IEU GWAS information

Trait: Number of children ever born measurement.

name	value
author	Howe LJ
consortium	Within family GWAS consortium
subcategory	NA
category	NA
build	HG19/GRCh37
population	European
trait	Number of children ever born measurement
sex	Males and Females
group_name	public
year	2022
unit	count
id	ieu-b-4827
ontology	EFO:0009102
note	Sibling estimate
sample_size	20095

Report information

name	value
gwas_id	ieu-b-4827
bcf_file	ieu-b-4827.vcf.gz
qc_metrics_file	qc_metrics.json
metadata	metadata.json
refdata	1kg_v3_nomult.bcf
compile_time	2022-01-05 09:33 UTC
build_version	master-74213fc-2021-03-26

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

{
    "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-b-4827,TotalVariants=7974415,VariantsNotRead=0,HarmonisedVariants=7974403,VariantsNotHarmonised=12,SwitchedAlleles=3531581,NormalisedVariants=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>",
    "Gwas2VCF_command": "--data /data/cromwell-executions/qc/12c0f2d3-8a27-4e2e-91d0-936762d9459e/call-vcf/inputs/-261044505/upload.txt.gz --id ieu-b-4827 --json /data/cromwell-executions/qc/12c0f2d3-8a27-4e2e-91d0-936762d9459e/call-vcf/inputs/-261044505/ieu-b-4827_data.json --ref /data/cromwell-executions/qc/12c0f2d3-8a27-4e2e-91d0-936762d9459e/call-vcf/inputs/1899004205/human_g1k_v37.fasta --dbsnp /data/cromwell-executions/qc/12c0f2d3-8a27-4e2e-91d0-936762d9459e/call-vcf/inputs/-307190728/dbsnp.v153.b37.vcf.gz --out /data/igd/ieu-b-4827/ieu-b-4827.vcf.gz --alias alias.txt; 1.3.0",
    "file_date": "2022-01-05T09:06:38.112860",
    "bcftools_viewVersion": "1.9+htslib-1.9",
    "bcftools_viewCommand": "view -h /data/cromwell-executions/qc/12c0f2d3-8a27-4e2e-91d0-936762d9459e/call-report/inputs/-261044505/ieu-b-4827.vcf.gz; Date=Wed Jan  5 09:27:02 2022"
}

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 /data/cromwell-executions/qc/12c0f2d3-8a27-4e2e-91d0-936762d9459e/call-ldsc/inputs/-261044505/ieu-b-4827.vcf.gz \
--ref-ld-chr /data/ref/eur_w_ld_chr/ \
--out /data/igd/ieu-b-4827/ldsc.txt \
--w-ld-chr /data/ref/eur_w_ld_chr/ 

Beginning analysis at Wed Jan  5 09:18:35 2022
Reading summary statistics from /data/cromwell-executions/qc/12c0f2d3-8a27-4e2e-91d0-936762d9459e/call-ldsc/inputs/-261044505/ieu-b-4827.vcf.gz ...
Read summary statistics for 7974332 SNPs.
Dropped 39132 SNPs with duplicated rs numbers.
Reading reference panel LD Score from /data/ref/eur_w_ld_chr/[1-22] ... (ldscore_fromlist)
Read reference panel LD Scores for 1290028 SNPs.
Removing partitioned LD Scores with zero variance.
Reading regression weight LD Score from /data/ref/eur_w_ld_chr/[1-22] ... (ldscore_fromlist)
Read regression weight LD Scores for 1290028 SNPs.
After merging with reference panel LD, 1202624 SNPs remain.
After merging with regression SNP LD, 1202624 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.03 (0.0215)
Lambda GC: 1.0299
Mean Chi^2: 1.027
Intercept: 1.0154 (0.0062)
Ratio: 0.5708 (0.2316)
Analysis finished at Wed Jan  5 09:20:21 2022
Total time elapsed: 1.0m:45.52s

QC metrics

Metrics

{
    "af_correlation": "NA",
    "inflation_factor": 1.0288,
    "mean_EFFECT": -0.0001,
    "n": 20095,
    "n_snps": 7974403,
    "n_clumped_hits": 0,
    "n_p_sig": 0,
    "n_mono": 0,
    "n_ns": 285241,
    "n_mac": 0,
    "is_snpid_unique": false,
    "n_miss_EFFECT": 0,
    "n_miss_SE": 0,
    "n_miss_PVAL": 0,
    "n_miss_AF": 7974403,
    "n_miss_AF_reference": 164849,
    "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": 1202624,
    "ldsc_nsnp_merge_regression_ld": 1202624,
    "ldsc_observed_scale_h2_beta": 0.03,
    "ldsc_observed_scale_h2_se": 0.0215,
    "ldsc_intercept_beta": 1.0154,
    "ldsc_intercept_se": 0.0062,
    "ldsc_lambda_gc": 1.0299,
    "ldsc_mean_chisq": 1.027,
    "ldsc_ratio": 0.5704
}

Flags

name	value
af_correlation	NA
inflation_factor	FALSE
n	FALSE
is_snpid_non_unique	TRUE
mean_EFFECT_nonfinite	FALSE
mean_EFFECT_05	FALSE
mean_EFFECT_01	FALSE
mean_chisq	FALSE
n_p_sig	FALSE
miss_EFFECT	FALSE
miss_SE	FALSE
miss_PVAL	FALSE
ldsc_ratio	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	logical.mean	logical.count	numeric.mean	numeric.sd	numeric.p0	numeric.p25	numeric.p50	numeric.p75	numeric.p100	numeric.hist
character	ID	22	0.9999972	3	58	0	7974245	0	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA
character	REF	0	1.0000000	1	43	0	16634	0	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA
character	ALT	0	1.0000000	1	44	0	6013	0	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA
logical	AF	7974403	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	8.648259e+00	5.755412e+00	1.0000e+00	4.000000e+00	8.000000e+00	1.300000e+01	2.200000e+01	▇▅▅▂▂
numeric	POS	0	1.0000000	NA	NA	NA	NA	NA	NA	NA	7.879905e+07	5.636303e+07	3.0200e+02	3.242980e+07	6.934579e+07	1.145649e+08	2.492223e+08	▇▆▅▂▁
numeric	EFFECT	0	1.0000000	NA	NA	NA	NA	NA	NA	NA	-1.282000e-04	2.807770e-02	-3.1560e-01	-1.310000e-02	-1.000000e-04	1.290000e-02	3.155000e-01	▁▁▇▁▁
numeric	SE	0	1.0000000	NA	NA	NA	NA	NA	NA	NA	2.372090e-02	1.451650e-02	1.0500e-02	1.310000e-02	1.740000e-02	2.970000e-02	9.200000e-02	▇▂▁▁▁
numeric	PVAL	0	1.0000000	NA	NA	NA	NA	NA	NA	NA	4.956973e-01	2.893364e-01	2.0000e-07	2.445001e-01	4.939000e-01	7.461996e-01	1.000000e+00	▇▇▇▇▇
numeric	PVAL_ztest	0	1.0000000	NA	NA	NA	NA	NA	NA	NA	4.956976e-01	2.893401e-01	2.0000e-07	2.445079e-01	4.938422e-01	7.461771e-01	1.000000e+00	▇▇▇▇▇
numeric	AF_reference	164849	0.9793277	NA	NA	NA	NA	NA	NA	NA	2.646304e-01	2.521037e-01	0.0000e+00	5.730830e-02	1.791130e-01	4.131390e-01	1.000000e+00	▇▃▂▁▁
numeric	N	0	1.0000000	NA	NA	NA	NA	NA	NA	NA	1.807242e+04	2.610279e+03	1.1364e+04	1.598200e+04	1.980800e+04	2.009500e+04	2.009500e+04	▁▁▁▁▇

Head and tail

CHROM	POS	ID	REF	ALT	EFFECT	SE	PVAL	PVAL_ztest	AF	AF_reference	N
1	693731	rs12238997	A	G	-0.0366	0.0229	0.1097999	0.1099866	NA	0.141773	12481
1	729679	rs4951859	C	G	0.0176	0.0214	0.4103997	0.4108323	NA	0.639976	11725
1	731718	rs142557973	T	C	-0.0370	0.0225	0.1002001	0.1000844	NA	0.154353	12481
1	734349	rs141242758	T	C	-0.0388	0.0226	0.0853493	0.0860131	NA	0.152556	12481
1	736289	rs79010578	T	A	-0.0226	0.0222	0.3099003	0.3086694	NA	0.139577	12010
1	752566	rs3094315	G	A	0.0156	0.0213	0.4643003	0.4639279	NA	0.718251	11725
1	752721	rs3131972	A	G	0.0163	0.0212	0.4423999	0.4419717	NA	0.653355	11725
1	753405	rs3115860	C	A	0.0329	0.0226	0.1457002	0.1454611	NA	0.751797	11725
1	753541	rs2073813	G	A	-0.0331	0.0219	0.1302999	0.1306826	NA	0.301917	12481
1	754182	rs3131969	A	G	0.0326	0.0225	0.1480001	0.1473686	NA	0.678514	11725

CHROM	POS	ID	REF	ALT	EFFECT	SE	PVAL	PVAL_ztest	AF	AF_reference	N
22	51218377	rs2519461	G	C	0.0069	0.0265	0.7942002	0.7945727	NA	0.0826677	13589
22	51219006	rs28729663	G	A	-0.0032	0.0214	0.8809000	0.8811333	NA	0.2052720	12514
22	51219387	rs9616832	T	C	0.0070	0.0265	0.7923991	0.7916636	NA	0.0654952	13589
22	51219704	rs147475742	G	A	-0.0068	0.0328	0.8368001	0.8357622	NA	0.0473243	12803
22	51221190	rs369304721	G	A	-0.0114	0.0303	0.7073006	0.7067402	NA	NA	13088
22	51221731	rs115055839	T	C	0.0060	0.0266	0.8222001	0.8215406	NA	0.0625000	13589
22	51222100	rs114553188	G	T	-0.0052	0.0295	0.8593000	0.8600809	NA	0.0880591	13592
22	51223637	rs375798137	G	A	-0.0121	0.0299	0.6853004	0.6857111	NA	0.0788738	13088
22	51229805	rs9616985	T	C	0.0086	0.0267	0.7462992	0.7473789	NA	0.0730831	13589
22	51237063	rs3896457	T	C	-0.0081	0.0164	0.6218004	0.6213751	NA	0.2050720	12010

bcf preview

1   693731  rs12238997  A   G   .   PASS    .   ES:SE:LP:SS:ID  -0.0366:0.0229:0.959398:12481:rs12238997
1   729679  rs4951859   C   G   .   PASS    .   ES:SE:LP:SS:ID  0.0176:0.0214:0.386793:11725:rs4951859
1   731718  rs58276399  T   C   .   PASS    .   ES:SE:LP:SS:ID  -0.037:0.0225:0.999132:12481:rs58276399
1   734349  rs141242758 T   C   .   PASS    .   ES:SE:LP:SS:ID  -0.0388:0.0226:1.0688:12481:rs141242758
1   736289  rs1254887344    T   A   .   PASS    .   ES:SE:LP:SS:ID  -0.0226:0.0222:0.508778:12010:rs1254887344
1   752566  rs3094315   G   A   .   PASS    .   ES:SE:LP:SS:ID  0.0156:0.0213:0.333201:11725:rs3094315
1   752721  rs3131972   A   G   .   PASS    .   ES:SE:LP:SS:ID  0.0163:0.0212:0.354185:11725:rs3131972
1   753405  rs3115860   C   A   .   PASS    .   ES:SE:LP:SS:ID  0.0329:0.0226:0.83654:11725:rs3115860
1   753541  rs1388595942    G   A   .   PASS    .   ES:SE:LP:SS:ID  -0.0331:0.0219:0.885056:12481:rs1388595942
1   754182  rs3131969   A   G   .   PASS    .   ES:SE:LP:SS:ID  0.0326:0.0225:0.829738:11725:rs3131969
1   754192  rs3131968   A   G   .   PASS    .   ES:SE:LP:SS:ID  0.0324:0.0225:0.823909:11725:rs3131968
1   754334  rs3131967   T   C   .   PASS    .   ES:SE:LP:SS:ID  0.0286:0.0225:0.692932:11725:rs3131967
1   754503  rs3115859   G   A   .   PASS    .   ES:SE:LP:SS:ID  0.013:0.0212:0.268572:11725:rs3115859
1   754964  rs3131966   C   T   .   PASS    .   ES:SE:LP:SS:ID  0.0146:0.0212:0.308388:11725:rs3131966
1   755775  rs3131965   A   G   .   PASS    .   ES:SE:LP:SS:ID  0.0114:0.0212:0.229443:11725:rs3131965
1   755890  rs1280367067    A   T   .   PASS    .   ES:SE:LP:SS:ID  0.0276:0.0226:0.65228:11725:rs1280367067
1   756604  rs3131962   A   G   .   PASS    .   ES:SE:LP:SS:ID  0.0288:0.0226:0.695509:11725:rs3131962
1   757640  rs3115853   G   A   .   PASS    .   ES:SE:LP:SS:ID  0.0303:0.0225:0.74958:11725:rs3115853
1   757734  rs1557551770    C   T   .   PASS    .   ES:SE:LP:SS:ID  0.0294:0.0226:0.712646:11725:rs1557551770
1   757936  rs1360886751    C   A   .   PASS    .   ES:SE:LP:SS:ID  0.0294:0.0226:0.712646:11725:rs1360886751
1   758144  rs3131956   A   G   .   PASS    .   ES:SE:LP:SS:ID  0.0295:0.0226:0.717831:11725:rs3131956
1   758626  rs3131954   C   T   .   PASS    .   ES:SE:LP:SS:ID  0.0278:0.0226:0.662341:11725:rs3131954
1   760912  rs1048488   C   T   .   PASS    .   ES:SE:LP:SS:ID  0.0122:0.0211:0.250496:11725:rs1048488
1   761147  rs3115850   T   C   .   PASS    .   ES:SE:LP:SS:ID  0.0128:0.0211:0.263843:11725:rs3115850
1   761732  rs2286139   C   T   .   PASS    .   ES:SE:LP:SS:ID  0.0262:0.0222:0.621966:11725:rs2286139
1   766007  rs61768174  A   C   .   PASS    .   ES:SE:LP:SS:ID  -0.0325:0.0236:0.774432:12481:rs61768174
1   768253  rs2977608   A   C   .   PASS    .   ES:SE:LP:SS:ID  0.0157:0.0177:0.427245:12481:rs2977608
1   768448  rs12562034  G   A   .   PASS    .   ES:SE:LP:SS:ID  -0.0007:0.0253:0.00935041:12010:rs12562034
1   769223  rs60320384  C   G   .   PASS    .   ES:SE:LP:SS:ID  -0.0296:0.022:0.749824:12481:rs60320384
1   771823  rs2977605   T   C   .   PASS    .   ES:SE:LP:SS:ID  0.0306:0.0226:0.755723:11725:rs2977605
1   771967  rs59066358  G   A   .   PASS    .   ES:SE:LP:SS:ID  -0.0286:0.022:0.715118:12481:rs59066358
1   772755  rs2905039   A   C   .   PASS    .   ES:SE:LP:SS:ID  0.0303:0.0226:0.74521:11725:rs2905039
1   777122  rs2980319   A   T   .   PASS    .   ES:SE:LP:SS:ID  0.0361:0.0225:0.965372:11725:rs2980319
1   777232  rs112618790 C   T   .   PASS    .   ES:SE:LP:SS:ID  0.0066:0.026:0.0969643:12481:rs112618790
1   778745  rs1055606   A   G   .   PASS    .   ES:SE:LP:SS:ID  -0.0321:0.0219:0.842846:12481:rs1055606
1   779322  rs4040617   A   G   .   PASS    .   ES:SE:LP:SS:ID  -0.0325:0.0219:0.859178:12481:rs4040617
1   780785  rs2977612   T   A   .   PASS    .   ES:SE:LP:SS:ID  0.0366:0.0224:0.988853:11725:rs2977612
1   781845  rs1391043716    A   G   .   PASS    .   ES:SE:LP:SS:ID  -0.0324:0.0237:0.768021:12481:rs1391043716
1   782981  rs6594026   C   T   .   PASS    .   ES:SE:LP:SS:ID  -0.0329:0.0219:0.878769:12481:rs6594026
1   785050  rs2905062   G   A   .   PASS    .   ES:SE:LP:SS:ID  0.0349:0.0224:0.925184:11725:rs2905062
1   785989  rs2980300   T   C   .   PASS    .   ES:SE:LP:SS:ID  0.0351:0.0224:0.933674:11725:rs2980300
1   787399  rs2905055   G   T   .   PASS    .   ES:SE:LP:SS:ID  0.0399:0.0222:1.14056:11725:rs2905055
1   787606  rs3863622   G   T   .   PASS    .   ES:SE:LP:SS:ID  -0.0336:0.0219:0.900665:12481:rs3863622
1   787685  rs2905054   G   T   .   PASS    .   ES:SE:LP:SS:ID  0.0398:0.0222:1.13354:11725:rs2905054
1   787844  rs2905053   C   T   .   PASS    .   ES:SE:LP:SS:ID  0.0377:0.0224:1.03423:11725:rs2905053
1   790465  rs61768207  G   A   .   PASS    .   ES:SE:LP:SS:ID  -0.0238:0.0239:0.494579:12481:rs61768207
1   791191  rs111818025 G   A   .   PASS    .   ES:SE:LP:SS:ID  -0.0325:0.022:0.859178:12481:rs111818025
1   791853  rs6684487   G   A   .   PASS    .   ES:SE:LP:SS:ID  0.012:0.026:0.191114:12481:rs6684487
1   794332  rs12127425  G   A   .   PASS    .   ES:SE:LP:SS:ID  0.0101:0.0283:0.142788:12481:rs12127425
1   795222  rs12131377  C   G   .   PASS    .   ES:SE:LP:SS:ID  0.0074:0.0282:0.100672:12481:rs12131377

Sidebar

IEU GWAS information

Report information

Summary

Summary {data-width=650}

Manhattan plot

QQ plot

AF plot

P-Z plot

beta_std plot

Metadata

LDSC

QC metrics

Metrics

Metrics

Flags

Definitions

Diagnostics

Details

Summary stats

Head and tail

bcf preview