IEU GWAS QC Report

name	value
id	UKB-b-1100
trait	Close to major road
note	24014: Output from GWAS pipeline using Phesant derived variables from UKBiobank
year	2018
author	Ben Elsworth
population	European
sex	Males and Females
sample_size	456380
ncase	31833
ncontrol	424547
units	SD
build	HG19/GRCh37
group_name	public
access	public
nsnp	9851867
mr	1
category	Binary
batch	UKB-b
sd	NULL
priority	1
consortium	MRC-IEU

name	value
gwas_id	ukb-b-1100
bcf_file	ukb-b-1100.vcf.gz
qc_metrics_file	qc_metrics.json
metadata	metadata.json
refdata	1kg_v3_nomult.bcf
compile_time	2020-05-10 01:24 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-b:1100,TotalVariants=9851866,VariantsNotRead=0,HarmonisedVariants=9851866,VariantsNotHarmonised=0,SwitchedAlleles=9851866,TotalControls=424547,TotalCases=31833,StudyType=CaseControl>",
    "contig": "<ID=1,length=249250621,assembly=GRCh37>",
    "contig.1": "<ID=2,length=243199373,assembly=GRCh37>",
    "contig.2": "<ID=3,length=198022430,assembly=GRCh37>",
    "contig.3": "<ID=4,length=191154276,assembly=GRCh37>",
    "contig.4": "<ID=5,length=180915260,assembly=GRCh37>",
    "contig.5": "<ID=6,length=171115067,assembly=GRCh37>",
    "contig.6": "<ID=7,length=159138663,assembly=GRCh37>",
    "contig.7": "<ID=8,length=146364022,assembly=GRCh37>",
    "contig.8": "<ID=9,length=141213431,assembly=GRCh37>",
    "contig.9": "<ID=10,length=135534747,assembly=GRCh37>",
    "contig.10": "<ID=11,length=135006516,assembly=GRCh37>",
    "contig.11": "<ID=12,length=133851895,assembly=GRCh37>",
    "contig.12": "<ID=13,length=115169878,assembly=GRCh37>",
    "contig.13": "<ID=14,length=107349540,assembly=GRCh37>",
    "contig.14": "<ID=15,length=102531392,assembly=GRCh37>",
    "contig.15": "<ID=16,length=90354753,assembly=GRCh37>",
    "contig.16": "<ID=17,length=81195210,assembly=GRCh37>",
    "contig.17": "<ID=18,length=78077248,assembly=GRCh37>",
    "contig.18": "<ID=19,length=59128983,assembly=GRCh37>",
    "contig.19": "<ID=20,length=63025520,assembly=GRCh37>",
    "contig.20": "<ID=21,length=48129895,assembly=GRCh37>",
    "contig.21": "<ID=22,length=51304566,assembly=GRCh37>",
    "contig.22": "<ID=X,length=155270560,assembly=GRCh37>",
    "contig.23": "<ID=Y,length=59373566,assembly=GRCh37>",
    "contig.24": "<ID=MT,length=16569,assembly=GRCh37>",
    "contig.25": "<ID=GL000207.1,length=4262,assembly=GRCh37>",
    "contig.26": "<ID=GL000226.1,length=15008,assembly=GRCh37>",
    "contig.27": "<ID=GL000229.1,length=19913,assembly=GRCh37>",
    "contig.28": "<ID=GL000231.1,length=27386,assembly=GRCh37>",
    "contig.29": "<ID=GL000210.1,length=27682,assembly=GRCh37>",
    "contig.30": "<ID=GL000239.1,length=33824,assembly=GRCh37>",
    "contig.31": "<ID=GL000235.1,length=34474,assembly=GRCh37>",
    "contig.32": "<ID=GL000201.1,length=36148,assembly=GRCh37>",
    "contig.33": "<ID=GL000247.1,length=36422,assembly=GRCh37>",
    "contig.34": "<ID=GL000245.1,length=36651,assembly=GRCh37>",
    "contig.35": "<ID=GL000197.1,length=37175,assembly=GRCh37>",
    "contig.36": "<ID=GL000203.1,length=37498,assembly=GRCh37>",
    "contig.37": "<ID=GL000246.1,length=38154,assembly=GRCh37>",
    "contig.38": "<ID=GL000249.1,length=38502,assembly=GRCh37>",
    "contig.39": "<ID=GL000196.1,length=38914,assembly=GRCh37>",
    "contig.40": "<ID=GL000248.1,length=39786,assembly=GRCh37>",
    "contig.41": "<ID=GL000244.1,length=39929,assembly=GRCh37>",
    "contig.42": "<ID=GL000238.1,length=39939,assembly=GRCh37>",
    "contig.43": "<ID=GL000202.1,length=40103,assembly=GRCh37>",
    "contig.44": "<ID=GL000234.1,length=40531,assembly=GRCh37>",
    "contig.45": "<ID=GL000232.1,length=40652,assembly=GRCh37>",
    "contig.46": "<ID=GL000206.1,length=41001,assembly=GRCh37>",
    "contig.47": "<ID=GL000240.1,length=41933,assembly=GRCh37>",
    "contig.48": "<ID=GL000236.1,length=41934,assembly=GRCh37>",
    "contig.49": "<ID=GL000241.1,length=42152,assembly=GRCh37>",
    "contig.50": "<ID=GL000243.1,length=43341,assembly=GRCh37>",
    "contig.51": "<ID=GL000242.1,length=43523,assembly=GRCh37>",
    "contig.52": "<ID=GL000230.1,length=43691,assembly=GRCh37>",
    "contig.53": "<ID=GL000237.1,length=45867,assembly=GRCh37>",
    "contig.54": "<ID=GL000233.1,length=45941,assembly=GRCh37>",
    "contig.55": "<ID=GL000204.1,length=81310,assembly=GRCh37>",
    "contig.56": "<ID=GL000198.1,length=90085,assembly=GRCh37>",
    "contig.57": "<ID=GL000208.1,length=92689,assembly=GRCh37>",
    "contig.58": "<ID=GL000191.1,length=106433,assembly=GRCh37>",
    "contig.59": "<ID=GL000227.1,length=128374,assembly=GRCh37>",
    "contig.60": "<ID=GL000228.1,length=129120,assembly=GRCh37>",
    "contig.61": "<ID=GL000214.1,length=137718,assembly=GRCh37>",
    "contig.62": "<ID=GL000221.1,length=155397,assembly=GRCh37>",
    "contig.63": "<ID=GL000209.1,length=159169,assembly=GRCh37>",
    "contig.64": "<ID=GL000218.1,length=161147,assembly=GRCh37>",
    "contig.65": "<ID=GL000220.1,length=161802,assembly=GRCh37>",
    "contig.66": "<ID=GL000213.1,length=164239,assembly=GRCh37>",
    "contig.67": "<ID=GL000211.1,length=166566,assembly=GRCh37>",
    "contig.68": "<ID=GL000199.1,length=169874,assembly=GRCh37>",
    "contig.69": "<ID=GL000217.1,length=172149,assembly=GRCh37>",
    "contig.70": "<ID=GL000216.1,length=172294,assembly=GRCh37>",
    "contig.71": "<ID=GL000215.1,length=172545,assembly=GRCh37>",
    "contig.72": "<ID=GL000205.1,length=174588,assembly=GRCh37>",
    "contig.73": "<ID=GL000219.1,length=179198,assembly=GRCh37>",
    "contig.74": "<ID=GL000224.1,length=179693,assembly=GRCh37>",
    "contig.75": "<ID=GL000223.1,length=180455,assembly=GRCh37>",
    "contig.76": "<ID=GL000195.1,length=182896,assembly=GRCh37>",
    "contig.77": "<ID=GL000212.1,length=186858,assembly=GRCh37>",
    "contig.78": "<ID=GL000222.1,length=186861,assembly=GRCh37>",
    "contig.79": "<ID=GL000200.1,length=187035,assembly=GRCh37>",
    "contig.80": "<ID=GL000193.1,length=189789,assembly=GRCh37>",
    "contig.81": "<ID=GL000194.1,length=191469,assembly=GRCh37>",
    "contig.82": "<ID=GL000225.1,length=211173,assembly=GRCh37>",
    "contig.83": "<ID=GL000192.1,length=547496,assembly=GRCh37>",
    "gwas_harmonisation_command": "--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/vcf_09_19b/bgzip_vcf/data.batch_24014.vcf.gz --id UKB-b:1100 --data /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/raw-output/data.batch_24014.txt.gz --cohort_cases 31833 --cohort_controls 424547 --ref /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/human_g1k_v37.fasta --json /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/ukb_gwas.json; 1.1.1",
    "file_date": "2019-09-12T19:32:31.885419",
    "bcftools_viewVersion": "1.9-74-g6af271c+htslib-1.9-64-g226b4a8",
    "bcftools_viewCommand": "view -T ^/mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-1100/mac_discard.txt -Oz /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-1100/UKB-b-1100_raw.vcf.gz; Date=Thu Oct 17 12:24:48 2019",
    "bcftools_viewCommand.1": "view -h /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukb-b-1100/ukb-b-1100.vcf.gz; Date=Sun May 10 01:16:02 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/public/UKB-b-1100/UKB-b-1100_data.vcf.gz \
--ref-ld-chr ../reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-1100/ldsc.txt \
--w-ld-chr ../reference/eur_w_ld_chr/ 

Beginning analysis at Thu Oct 17 14:40:18 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-1100/UKB-b-1100_data.vcf.gz ...
Read summary statistics for 7595574 SNPs.
Dropped 5341 SNPs with duplicated rs numbers.
Reading reference panel LD Score from ../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 ../reference/eur_w_ld_chr/[1-22] ...
Read regression weight LD Scores for 1290028 SNPs.
After merging with reference panel LD, 1277591 SNPs remain.
After merging with regression SNP LD, 1277591 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0004 (0.001)
Lambda GC: 1.0367
Mean Chi^2: 1.0366
Intercept: 1.0334 (0.0058)
Ratio: 0.9118 (0.159)
Analysis finished at Thu Oct 17 14:41:47 2019
Total time elapsed: 1.0m:28.81s

{
    "af_correlation": 0.9404,
    "inflation_factor": 1.0475,
    "mean_EFFECT": 7.3662e-06,
    "n": "-Inf",
    "n_snps": 9851866,
    "n_clumped_hits": 1,
    "n_p_sig": 2,
    "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": 70554,
    "n_est": "NA",
    "ratio_se_n": "NA",
    "mean_diff": "NaN",
    "ratio_diff": "NaN",
    "sd_y_est1": "NaN",
    "sd_y_est2": "NA",
    "r2_sum1": 0,
    "r2_sum2": 0,
    "r2_sum3": 0,
    "r2_sum4": 0,
    "ldsc_nsnp_merge_refpanel_ld": 1277591,
    "ldsc_nsnp_merge_regression_ld": 1277591,
    "ldsc_observed_scale_h2_beta": 0.0004,
    "ldsc_observed_scale_h2_se": 0.001,
    "ldsc_intercept_beta": 1.0334,
    "ldsc_intercept_se": 0.0058,
    "ldsc_lambda_gc": 1.0367,
    "ldsc_mean_chisq": 1.0366,
    "ldsc_ratio": 0.9126
}

name	value
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

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	logical.mean	logical.count	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	logical.mean	logical.count	numeric.mean	numeric.sd	numeric.p0	numeric.p25	numeric.p50	numeric.p75	numeric.p100	numeric.hist
character	ID	0	1.0000000	3	58	0	7590256	0	NA	NA	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	NA	NA
character	ALT	0	1.0000000	1	1	0	4	0	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA
logical	N	7595574	0.0000000	NA	NA	NA	NA	NA	NaN	:	NA	NA	NA	NA	NA	NA	NA	NA
numeric	CHROM	0	1.0000000	NA	NA	NA	NA	NA	NA	NA	8.663172e+00	5.764444e+00	1.0000000	4.000000e+00	8.000000e+00	1.300000e+01	2.200000e+01	▇▅▅▂▂
numeric	POS	0	1.0000000	NA	NA	NA	NA	NA	NA	NA	7.866593e+07	5.643884e+07	828.0000000	3.219481e+07	6.910630e+07	1.145586e+08	2.492385e+08	▇▆▅▂▁
numeric	EFFECT	0	1.0000000	NA	NA	NA	NA	NA	NA	NA	7.400000e-06	1.207000e-03	-0.0117779	-5.873000e-04	1.800000e-06	5.933000e-04	1.093180e-02	▁▁▇▁▁
numeric	SE	0	1.0000000	NA	NA	NA	NA	NA	NA	NA	1.041500e-03	5.704000e-04	0.0005146	5.897000e-04	7.947000e-04	1.346400e-03	6.175800e-03	▇▂▁▁▁
numeric	PVAL	0	1.0000000	NA	NA	NA	NA	NA	NA	NA	4.938405e-01	2.901117e-01	0.0000000	2.399999e-01	4.899999e-01	7.400005e-01	1.000000e+00	▇▇▇▇▇
numeric	PVAL_ztest	0	1.0000000	NA	NA	NA	NA	NA	NA	NA	4.938400e-01	2.900854e-01	0.0000000	2.404563e-01	4.924915e-01	7.447235e-01	1.000000e+00	▇▇▇▇▇
numeric	AF	0	1.0000000	NA	NA	NA	NA	NA	NA	NA	2.571743e-01	2.608438e-01	0.0109950	4.394100e-02	1.530970e-01	4.061970e-01	9.890050e-01	▇▂▂▁▁
numeric	AF_reference	70554	0.9907112	NA	NA	NA	NA	NA	NA	NA	2.561020e-01	2.526931e-01	0.0000000	4.852240e-02	1.673320e-01	4.003590e-01	1.000000e+00	▇▃▂▁▁

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	49298	rs200943160	T	C	-0.0002076	0.0009470	0.8300000	0.8264982	0.623756	0.7821490	NA
1	54676	rs2462492	C	T	0.0001980	0.0009384	0.8300000	0.8328483	0.400407	NA	NA
1	86028	rs114608975	T	C	-0.0001361	0.0015004	0.9299999	0.9277285	0.103555	0.0277556	NA
1	91536	rs6702460	G	T	0.0009102	0.0009238	0.3200000	0.3244631	0.456805	0.4207270	NA
1	234313	rs8179466	C	T	-0.0015067	0.0018209	0.4100001	0.4079822	0.074538	NA	NA
1	534192	rs6680723	C	T	-0.0020532	0.0010551	0.0519996	0.0516664	0.240997	NA	NA
1	546697	rs12025928	A	G	0.0018210	0.0013170	0.1700000	0.1667699	0.913520	NA	NA
1	693731	rs12238997	A	G	0.0002076	0.0008841	0.8100000	0.8143769	0.116381	0.1417730	NA
1	705882	rs72631875	G	A	-0.0017928	0.0012966	0.1700000	0.1667773	0.067232	0.0315495	NA
1	706368	rs55727773	A	G	-0.0006041	0.0006552	0.3599996	0.3565190	0.515569	0.2751600	NA

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
22	51219006	rs28729663	G	A	0.0002766	0.0007903	0.7300002	0.7263333	0.137926	0.2052720	NA
22	51219387	rs9616832	T	C	-0.0004910	0.0010260	0.6300007	0.6322585	0.073706	0.0654952	NA
22	51219704	rs147475742	G	A	-0.0004891	0.0013752	0.7199992	0.7220747	0.041920	0.0473243	NA
22	51221190	rs369304721	G	A	-0.0003884	0.0013731	0.7800007	0.7773092	0.049688	NA	NA
22	51221731	rs115055839	T	C	-0.0005206	0.0010266	0.6100002	0.6120805	0.073200	0.0625000	NA
22	51222100	rs114553188	G	T	0.0013116	0.0012084	0.2800000	0.2777347	0.054461	0.0880591	NA
22	51223637	rs375798137	G	A	0.0013801	0.0012142	0.2599998	0.2556873	0.054091	0.0788738	NA
22	51229805	rs9616985	T	C	-0.0005831	0.0010303	0.5700002	0.5714055	0.073035	0.0730831	NA
22	51232488	rs376461333	A	G	0.0044606	0.0024266	0.0659994	0.0660340	0.020045	NA	NA
22	51237063	rs3896457	T	C	-0.0009694	0.0006300	0.1199999	0.1238693	0.297983	0.2050720	NA

1   49298   rs10399793  T   C   .   PASS    AF=0.623756 ES:SE:LP:AF:ID  -0.00020758:0.000947011:0.0809219:0.623756:rs10399793
1   54676   rs2462492   C   T   .   PASS    AF=0.400407 ES:SE:LP:AF:ID  0.000198049:0.000938399:0.0809219:0.400407:rs2462492
1   86028   rs114608975 T   C   .   PASS    AF=0.103555 ES:SE:LP:AF:ID  -0.000136091:0.0015004:0.0315171:0.103555:rs114608975
1   91536   rs6702460   G   T   .   PASS    AF=0.456805 ES:SE:LP:AF:ID  0.000910235:0.000923789:0.49485:0.456805:rs6702460
1   234313  rs8179466   C   T   .   PASS    AF=0.074538 ES:SE:LP:AF:ID  -0.00150667:0.00182086:0.387216:0.074538:rs8179466
1   534192  rs6680723   C   T   .   PASS    AF=0.240997 ES:SE:LP:AF:ID  -0.0020532:0.00105514:1.284:0.240997:rs6680723
1   546697  rs12025928  A   G   .   PASS    AF=0.91352  ES:SE:LP:AF:ID  0.00182096:0.001317:0.769551:0.91352:rs12025928
1   693731  rs12238997  A   G   .   PASS    AF=0.116381 ES:SE:LP:AF:ID  0.000207563:0.000884062:0.091515:0.116381:rs12238997
1   705882  rs72631875  G   A   .   PASS    AF=0.067232 ES:SE:LP:AF:ID  -0.00179275:0.00129662:0.769551:0.067232:rs72631875
1   706368  rs12029736  A   G   .   PASS    AF=0.515569 ES:SE:LP:AF:ID  -0.000604123:0.000655218:0.443698:0.515569:rs12029736
1   714596  rs149887893 T   C   .   PASS    AF=0.033    ES:SE:LP:AF:ID  0.00271214:0.00165161:1:0.033:rs149887893
1   715265  rs12184267  C   T   .   PASS    AF=0.036611 ES:SE:LP:AF:ID  0.00253467:0.00150029:1.04096:0.036611:rs12184267
1   715367  rs12184277  A   G   .   PASS    AF=0.036726 ES:SE:LP:AF:ID  0.00250348:0.00149462:1.02687:0.036726:rs12184277
1   717485  rs12184279  C   A   .   PASS    AF=0.036422 ES:SE:LP:AF:ID  0.00247305:0.00150547:1:0.036422:rs12184279
1   717587  rs144155419 G   A   .   PASS    AF=0.01643  ES:SE:LP:AF:ID  0.0020433:0.00231558:0.420216:0.01643:rs144155419
1   720381  rs116801199 G   T   .   PASS    AF=0.036964 ES:SE:LP:AF:ID  0.00263826:0.00148872:1.11919:0.036964:rs116801199
1   721290  rs12565286  G   C   .   PASS    AF=0.037061 ES:SE:LP:AF:ID  0.00240118:0.00148362:0.958607:0.037061:rs12565286
1   722670  rs116030099 T   C   .   PASS    AF=0.101221 ES:SE:LP:AF:ID  -0.000931662:0.00108079:0.408935:0.101221:rs116030099
1   723891  rs2977670   G   C   .   PASS    AF=0.959116 ES:SE:LP:AF:ID  -0.00341248:0.00143106:1.76955:0.959116:rs2977670
1   724849  rs12126395  C   A   .   PASS    AF=0.031451 ES:SE:LP:AF:ID  -0.00114732:0.00259649:0.180456:0.031451:rs12126395
1   725060  rs865924913 A   T   .   PASS    AF=0.053252 ES:SE:LP:AF:ID  -0.0024056:0.00206649:0.619789:0.053252:rs865924913
1   726794  rs28454925  C   G   .   PASS    AF=0.036579 ES:SE:LP:AF:ID  0.00248974:0.00149325:1.02228:0.036579:rs28454925
1   729632  rs116720794 C   T   .   PASS    AF=0.0369   ES:SE:LP:AF:ID  0.0024258:0.00147957:1:0.0369:rs116720794
1   729679  rs4951859   C   G   .   PASS    AF=0.843173 ES:SE:LP:AF:ID  -0.00127817:0.000766241:1.02228:0.843173:rs4951859
1   730087  rs148120343 T   C   .   PASS    AF=0.055948 ES:SE:LP:AF:ID  0.00112489:0.00124041:0.443698:0.055948:rs148120343
1   731718  rs58276399  T   C   .   PASS    AF=0.12237  ES:SE:LP:AF:ID  0.000398432:0.000838603:0.200659:0.12237:rs58276399
1   732989  rs369030935 C   T   .   PASS    AF=0.025756 ES:SE:LP:AF:ID  -0.000913941:0.00206168:0.180456:0.025756:rs369030935
1   734349  rs141242758 T   C   .   PASS    AF=0.121613 ES:SE:LP:AF:ID  0.00044479:0.000838945:0.221849:0.121613:rs141242758
1   736289  rs79010578  T   A   .   PASS    AF=0.132352 ES:SE:LP:AF:ID  0.000983906:0.000826978:0.638272:0.132352:rs79010578
1   736689  rs181876450 T   C   .   PASS    AF=0.011107 ES:SE:LP:AF:ID  0.00370197:0.003012:0.657577:0.011107:rs181876450
1   752478  rs146277091 G   A   .   PASS    AF=0.036814 ES:SE:LP:AF:ID  0.00245959:0.00146461:1.03152:0.036814:rs146277091
1   752566  rs3094315   G   A   .   PASS    AF=0.838895 ES:SE:LP:AF:ID  -0.00137513:0.000742015:1.19382:0.838895:rs3094315
1   752721  rs3131972   A   G   .   PASS    AF=0.838528 ES:SE:LP:AF:ID  -0.0013659:0.000741226:1.18709:0.838528:rs3131972
1   753405  rs3115860   C   A   .   PASS    AF=0.869711 ES:SE:LP:AF:ID  -0.000747427:0.000795284:0.455932:0.869711:rs3115860
1   753541  rs2073813   G   A   .   PASS    AF=0.129936 ES:SE:LP:AF:ID  0.000697854:0.000796924:0.420216:0.129936:rs2073813
1   754063  rs12184312  G   T   .   PASS    AF=0.037328 ES:SE:LP:AF:ID  0.00226634:0.00143968:0.920819:0.037328:rs12184312
1   754105  rs12184325  C   T   .   PASS    AF=0.037572 ES:SE:LP:AF:ID  0.00219976:0.00143056:0.920819:0.037572:rs12184325
1   754182  rs3131969   A   G   .   PASS    AF=0.869056 ES:SE:LP:AF:ID  -0.000741347:0.000793742:0.455932:0.869056:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.869154 ES:SE:LP:AF:ID  -0.000675212:0.000794057:0.39794:0.869154:rs3131968
1   754211  rs12184313  G   A   .   PASS    AF=0.037531 ES:SE:LP:AF:ID  0.00224518:0.00143675:0.920819:0.037531:rs12184313
1   754334  rs3131967   T   C   .   PASS    AF=0.86906  ES:SE:LP:AF:ID  -0.000747357:0.00079373:0.455932:0.86906:rs3131967
1   754503  rs3115859   G   A   .   PASS    AF=0.837976 ES:SE:LP:AF:ID  -0.0013505:0.000739146:1.16749:0.837976:rs3115859
1   754629  rs10454459  A   G   .   PASS    AF=0.037544 ES:SE:LP:AF:ID  0.00217875:0.00143878:0.886057:0.037544:rs10454459
1   754964  rs3131966   C   T   .   PASS    AF=0.838606 ES:SE:LP:AF:ID  -0.00135004:0.00074122:1.16115:0.838606:rs3131966
1   755240  rs181660517 T   G   .   PASS    AF=0.013775 ES:SE:LP:AF:ID  -0.00183586:0.00258741:0.318759:0.013775:rs181660517
1   755775  rs3131965   A   G   .   PASS    AF=0.839716 ES:SE:LP:AF:ID  -0.00142705:0.000751248:1.24413:0.839716:rs3131965
1   755890  rs3115858   A   T   .   PASS    AF=0.869338 ES:SE:LP:AF:ID  -0.000744517:0.000792802:0.455932:0.869338:rs3115858
1   756604  rs3131962   A   G   .   PASS    AF=0.868886 ES:SE:LP:AF:ID  -0.000776084:0.000790813:0.481486:0.868886:rs3131962
1   757640  rs3115853   G   A   .   PASS    AF=0.867838 ES:SE:LP:AF:ID  -0.000629532:0.000789298:0.366532:0.867838:rs3115853
1   757734  rs4951929   C   T   .   PASS    AF=0.869028 ES:SE:LP:AF:ID  -0.000740837:0.000791453:0.455932:0.869028:rs4951929

IEU GWAS information

Report information