG19/GRCh37>",
    "contig.79": "<ID=GL000200.1,length=187035,assembly=HG19/GRCh37>",
    "contig.80": "<ID=GL000193.1,length=189789,assembly=HG19/GRCh37>",
    "contig.81": "<ID=GL000194.1,length=191469,assembly=HG19/GRCh37>",
    "contig.82": "<ID=GL000225.1,length=211173,assembly=HG19/GRCh37>",
    "contig.83": "<ID=GL000192.1,length=547496,assembly=HG19/GRCh37>",
    "gwas_harmonisation_command": "--json /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-1082/ieu-a-1082_data.json --ref /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/QC/genomes/b37/human_g1k_v37.fasta; 1.1.1",
    "file_date": "2020-02-04T07:49:54.862254",
    "bcftools_annotateVersion": "1.9-74-g6af271c+htslib-1.9-64-g226b4a8",
    "bcftools_annotateCommand": "annotate -a /mnt/storage/home/gh13047/mr-eve/vcf-reference-datasets/dbsnp/dbsnp.v153.b37.vcf.gz -c ID -o /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-1082/ieu-a-1082.vcf.gz -O z /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-1082/ieu-a-1082_data.vcf.gz; Date=Tue Feb  4 20:18:59 2020",
    "bcftools_viewVersion": "1.9-74-g6af271c+htslib-1.9-64-g226b4a8",
    "bcftools_viewCommand": "view -h /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ieu-a-1082/ieu-a-1082.vcf.gz; Date=Sat May  9 21:43:24 2020"
}

*********************************************************************
* 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-1082/ieu-a-1082.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-1082/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 20:59:38 2020
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-1082/ieu-a-1082.vcf.gz ...
Read summary statistics for 571078 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, 458290 SNPs remain.
After merging with regression SNP LD, 458290 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 4.3408 (0.5693)
Lambda GC: 1.201
Mean Chi^2: 1.3166
Intercept: 1.2273 (0.009)
Ratio: 0.7179 (0.0284)
Analysis finished at Tue Feb  4 20:59:52 2020
Total time elapsed: 13.45s

{
    "af_correlation": 0.9029,
    "inflation_factor": 1.2053,
    "mean_EFFECT": 0.0002,
    "n": 1187,
    "n_snps": 571078,
    "n_clumped_hits": 347,
    "n_p_sig": 795,
    "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": 3569,
    "n_est": 1179.0631,
    "ratio_se_n": 0.9967,
    "mean_diff": -0.0004,
    "ratio_diff": 1.459,
    "sd_y_est1": 2.0338,
    "sd_y_est2": 2.0269,
    "r2_sum1": 200.757,
    "r2_sum2": 48.5371,
    "r2_sum3": 48.8638,
    "r2_sum4": 29.028,
    "ldsc_nsnp_merge_refpanel_ld": 458290,
    "ldsc_nsnp_merge_regression_ld": 458290,
    "ldsc_observed_scale_h2_beta": 4.3408,
    "ldsc_observed_scale_h2_se": 0.5693,
    "ldsc_intercept_beta": 1.2273,
    "ldsc_intercept_se": 0.009,
    "ldsc_lambda_gc": 1.201,
    "ldsc_mean_chisq": 1.3166,
    "ldsc_ratio": 0.7179
}

name	value
name	value
af_correlation	FALSE
inflation_factor	TRUE
n	TRUE
is_snpid_non_unique	FALSE
mean_EFFECT_nonfinite	FALSE
mean_EFFECT_05	FALSE
mean_EFFECT_01	FALSE
mean_chisq	TRUE
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	TRUE
r2_sum2	TRUE
r2_sum3	TRUE
r2_sum4	TRUE

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	4	33	0	571078	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	9.240865e+00	6.157312e+00	1.0000000	4.000000e+00	8.000000e+00	1.400000e+01	2.400000e+01	▇▆▅▃▂
numeric	POS	0	1.0000000	NA	NA	NA	NA	NA	7.716883e+07	5.667229e+07	8547.0000000	3.013598e+07	6.762251e+07	1.140089e+08	2.491747e+08	▇▆▃▂▁
numeric	EFFECT	0	1.0000000	NA	NA	NA	NA	NA	2.234000e-04	1.284808e-01	-4.6511100	-7.510750e-02	0.000000e+00	7.601750e-02	5.390440e+00	▁▁▇▁▁
numeric	SE	0	1.0000000	NA	NA	NA	NA	NA	1.061470e-01	2.619420e-02	0.0832000	8.622000e-02	9.584000e-02	1.177000e-01	1.003000e+00	▇▁▁▁▁
numeric	PVAL	0	1.0000000	NA	NA	NA	NA	NA	4.697693e-01	2.966296e-01	0.0000000	2.061000e-01	4.590003e-01	7.272002e-01	1.000000e+00	▇▆▆▆▆
numeric	PVAL_ztest	0	1.0000000	NA	NA	NA	NA	NA	4.698686e-01	2.965496e-01	0.0000000	2.063543e-01	4.589897e-01	7.270172e-01	1.000000e+00	▇▆▆▆▆
numeric	AF	0	1.0000000	NA	NA	NA	NA	NA	3.836163e-01	2.448132e-01	0.0500000	1.720000e-01	3.332000e-01	5.656000e-01	9.499600e-01	▇▆▅▃▂
numeric	AF_reference	3569	0.9937504	NA	NA	NA	NA	NA	3.839601e-01	2.324002e-01	0.0001997	1.896960e-01	3.370610e-01	5.549120e-01	9.899340e-01	▇▇▅▃▂
numeric	N	0	1.0000000	NA	NA	NA	NA	NA	1.187000e+03	0.000000e+00	1187.0000000	1.187000e+03	1.187000e+03	1.187000e+03	1.187000e+03	▁▁▇▁▁

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	752566	rs3094315	G	A	0.0690286	0.10620	0.5157996	0.5157007	0.81200	0.718251	1187
1	752721	rs3131972	A	G	0.0627268	0.10580	0.5533998	0.5532609	0.81040	0.653355	1187
1	768448	rs12562034	G	A	0.1578580	0.12870	0.2198002	0.2199888	0.12290	0.191893	1187
1	798959	rs11240777	G	A	-0.0196926	0.09714	0.8395000	0.8393508	0.24140	0.409944	1187
1	838555	rs4970383	C	A	-0.1118260	0.09675	0.2477998	0.2477530	0.24660	0.336262	1187
1	846808	rs4475691	C	T	-0.1192340	0.10010	0.2334001	0.2335952	0.21950	0.254792	1187
1	854250	rs7537756	A	G	-0.1578240	0.09930	0.1117000	0.1119779	0.22390	0.215655	1187
1	873558	rs1110052	G	T	-0.3293040	0.08771	0.0001685	0.0001737	0.61940	0.494609	1187
1	882033	rs2272756	G	A	-0.1368510	0.09708	0.1584999	0.1586364	0.23950	0.136781	1187
1	888659	rs3748597	T	C	-0.3393250	0.16150	0.0347600	0.0356336	0.92285	0.922724	1187

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
24	23452965	rs9786576	C	T	0.767224	0.2554	0.0024700	0.0026645	0.6413	0.8264	1187
24	23550924	rs2033003	C	A	0.646454	0.2510	0.0096590	0.0100091	0.5784	0.5061	1187
24	23984056	rs1276034	A	G	0.769381	0.2544	0.0023130	0.0024921	0.6341	0.8248	1187
24	23992762	rs1276033	A	C	0.838404	0.2575	0.0010200	0.0011302	0.6410	NA	1187
24	24359931	rs9786095	C	T	0.449801	0.3790	0.2325000	0.2353026	0.1273	NA	1187
24	24437979	rs9786856	C	T	0.449801	0.3790	0.2325000	0.2353026	0.1273	0.2612	1187
24	24444622	rs7893048	T	C	0.764643	0.2562	0.0026350	0.0028399	0.6374	0.8273	1187
24	25029969	rs158435	T	G	0.877070	0.2590	0.0006302	0.0007082	0.6241	NA	1187
24	28650343	rs9786795	G	C	0.492254	0.3766	0.1879001	0.1911786	0.1304	0.3114	1187
24	28699018	rs2049642	G	A	0.575489	0.2867	0.0434000	0.0447192	0.2609	0.3771	1187

1   752566  rs3094315   G   A   .   PASS    AF=0.812    ES:SE:LP:AF:SS:ID   0.0690286:0.1062:0.287519:0.812:1187:rs3094315
1   752721  rs3131972   A   G   .   PASS    AF=0.8104   ES:SE:LP:AF:SS:ID   0.0627268:0.1058:0.256961:0.8104:1187:rs3131972
1   768448  rs12562034  G   A   .   PASS    AF=0.1229   ES:SE:LP:AF:SS:ID   0.157858:0.1287:0.657972:0.1229:1187:rs12562034
1   798959  rs11240777  G   A   .   PASS    AF=0.2414   ES:SE:LP:AF:SS:ID   -0.0196926:0.09714:0.0759793:0.2414:1187:rs11240777
1   838555  rs4970383   C   A   .   PASS    AF=0.2466   ES:SE:LP:AF:SS:ID   -0.111826:0.09675:0.605899:0.2466:1187:rs4970383
1   846808  rs4475691   C   T   .   PASS    AF=0.2195   ES:SE:LP:AF:SS:ID   -0.119234:0.1001:0.631899:0.2195:1187:rs4475691
1   854250  rs7537756   A   G   .   PASS    AF=0.2239   ES:SE:LP:AF:SS:ID   -0.157824:0.0993:0.951947:0.2239:1187:rs7537756
1   873558  rs1110052   G   T   .   PASS    AF=0.6194   ES:SE:LP:AF:SS:ID   -0.329304:0.08771:3.7734:0.6194:1187:rs1110052
1   882033  rs2272756   G   A   .   PASS    AF=0.2395   ES:SE:LP:AF:SS:ID   -0.136851:0.09708:0.799971:0.2395:1187:rs2272756
1   888659  rs3748597   T   C   .   PASS    AF=0.92285  ES:SE:LP:AF:SS:ID   -0.339325:0.1615:1.45892:0.92285:1187:rs3748597
1   891945  rs13303106  A   G   .   PASS    AF=0.5893   ES:SE:LP:AF:SS:ID   -0.0305292:0.0846:0.142547:0.5893:1187:rs13303106
1   894573  rs13303010  G   A   .   PASS    AF=0.868    ES:SE:LP:AF:SS:ID   -0.360468:0.127:2.35694:0.868:1187:rs13303010
1   910935  rs2340592   G   A   .   PASS    AF=0.1812   ES:SE:LP:AF:SS:ID   -0.0462534:0.1093:0.172437:0.1812:1187:rs2340592
1   918384  rs13303118  G   T   .   PASS    AF=0.5733   ES:SE:LP:AF:SS:ID   -0.07139:0.0842:0.405055:0.5733:1187:rs13303118
1   918573  rs2341354   A   G   .   PASS    AF=0.5813   ES:SE:LP:AF:SS:ID   -0.0657877:0.08441:0.358129:0.5813:1187:rs2341354
1   924898  rs6665000   C   A   .   PASS    AF=0.92285  ES:SE:LP:AF:SS:ID   0.0560414:0.1554:0.143694:0.92285:1187:rs6665000
1   927309  rs2341362   T   C   .   PASS    AF=0.92291  ES:SE:LP:AF:SS:ID   0.0576291:0.1554:0.148253:0.92291:1187:rs2341362
1   928836  rs9777703   C   T   .   PASS    AF=0.92249  ES:SE:LP:AF:SS:ID   0.0712812:0.1549:0.190238:0.92249:1187:rs9777703
1   932457  rs1891910   G   A   .   PASS    AF=0.1775   ES:SE:LP:AF:SS:ID   0.0843411:0.1095:0.355266:0.1775:1187:rs1891910
1   944564  rs3128117   T   C   .   PASS    AF=0.3465   ES:SE:LP:AF:SS:ID   0.0285875:0.08754:0.129889:0.3465:1187:rs3128117
1   947034  rs2465126   G   A   .   PASS    AF=0.90733  ES:SE:LP:AF:SS:ID   0.0999308:0.1427:0.315693:0.90733:1187:rs2465126
1   948692  rs2341365   G   A   .   PASS    AF=0.90944  ES:SE:LP:AF:SS:ID   0.0831642:0.1443:0.248644:0.90944:1187:rs2341365
1   948921  rs15842 T   C   .   PASS    AF=0.91319  ES:SE:LP:AF:SS:ID   0.146414:0.1472:0.495529:0.91319:1187:rs15842
1   959842  rs2710888   C   T   .   PASS    AF=0.3416   ES:SE:LP:AF:SS:ID   -0.0734313:0.08802:0.393404:0.3416:1187:rs2710888
1   962210  rs3128126   A   G   .   PASS    AF=0.3644   ES:SE:LP:AF:SS:ID   -0.151637:0.08647:1.10007:0.3644:1187:rs3128126
1   977780  rs2710875   C   T   .   PASS    AF=0.8842   ES:SE:LP:AF:SS:ID   -0.10436:0.131:0.372122:0.8842:1187:rs2710875
1   990417  rs2465136   T   C   .   PASS    AF=0.3163   ES:SE:LP:AF:SS:ID   -0.0842516:0.08926:0.462055:0.3163:1187:rs2465136
1   994391  rs2488991   G   T   .   PASS    AF=0.8568   ES:SE:LP:AF:SS:ID   -0.176471:0.1203:0.8471:0.8568:1187:rs2488991
1   998395  rs7526076   A   G   .   PASS    AF=0.7578   ES:SE:LP:AF:SS:ID   -0.00697561:0.09713:0.0261336:0.7578:1187:rs7526076
1   1005806 rs3934834   C   T   .   PASS    AF=0.1854   ES:SE:LP:AF:SS:ID   -0.240035:0.1063:1.62397:0.1854:1187:rs3934834
1   1017197 rs3766192   C   T   .   PASS    AF=0.5202   ES:SE:LP:AF:SS:ID   0.0979436:0.0833:0.620332:0.5202:1187:rs3766192
1   1017587 rs3766191   C   T   .   PASS    AF=0.1847   ES:SE:LP:AF:SS:ID   -0.237369:0.1064:1.59363:0.1847:1187:rs3766191
1   1018704 rs9442372   A   G   .   PASS    AF=0.5299   ES:SE:LP:AF:SS:ID   0.0956302:0.08336:0.599462:0.5299:1187:rs9442372
1   1021346 rs10907177  A   G   .   PASS    AF=0.1955   ES:SE:LP:AF:SS:ID   -0.171738:0.1042:1.00406:0.1955:1187:rs10907177
1   1021415 rs3737728   A   G   .   PASS    AF=0.7281   ES:SE:LP:AF:SS:ID   -0.0506931:0.09374:0.22856:0.7281:1187:rs3737728
1   1021583 rs10907178  A   C   .   PASS    AF=0.1955   ES:SE:LP:AF:SS:ID   -0.177215:0.1047:1.04436:0.1955:1187:rs10907178
1   1021695 rs9442398   A   G   .   PASS    AF=0.72 ES:SE:LP:AF:SS:ID   -0.0372958:0.09287:0.161277:0.72:1187:rs9442398
1   1025301 rs9442400   T   C   .   PASS    AF=0.91912  ES:SE:LP:AF:SS:ID   -0.24686:0.1561:0.947306:0.91912:1187:rs9442400
1   1030565 rs6687776   C   T   .   PASS    AF=0.1912   ES:SE:LP:AF:SS:ID   -0.176737:0.1051:1.03433:0.1912:1187:rs6687776
1   1036959 rs11579015  T   C   .   PASS    AF=0.1516   ES:SE:LP:AF:SS:ID   -0.282761:0.1148:1.86519:0.1516:1187:rs11579015
1   1040026 rs6671356   T   C   .   PASS    AF=0.1771   ES:SE:LP:AF:SS:ID   -0.129881:0.1084:0.637141:0.1771:1187:rs6671356
1   1060174 rs7548798   C   T   .   PASS    AF=0.2728   ES:SE:LP:AF:SS:ID   0.0934903:0.09388:0.494036:0.2728:1187:rs7548798
1   1061262 rs12757754  A   G   .   PASS    AF=0.155    ES:SE:LP:AF:SS:ID   -0.260197:0.1139:1.65659:0.155:1187:rs12757754
1   1062638 rs9442373   C   A   .   PASS    AF=0.5527   ES:SE:LP:AF:SS:ID   -0.0188218:0.08368:0.0842309:0.5527:1187:rs9442373
1   1064979 rs2298217   C   T   .   PASS    AF=0.1647   ES:SE:LP:AF:SS:ID   -0.190676:0.1113:1.06344:0.1647:1187:rs2298217
1   1066403 rs10907182  T   C   .   PASS    AF=0.6004   ES:SE:LP:AF:SS:ID   -0.0971267:0.0858:0.586365:0.6004:1187:rs10907182
1   1087683 rs9442380   T   C   .   PASS    AF=0.91955  ES:SE:LP:AF:SS:ID   0.162872:0.1516:0.549135:0.91955:1187:rs9442380
1   1097335 rs9442385   T   G   .   PASS    AF=0.91997  ES:SE:LP:AF:SS:ID   0.103806:0.1524:0.305044:0.91997:1187:rs9442385
1   1099342 rs9660710   A   C   .   PASS    AF=0.92628  ES:SE:LP:AF:SS:ID   0.168892:0.1578:0.546376:0.92628:1187:rs9660710
1   1100217 rs1891905   C   T   .   PASS    AF=0.93708  ES:SE:LP:AF:SS:ID   0.302863:0.1694:1.13674:0.93708:1187:rs1891905

IEU GWAS information

Report information