IEU GWAS QC Report

name	value
id	ukb-d-1448_4
trait	Bread type: Other type of bread
category	Binary
ncase	14441
ncontrol	333983
sample_size	348424
sex	Males and females
population	European
group_name	public
access	public
build	HG19/GRCh37
author	Neale lab
year	2018
mr	1
nsnp	13586247

name	value
gwas_id	ukb-d-1448_4
bcf_file	ukb-d-1448_4.vcf.gz
qc_metrics_file	qc_metrics.json
metadata	metadata.json
refdata	1kg_v3_nomult.bcf
compile_time	2020-05-10 10:07 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=ukb-d-1448_4,TotalVariants=13586246,VariantsNotRead=0,HarmonisedVariants=13586246,VariantsNotHarmonised=0,SwitchedAlleles=229,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/ukb-d-import/processed/ukb-d-1448_4/ukb-d-1448_4_data.json --ref /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/QC/genomes/b37/human_g1k_v37.fasta; 1.1.1",
    "file_date": "2019-11-25T15:23:51.893466",
    "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/ukb-d-import/processed/ukb-d-1448_4/ukb-d-1448_4.vcf.gz -O z /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-1448_4/ukb-d-1448_4_data.vcf.gz; Date=Mon Nov 25 16:19:00 2019",
    "bcftools_viewVersion": "1.9-74-g6af271c+htslib-1.9-64-g226b4a8",
    "bcftools_viewCommand": "view -h /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukb-d-1448_4/ukb-d-1448_4.vcf.gz; Date=Sun May 10 09:38:51 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/ukb-d-import/processed/ukb-d-1448_4/ukb-d-1448_4.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-1448_4/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 17:05:26 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-1448_4/ukb-d-1448_4.vcf.gz ...
Read summary statistics for 13586246 SNPs.
Dropped 12712 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: 0.0048 (0.0015)
Lambda GC: 1.0244
Mean Chi^2: 1.0296
Intercept: 0.9967 (0.0066)
Ratio < 0 (usually indicates GC correction).
Analysis finished at Mon Nov 25 17:07:50 2019
Total time elapsed: 2.0m:24.05s

{
    "af_correlation": 0.9521,
    "inflation_factor": 1.0158,
    "mean_EFFECT": 5.3701e-06,
    "n": 348424,
    "n_snps": 13586246,
    "n_clumped_hits": 4,
    "n_p_sig": 5569,
    "n_mono": 0,
    "n_ns": 1251794,
    "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": 569238,
    "n_est": 349804.5117,
    "ratio_se_n": 1.002,
    "mean_diff": 0,
    "ratio_diff": 30.9029,
    "sd_y_est1": 0.1997,
    "sd_y_est2": 0.2001,
    "r2_sum1": 0,
    "r2_sum2": 0.0008,
    "r2_sum3": 0.0008,
    "r2_sum4": 0.0007,
    "ldsc_nsnp_merge_refpanel_ld": 1283504,
    "ldsc_nsnp_merge_regression_ld": 1283504,
    "ldsc_observed_scale_h2_beta": 0.0048,
    "ldsc_observed_scale_h2_se": 0.0015,
    "ldsc_intercept_beta": 0.9967,
    "ldsc_intercept_se": 0.0066,
    "ldsc_lambda_gc": 1.0244,
    "ldsc_mean_chisq": 1.0296,
    "ldsc_ratio": -0.1115
}

name	value
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	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

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	3	94	0	13574198	0	NA	NA	NA	NA	NA	NA	NA	NA
character	REF	0	1.0000000	1	100	0	57084	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	9.051300e+00	6.184955e+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	7.902529e+07	5.591512e+07	3.02000e+02	3.293080e+07	7.013840e+07	1.148599e+08	2.492309e+08	▇▆▅▂▁
numeric	EFFECT	0	1.0000000	NA	NA	NA	NA	NA	5.400000e-06	2.793300e-03	-3.20578e-02	-7.547000e-04	-8.400000e-06	7.375000e-04	3.854270e-02	▁▁▇▁▁
numeric	SE	0	1.0000000	NA	NA	NA	NA	NA	2.010700e-03	1.939600e-03	3.92500e-04	5.725000e-04	1.054900e-03	2.889400e-03	9.795100e-03	▇▂▁▁▁
numeric	PVAL	0	1.0000000	NA	NA	NA	NA	NA	4.971689e-01	2.898802e-01	0.00000e+00	2.456999e-01	4.966289e-01	7.480455e-01	1.000000e+00	▇▇▇▇▇
numeric	PVAL_ztest	0	1.0000000	NA	NA	NA	NA	NA	4.971684e-01	2.898805e-01	0.00000e+00	2.456991e-01	4.966282e-01	7.480454e-01	1.000000e+00	▇▇▇▇▇
numeric	AF	0	1.0000000	NA	NA	NA	NA	NA	1.908060e-01	2.544035e-01	1.00000e-03	7.430600e-03	6.003200e-02	2.953218e-01	9.990000e-01	▇▂▁▁▁
numeric	AF_reference	569238	0.9581019	NA	NA	NA	NA	NA	1.963368e-01	2.471016e-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	3.484240e+05	0.000000e+00	3.48424e+05	3.484240e+05	3.484240e+05	3.484240e+05	3.484240e+05	▁▁▇▁▁

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	692794	rs530212009	CA	C	-0.0003379	0.0008383	0.6868407	0.6868404	0.1105660	0.1894970	348424
1	693731	rs12238997	A	G	0.0001034	0.0007920	0.8961401	0.8961397	0.1157510	0.1417730	348424
1	707522	rs371890604	G	C	-0.0000287	0.0008903	0.9742820	0.9742816	0.0972257	0.1293930	348424
1	717587	rs144155419	G	A	0.0001579	0.0021276	0.9408210	0.9408215	0.0156497	0.0045926	348424
1	723329	rs189787166	A	T	-0.0080963	0.0062668	0.1963799	0.1963794	0.0017334	0.0003994	348424
1	730087	rs148120343	T	C	0.0005446	0.0011036	0.6216930	0.6216935	0.0564055	0.0127796	348424
1	731718	rs142557973	T	C	0.0004984	0.0007511	0.5069440	0.5069438	0.1216490	0.1543530	348424
1	732032	rs61770163	A	C	0.0000996	0.0008012	0.9011060	0.9011056	0.1210850	0.1555510	348424
1	734349	rs141242758	T	C	0.0004245	0.0007515	0.5721620	0.5721615	0.1208790	0.1525560	348424
1	740284	rs61770167	C	T	-0.0032396	0.0034339	0.3454673	0.3454650	0.0057964	0.0023962	348424

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
23	154923311	rs141127553	C	T	0.0011491	0.0008664	0.1847681	0.1847677	0.0560551	0.0309934	348424
23	154923374	rs111332691	T	A	-0.0006187	0.0009523	0.5158934	0.5158925	0.0446955	0.0116556	348424
23	154925045	rs509981	C	T	0.0002826	0.0004575	0.5368686	0.5368685	0.2457460	0.3634440	348424
23	154925895	rs538470	C	T	0.0001576	0.0004680	0.7362512	0.7362518	0.2420510	0.3634440	348424
23	154927581	rs644138	G	A	0.0005259	0.0004304	0.2217318	0.2217311	0.3021920	0.4635760	348424
23	154929412	rs557132	C	T	0.0002772	0.0004577	0.5446782	0.5446773	0.2455970	0.3568210	348424
23	154929637	rs35185538	CT	C	0.0000620	0.0004776	0.8967909	0.8967910	0.2297910	0.3011920	348424
23	154929952	rs4012982	CAA	C	0.0004138	0.0004813	0.3899079	0.3899071	0.2395410	0.3165560	348424
23	154930230	rs781880	A	G	0.0002911	0.0004576	0.5247023	0.5247015	0.2460140	0.3618540	348424
23	154930487	rs781879	T	A	0.0006896	0.0015693	0.6603467	0.6603472	0.0195723	0.1263580	348424

1   692794  rs530212009 CA  C   .   PASS    AF=0.110566 ES:SE:LP:AF:SS:ID   -0.00033794:0.000838256:0.163144:0.110566:348424:1_692794_CA_C
1   693731  rs12238997  A   G   .   PASS    AF=0.115751 ES:SE:LP:AF:SS:ID   0.000103383:0.000791968:0.0476241:0.115751:348424:rs12238997
1   707522  rs371890604 G   C   .   PASS    AF=0.0972257    ES:SE:LP:AF:SS:ID   -2.87015e-05:0.000890277:0.0113153:0.0972257:348424:rs371890604
1   717587  rs144155419 G   A   .   PASS    AF=0.0156497    ES:SE:LP:AF:SS:ID   0.000157949:0.00212762:0.026493:0.0156497:348424:rs144155419
1   723329  rs189787166 A   T   .   PASS    AF=0.00173336   ES:SE:LP:AF:SS:ID   -0.00809629:0.00626679:0.706903:0.00173336:348424:rs189787166
1   730087  rs148120343 T   C   .   PASS    AF=0.0564055    ES:SE:LP:AF:SS:ID   0.000544588:0.00110363:0.206424:0.0564055:348424:rs148120343
1   731718  rs58276399  T   C   .   PASS    AF=0.121649 ES:SE:LP:AF:SS:ID   0.000498433:0.0007511:0.29504:0.121649:348424:rs58276399
1   732032  rs61770163  A   C   .   PASS    AF=0.121085 ES:SE:LP:AF:SS:ID   9.95599e-05:0.000801191:0.0452241:0.121085:348424:rs61770163
1   734349  rs141242758 T   C   .   PASS    AF=0.120879 ES:SE:LP:AF:SS:ID   0.000424509:0.000751515:0.242481:0.120879:348424:rs141242758
1   740284  rs61770167  C   T   .   PASS    AF=0.00579641   ES:SE:LP:AF:SS:ID   -0.00323958:0.00343386:0.461593:0.00579641:348424:rs61770167
1   742813  rs112573343 C   T   .   PASS    AF=0.00188398   ES:SE:LP:AF:SS:ID   0.00456561:0.00647098:0.318336:0.00188398:348424:rs112573343
1   749963  rs529266287 T   TAA .   PASS    AF=0.869838 ES:SE:LP:AF:SS:ID   -0.000255566:0.000740891:0.136596:0.869838:348424:rs529266287
1   750230  rs190826124 G   C   .   PASS    AF=0.00153811   ES:SE:LP:AF:SS:ID   -0.00547672:0.00668548:0.384392:0.00153811:348424:rs190826124
1   751343  rs28544273  T   A   .   PASS    AF=0.122804 ES:SE:LP:AF:SS:ID   0.000311603:0.000733837:0.173204:0.122804:348424:rs28544273
1   751488  rs200141114 G   GA  .   PASS    AF=0.142609 ES:SE:LP:AF:SS:ID   0.000755144:0.000725276:0.526087:0.142609:348424:rs200141114
1   751756  rs28527770  T   C   .   PASS    AF=0.12292  ES:SE:LP:AF:SS:ID   0.000332069:0.000732812:0.186789:0.12292:348424:rs28527770
1   753405  rs3115860   C   A   .   PASS    AF=0.870978 ES:SE:LP:AF:SS:ID   -0.000467723:0.000714042:0.290353:0.870978:348424:rs3115860
1   753425  rs3131970   T   C   .   PASS    AF=0.87557  ES:SE:LP:AF:SS:ID   -0.000333923:0.000725914:0.190094:0.87557:348424:rs3131970
1   753541  rs2073813   G   A   .   PASS    AF=0.128532 ES:SE:LP:AF:SS:ID   0.000425403:0.000715829:0.257805:0.128532:348424:rs2073813
1   754105  rs12184325  C   T   .   PASS    AF=0.036325 ES:SE:LP:AF:SS:ID   -0.000447145:0.00129903:0.13627:0.036325:348424:rs12184325
1   754182  rs3131969   A   G   .   PASS    AF=0.870576 ES:SE:LP:AF:SS:ID   -0.000430113:0.000713316:0.26239:0.870576:348424:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.87068  ES:SE:LP:AF:SS:ID   -0.000451321:0.000713644:0.278095:0.87068:348424:rs3131968
1   754334  rs3131967   T   C   .   PASS    AF=0.870573 ES:SE:LP:AF:SS:ID   -0.000426587:0.00071329:0.259792:0.870573:348424:rs3131967
1   754433  rs150578204 G   A   .   PASS    AF=0.00504313   ES:SE:LP:AF:SS:ID   -0.00385499:0.0036612:0.534063:0.00504313:348424:rs150578204
1   754458  rs142682604 G   T   .   PASS    AF=0.00501098   ES:SE:LP:AF:SS:ID   -0.00385701:0.00367084:0.532555:0.00501098:348424:rs142682604
1   755435  rs184270342 T   G   .   PASS    AF=0.0055674    ES:SE:LP:AF:SS:ID   -0.000569327:0.00355342:0.059131:0.0055674:348424:rs184270342
1   755890  rs3115858   A   T   .   PASS    AF=0.870647 ES:SE:LP:AF:SS:ID   -0.000484051:0.00071202:0.303982:0.870647:348424:rs3115858
1   756434  rs61768170  G   C   .   PASS    AF=0.12589  ES:SE:LP:AF:SS:ID   0.000432783:0.000726534:0.258543:0.12589:348424:rs61768170
1   756604  rs3131962   A   G   .   PASS    AF=0.870217 ES:SE:LP:AF:SS:ID   -0.000460418:0.000710321:0.286621:0.870217:348424:rs3131962
1   757640  rs3115853   G   A   .   PASS    AF=0.869504 ES:SE:LP:AF:SS:ID   -0.000450258:0.000709658:0.279201:0.869504:348424:rs3115853
1   757734  rs4951929   C   T   .   PASS    AF=0.870367 ES:SE:LP:AF:SS:ID   -0.000467835:0.000710918:0.29201:0.870367:348424:rs4951929
1   757936  rs4951862   C   A   .   PASS    AF=0.870372 ES:SE:LP:AF:SS:ID   -0.000467266:0.000710969:0.291548:0.870372:348424:rs4951862
1   758144  rs3131956   A   G   .   PASS    AF=0.870381 ES:SE:LP:AF:SS:ID   -0.000469094:0.000710991:0.292942:0.870381:348424:rs3131956
1   758626  rs3131954   C   T   .   PASS    AF=0.870823 ES:SE:LP:AF:SS:ID   -0.000454145:0.000712802:0.280633:0.870823:348424:rs3131954
1   759293  rs10157329  T   A   .   PASS    AF=0.0987831    ES:SE:LP:AF:SS:ID   0.000116354:0.00082817:0.0514555:0.0987831:348424:rs10157329
1   759600  rs545998451 AGT A   .   PASS    AF=0.00644687   ES:SE:LP:AF:SS:ID   -0.000530352:0.00321131:0.0610677:0.00644687:348424:1_759600_AGT_A
1   759837  rs3115851   T   A   .   PASS    AF=0.874731 ES:SE:LP:AF:SS:ID   -0.000394349:0.000723467:0.232327:0.874731:348424:rs3115851
1   761732  rs2286139   C   T   .   PASS    AF=0.864126 ES:SE:LP:AF:SS:ID   -0.000460728:0.000709402:0.287315:0.864126:348424:rs2286139
1   761752  rs1057213   C   T   .   PASS    AF=0.8695   ES:SE:LP:AF:SS:ID   -0.000548916:0.00071629:0.353127:0.8695:348424:rs1057213
1   762273  rs3115849   G   A   .   PASS    AF=0.866446 ES:SE:LP:AF:SS:ID   -0.000453131:0.00071644:0.278126:0.866446:348424:rs3115849
1   762485  rs12095200  C   A   .   PASS    AF=0.0987204    ES:SE:LP:AF:SS:ID   -0.000361794:0.00085784:0.171851:0.0987204:348424:rs12095200
1   762589  rs3115848   G   C   .   PASS    AF=0.871633 ES:SE:LP:AF:SS:ID   -0.000328824:0.000724639:0.187093:0.871633:348424:rs3115848
1   762592  rs3131950   C   G   .   PASS    AF=0.871633 ES:SE:LP:AF:SS:ID   -0.000328805:0.000724639:0.187081:0.871633:348424:rs3131950
1   762601  rs3131949   T   C   .   PASS    AF=0.871633 ES:SE:LP:AF:SS:ID   -0.00032967:0.000724653:0.187651:0.871633:348424:rs3131949
1   762632  rs3131948   T   A   .   PASS    AF=0.872009 ES:SE:LP:AF:SS:ID   -0.000361361:0.000725076:0.208858:0.872009:348424:rs3131948
1   764191  rs7515915   T   G   .   PASS    AF=0.125467 ES:SE:LP:AF:SS:ID   0.00037629:0.000725651:0.218912:0.125467:348424:rs7515915
1   766007  rs61768174  A   C   .   PASS    AF=0.105397 ES:SE:LP:AF:SS:ID   0.000487987:0.000789742:0.270319:0.105397:348424:rs61768174
1   766105  rs2519015   T   A   .   PASS    AF=0.855446 ES:SE:LP:AF:SS:ID   -0.000393123:0.000709108:0.237088:0.855446:348424:rs2519015
1   767393  rs538667473 A   C   .   PASS    AF=0.0016537    ES:SE:LP:AF:SS:ID   -0.00648099:0.00628127:0.519752:0.0016537:348424:rs538667473
1   768116  rs376645387 A   AGTTTT  .   PASS    AF=0.838377 ES:SE:LP:AF:SS:ID   -0.00166355:0.000698784:1.76237:0.838377:348424:rs376645387

IEU GWAS information

Report information