Sidebar

IEU GWAS information

Trait: High light scatter reticulocyte count.

name	value
id	ukb-d-30300_irnt
trait	High light scatter reticulocyte count
category	Continuous
sample_size	344729
sex	Males and females
population	European
group_name	public
access	public
build	HG19/GRCh37
author	Neale lab
year	2018
mr	1
nsnp	13586218

Report information

name	value
gwas_id	ukb-d-30300_irnt
bcf_file	ukb-d-30300_irnt.vcf.gz
qc_metrics_file	qc_metrics.json
metadata	metadata.json
refdata	1kg_v3_nomult.bcf
compile_time	2020-05-10 23:24 BST
build_version	run_igd-8f4f4c9-2020-05-09

Summary

Summary {data-width=650}

Manhattan plot

manhattan_plot

QQ plot

qq_plot

AF plot

$af_plot$

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=ukb-d-30300_irnt,TotalVariants=13586217,VariantsNotRead=0,HarmonisedVariants=13586217,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-30300_irnt/ukb-d-30300_irnt_data.json --ref /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/QC/genomes/b37/human_g1k_v37.fasta; 1.1.1",
    "file_date": "2019-11-25T13:28:49.063694",
    "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-30300_irnt/ukb-d-30300_irnt.vcf.gz -O z /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-30300_irnt/ukb-d-30300_irnt_data.vcf.gz; Date=Mon Nov 25 14:18:32 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-30300_irnt/ukb-d-30300_irnt.vcf.gz; Date=Sun May 10 23:23:03 2020"
}

LDSC

*********************************************************************
* LD Score Regression (LDSC)
* Version 1.0.1
* (C) 2014-2019 Brendan Bulik-Sullivan and Hilary Finucane
* Broad Institute of MIT and Harvard / MIT Department of Mathematics
* GNU General Public License v3
*********************************************************************
Call: 
./ldsc.py \
--h2 /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-30300_irnt/ukb-d-30300_irnt.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-30300_irnt/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 14:53:36 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-30300_irnt/ukb-d-30300_irnt.vcf.gz ...
Read summary statistics for 13586217 SNPs.
Dropped 12711 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: 0.1909 (0.0142)
Lambda GC: 1.6958
Mean Chi^2: 2.523
Intercept: 1.1613 (0.0201)
Ratio: 0.1059 (0.0132)
Analysis finished at Mon Nov 25 14:55:59 2019
Total time elapsed: 2.0m:23.05s

QC metrics

Metrics

{
    "af_correlation": 0.9521,
    "inflation_factor": 1.4388,
    "mean_EFFECT": -9.8977e-06,
    "n": 344729,
    "n_snps": 13586217,
    "n_clumped_hits": 310,
    "n_p_sig": 79632,
    "n_mono": 0,
    "n_ns": 1251786,
    "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": 569217,
    "n_est": 346035.0069,
    "ratio_se_n": 1.0019,
    "mean_diff": 8.3532e-07,
    "ratio_diff": 0.9578,
    "sd_y_est1": 0.9944,
    "sd_y_est2": 0.9963,
    "r2_sum1": 0.0995,
    "r2_sum2": 0.1006,
    "r2_sum3": 0.1002,
    "r2_sum4": 0.1003,
    "ldsc_nsnp_merge_refpanel_ld": 1283504,
    "ldsc_nsnp_merge_regression_ld": 1283504,
    "ldsc_observed_scale_h2_beta": 0.1909,
    "ldsc_observed_scale_h2_se": 0.0142,
    "ldsc_intercept_beta": 1.1613,
    "ldsc_intercept_se": 0.0201,
    "ldsc_lambda_gc": 1.6958,
    "ldsc_mean_chisq": 2.523,
    "ldsc_ratio": 0.1059
}

Flags

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

Definitions

General metrics

af_correlation: Correlation coefficient between AF and AF_reference.
inflation_factor (lambda): Genomic inflation factor.
mean_EFFECT: Mean of EFFECT size.
n: Maximum value of reported sample size across all SNPs, $n$.
n_clumped_hits: Number of clumped hits.
n_snps: Number of SNPs
n_p_sig: Number of SNPs with pvalue below 5e-8.
n_mono: Number of monomorphic (MAF == 1 or MAF == 0) SNPs.
n_ns: Number of SNPs with nonsense values:
- alleles other than A, C, G or T.
- P-values < 0 or > 1.
- negative or infinite standard errors (<= 0 or = Infinity).
- infinite beta estimates or allele frequencies < 0 or > 1.
n_mac: Number of cases where MAC ($2 \times N \times MAF$) is less than 6.
is_snpid_unique: true if the combination of ID REF ALT is unique and therefore no duplication in snpid.
n_miss_<*>: Number of NA observations for <*> column.

se_n metrics

n_est: Estimated sample size value, $\widehat{n}$.
ratio_se_n: $\texttt{ratio_se_n} = \frac{\sqrt{\widehat{n}}}{\sqrt{n}}$. We expect ratio_se_n to be 1. When it is not 1, it implies that the trait did not have a variance of 1, the reported sample size is wrong, or that the SNP-level effective sample sizes differ markedly from the reported sample size.
mean_diff: $\texttt{mean_diff} = \sum_{j} \frac{\widehat{\beta_j^{std}} - \beta_j}{\texttt{n_snps}}$, mean difference between the standardised beta, predicted from P-values, and the observed beta. The difference should be very close to zero if trait has a variance of 1.
- $\widehat{\beta_j^{std}} = \sqrt{\frac{{z}_j^2 / ({z}_j^2 + n -2)}{2 \times {MAF}_j \times (1 - {MAF}_j)}} \times sign({z}_j)$,
- ${z}_j = \frac{\beta_j}{{se}_j}$,
- and $\beta_j$ is the reported effect size.
ratio_diff: $\texttt{ratio_diff} = |\frac{\texttt{mean_diff}}{\texttt{mean_diff2}}|$, absolute ratio between the mean of diff and the mean of diff2 (expected difference between the standardised beta predicted from P-values, and the standardised beta derived from the observed beta divided by the predicted SD; NOT reported). The ratio should be close to 1. If different from 1, then implies that the betas are not in a standard deviation scale.
- $\texttt{mean_diff2} = \sum_{j} \frac{\widehat{\beta_j^{std}} - \beta^{\prime}_j}{\texttt{n_snps}}$
- $\beta^{\prime}_j = \frac{\beta_j}{\widehat{\texttt{sd2}}_{y}}$
sd_y_est1: The standard deviation for the trait inferred from the reported sample size, median standard errors for the SNP-trait assocations and SNP variances.
- $\widehat{\texttt{sd1}}_{y} = \frac{\sqrt{n} \times median({se}_j)}{C}$,
- $C = median(\frac{1}{\sqrt{2 \times {MAF}_j \times (1 - {MAF}_j)}})$,
- and ${se}_j$ is the reported standard error.
sd_y_est2: The standard deviation for the trait inferred from the reported sample size, Z statistics for the SNP-trait effects (beta/se) and allele frequency.
- $\widehat{\texttt{sd2}}_{y} = median(\widehat{sd_j})$,
- $\widehat{sd_j} = \frac{\beta_j}{\widehat{\beta_j^{std}}}$,

r2 metrics

Sum of variance explained, calculated from the clumped top hits sample.

r2_sum<*>: r2 statistics under various assumptions
- 1: $r^2 = \sum_j{\frac{2 \times \beta_j^2 \times {MAF}_j \times (1 - {MAF}_j)}{\texttt{var1}}}$, $\texttt{var1} = 1$.
- 2: $r^2 = \sum_j{\frac{2 \times \beta_j^2 \times {MAF}_j \times (1 - {MAF}_j)}{\texttt{var2}}}$, $\texttt{var2} = {\widehat{\texttt{sd1}}_{y}}^2$,
- 3: $r^2 = \sum_j{\frac{2 \times \beta_j^2 \times {MAF}_j \times (1 - {MAF}_j)}{\texttt{var3}}}$, $\texttt{var3} = {\widehat{\texttt{sd2}}_{y}}^2$,
- 4: $r^2 = \sum_j{\frac{F_j}{F_j + n - 2}}$, $F = \frac{\beta_j^2}{{se}_j^2}$.

LDSC metrics

Metrics from LD regression

ldsc_nsnp_merge_refpanel_ld: Number of remaining SNPs after merging with reference panel LD.
ldsc_nsnp_merge_regression_ld: Number of remaining SNPs after merging with regression SNP LD.
ldsc_observed_scale_h2_{beta,se} Coefficient value and SE for total observed scale h2.
ldsc_intercept_{beta,se}: Coefficient value and SE for intercept. Intercept is expected to be 1.
ldsc_lambda_gc: Lambda GC statistics.
ldsc_mean_chisq: Mean $\chi^2$ statistics.
ldsc_ratio: $\frac{\texttt{ldsc_intercept_beta} - 1}{\texttt{ldsc_mean_chisq} - 1}$, the proportion of the inflation in the mean $\chi^2$ that the LD Score regression intercepts ascribes to causes other than polygenic heritability. The value of ratio should be close to zero, though in practice values of 0.1-0.2 are not uncommon, probably due to sample/reference LD Score mismatch or model misspecification (e.g., low LD variants have slightly higher $h^2$ per SNP).

Flags

When a metric needs attention, the flag should return TRUE.

af_correlation: abs(af_correlation) < 0.7.
inflation_factor: inflation_factor > 1.2.
n: n (max reported sample size) < 10000.
is_snpid_non_unique: NOT is_snpid_unique.
mean_EFFECT_nonfinite: mean(EFFECT) is NA, NaN, or Inf.
mean_EFFECT_05: abs(mean(EFFECT)) > 0.5.
mean_EFFECT_01: abs(mean(EFFECT)) > 0.1.
mean_chisq: ldsc_mean_chisq > 1.3 or ldsc_mean_chisq < 0.7.
n_p_sig: n_p_sig > 1000.
miss_<*>: n_miss_<*> / n_snps > 0.01.
ldsc_ratio: ldsc_ratio > 0.5
ldsc_intercept_beta: ldsc_intercept_beta > 1.5
n_clumped_hits: n_clumped_hits > 1000
r2_sum<*>: r2_sum<*> > 0.5

Plots

Manhattan plot
- Red line: $-log_{10}^{5 \times 10^{-8}}$
- Blue line: $-log_{10}^{5 \times 10^{-5}}$
QQ plot
AF plot
P-Z plot
beta_std plot: Scatter plot between $\widehat{\beta_j^{std}}$ and $\beta_j$

Diagnostics

Details

Summary stats

skim_type	skim_variable	n_missing	complete_rate	character.min	character.max	character.empty	character.n_unique	character.whitespace	numeric.mean	numeric.sd	numeric.p0	numeric.p25	numeric.p50	numeric.p75	numeric.p100	numeric.hist
character	ID	0	1.0000000	3	94	0	13574170	0	NA	NA	NA	NA	NA	NA	NA	NA
character	REF	0	1.0000000	1	100	0	57082	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	9.051358e+00	6.184962e+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	7.902498e+07	5.591474e+07	3.02000e+02	3.293100e+07	7.013848e+07	1.148588e+08	2.492309e+08	▇▆▅▂▁
numeric	EFFECT	0	1.0000000	NA	NA	NA	NA	NA	-9.900000e-06	1.512420e-02	-2.47658e-01	-4.689400e-03	1.550000e-05	4.701400e-03	3.552080e-01	▁▂▇▁▁
numeric	SE	0	1.0000000	NA	NA	NA	NA	NA	1.006380e-02	9.708000e-03	1.96830e-03	2.865100e-03	5.279900e-03	1.446170e-02	4.937340e-02	▇▂▁▁▁
numeric	PVAL	0	1.0000000	NA	NA	NA	NA	NA	4.397820e-01	3.053733e-01	0.00000e+00	1.597158e-01	4.184784e-01	7.042405e-01	1.000000e+00	▇▅▅▅▅
numeric	PVAL_ztest	0	1.0000000	NA	NA	NA	NA	NA	4.397815e-01	3.053735e-01	0.00000e+00	1.597154e-01	4.184775e-01	7.042402e-01	1.000000e+00	▇▅▅▅▅
numeric	AF	0	1.0000000	NA	NA	NA	NA	NA	1.908069e-01	2.544041e-01	1.00000e-03	7.430400e-03	6.003420e-02	2.953250e-01	9.989990e-01	▇▂▁▁▁
numeric	AF_reference	569217	0.9581033	NA	NA	NA	NA	NA	1.963367e-01	2.471015e-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	3.447290e+05	0.000000e+00	3.44729e+05	3.447290e+05	3.447290e+05	3.447290e+05	3.447290e+05	▁▁▇▁▁

Head and tail

CHROM	POS	ID	REF	ALT	EFFECT	SE	PVAL	PVAL_ztest	AF	AF_reference	N
1	692794	rs530212009	CA	C	-0.0046872	0.0041941	0.2637491	0.2637481	0.1106300	0.1894970	344729
1	693731	rs12238997	A	G	-0.0019786	0.0039630	0.6175967	0.6175958	0.1158130	0.1417730	344729
1	707522	rs371890604	G	C	-0.0014006	0.0044573	0.7533452	0.7533464	0.0972243	0.1293930	344729
1	717587	rs144155419	G	A	-0.0112787	0.0106135	0.2879320	0.2879294	0.0157292	0.0045926	344729
1	723329	rs189787166	A	T	0.0083889	0.0315333	0.7902127	0.7902135	0.0017197	0.0003994	344729
1	730087	rs148120343	T	C	-0.0056079	0.0055166	0.3093699	0.3093684	0.0564849	0.0127796	344729
1	731718	rs142557973	T	C	-0.0019878	0.0037584	0.5968703	0.5968715	0.1217300	0.1543530	344729
1	732032	rs61770163	A	C	-0.0020128	0.0040097	0.6156814	0.6156806	0.1211220	0.1555510	344729
1	734349	rs141242758	T	C	-0.0018605	0.0037604	0.6207604	0.6207603	0.1209620	0.1525560	344729
1	740284	rs61770167	C	T	0.0199561	0.0172172	0.2464257	0.2464239	0.0057743	0.0023962	344729

CHROM	POS	ID	REF	ALT	EFFECT	SE	PVAL	PVAL_ztest	AF	AF_reference	N
23	154923311	rs141127553	C	T	0.0083554	0.0043394	0.0541714	0.0541701	0.0561570	0.0309934	344729
23	154923374	rs111332691	T	A	0.0018964	0.0047690	0.6908965	0.6908957	0.0447961	0.0116556	344729
23	154925045	rs509981	C	T	-0.0081327	0.0022950	0.0003946	0.0003946	0.2456220	0.3634440	344729
23	154925895	rs538470	C	T	-0.0081477	0.0023475	0.0005189	0.0005188	0.2419530	0.3634440	344729
23	154927581	rs644138	G	A	-0.0052213	0.0021583	0.0155579	0.0155572	0.3021780	0.4635760	344729
23	154929412	rs557132	C	T	-0.0080627	0.0022957	0.0004446	0.0004445	0.2454760	0.3568210	344729
23	154929637	rs35185538	CT	C	-0.0074542	0.0023959	0.0018632	0.0018630	0.2297040	0.3011920	344729
23	154929952	rs4012982	CAA	C	-0.0082285	0.0024146	0.0006549	0.0006549	0.2394410	0.3165560	344729
23	154930230	rs781880	A	G	-0.0082451	0.0022952	0.0003279	0.0003278	0.2458870	0.3618540	344729
23	154930487	rs781879	T	A	0.0018604	0.0078791	0.8133420	0.8133418	0.0195262	0.1263580	344729

bcf preview

1   692794  rs530212009 CA  C   .   PASS    AF=0.11063  ES:SE:LP:AF:SS:ID   -0.00468717:0.00419405:0.578809:0.11063:344729:1_692794_CA_C
1   693731  rs12238997  A   G   .   PASS    AF=0.115813 ES:SE:LP:AF:SS:ID   -0.00197855:0.00396296:0.209295:0.115813:344729:rs12238997
1   707522  rs371890604 G   C   .   PASS    AF=0.0972243    ES:SE:LP:AF:SS:ID   -0.00140063:0.00445734:0.123006:0.0972243:344729:rs371890604
1   717587  rs144155419 G   A   .   PASS    AF=0.0157292    ES:SE:LP:AF:SS:ID   -0.0112787:0.0106135:0.54071:0.0157292:344729:rs144155419
1   723329  rs189787166 A   T   .   PASS    AF=0.00171967   ES:SE:LP:AF:SS:ID   0.00838891:0.0315333:0.102256:0.00171967:344729:rs189787166
1   730087  rs148120343 T   C   .   PASS    AF=0.0564849    ES:SE:LP:AF:SS:ID   -0.00560793:0.00551664:0.509522:0.0564849:344729:rs148120343
1   731718  rs58276399  T   C   .   PASS    AF=0.12173  ES:SE:LP:AF:SS:ID   -0.00198782:0.00375837:0.22412:0.12173:344729:rs58276399
1   732032  rs61770163  A   C   .   PASS    AF=0.121122 ES:SE:LP:AF:SS:ID   -0.00201278:0.00400967:0.210644:0.121122:344729:rs61770163
1   734349  rs141242758 T   C   .   PASS    AF=0.120962 ES:SE:LP:AF:SS:ID   -0.00186052:0.00376035:0.207076:0.120962:344729:rs141242758
1   740284  rs61770167  C   T   .   PASS    AF=0.00577432   ES:SE:LP:AF:SS:ID   0.0199561:0.0172172:0.608314:0.00577432:344729:rs61770167
1   742813  rs112573343 C   T   .   PASS    AF=0.0018795    ES:SE:LP:AF:SS:ID   0.0142087:0.0325169:0.179051:0.0018795:344729:rs112573343
1   749963  rs529266287 T   TAA .   PASS    AF=0.869782 ES:SE:LP:AF:SS:ID   0.00295991:0.00370759:0.371944:0.869782:344729:rs529266287
1   750230  rs190826124 G   C   .   PASS    AF=0.00153601   ES:SE:LP:AF:SS:ID   -0.00410568:0.0334925:0.0445836:0.00153601:344729:rs190826124
1   751343  rs28544273  T   A   .   PASS    AF=0.122886 ES:SE:LP:AF:SS:ID   -0.00269892:0.00367132:0.335116:0.122886:344729:rs28544273
1   751488  rs200141114 G   GA  .   PASS    AF=0.142712 ES:SE:LP:AF:SS:ID   7.05361e-05:0.00362891:0.00678781:0.142712:344729:rs200141114
1   751756  rs28527770  T   C   .   PASS    AF=0.123004 ES:SE:LP:AF:SS:ID   -0.00273519:0.00366619:0.341385:0.123004:344729:rs28527770
1   753405  rs3115860   C   A   .   PASS    AF=0.870907 ES:SE:LP:AF:SS:ID   0.00143037:0.00357277:0.161846:0.870907:344729:rs3115860
1   753425  rs3131970   T   C   .   PASS    AF=0.875493 ES:SE:LP:AF:SS:ID   0.0017785:0.00363181:0.204575:0.875493:344729:rs3131970
1   753541  rs2073813   G   A   .   PASS    AF=0.128617 ES:SE:LP:AF:SS:ID   -0.00245783:0.00358165:0.307532:0.128617:344729:rs2073813
1   754105  rs12184325  C   T   .   PASS    AF=0.0363561    ES:SE:LP:AF:SS:ID   -0.00858942:0.00649905:0.729815:0.0363561:344729:rs12184325
1   754182  rs3131969   A   G   .   PASS    AF=0.8705   ES:SE:LP:AF:SS:ID   0.00176039:0.003569:0.206322:0.8705:344729:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.870603 ES:SE:LP:AF:SS:ID   0.00178854:0.00357059:0.210112:0.870603:344729:rs3131968
1   754334  rs3131967   T   C   .   PASS    AF=0.870495 ES:SE:LP:AF:SS:ID   0.00174118:0.00356885:0.20368:0.870495:344729:rs3131967
1   754433  rs150578204 G   A   .   PASS    AF=0.00505869   ES:SE:LP:AF:SS:ID   -0.0110453:0.0182915:0.26285:0.00505869:344729:rs150578204
1   754458  rs142682604 G   T   .   PASS    AF=0.00502542   ES:SE:LP:AF:SS:ID   -0.0110563:0.0183406:0.262314:0.00502542:344729:rs142682604
1   755435  rs184270342 T   G   .   PASS    AF=0.00558651   ES:SE:LP:AF:SS:ID   0.0126807:0.0177394:0.323568:0.00558651:344729:rs184270342
1   755890  rs3115858   A   T   .   PASS    AF=0.870579 ES:SE:LP:AF:SS:ID   0.00135481:0.00356259:0.152593:0.870579:344729:rs3115858
1   756434  rs61768170  G   C   .   PASS    AF=0.125958 ES:SE:LP:AF:SS:ID   -0.00207784:0.00363536:0.245943:0.125958:344729:rs61768170
1   756604  rs3131962   A   G   .   PASS    AF=0.870143 ES:SE:LP:AF:SS:ID   0.00134171:0.00355399:0.151328:0.870143:344729:rs3131962
1   757640  rs3115853   G   A   .   PASS    AF=0.869424 ES:SE:LP:AF:SS:ID   0.00134965:0.00355068:0.152511:0.869424:344729:rs3115853
1   757734  rs4951929   C   T   .   PASS    AF=0.870297 ES:SE:LP:AF:SS:ID   0.00129158:0.00355708:0.144766:0.870297:344729:rs4951929
1   757936  rs4951862   C   A   .   PASS    AF=0.870303 ES:SE:LP:AF:SS:ID   0.00128902:0.00355733:0.144428:0.870303:344729:rs4951862
1   758144  rs3131956   A   G   .   PASS    AF=0.870312 ES:SE:LP:AF:SS:ID   0.00130063:0.00355745:0.145901:0.870312:344729:rs3131956
1   758626  rs3131954   C   T   .   PASS    AF=0.870753 ES:SE:LP:AF:SS:ID   0.00149316:0.0035665:0.170398:0.870753:344729:rs3131954
1   759293  rs10157329  T   A   .   PASS    AF=0.0987463    ES:SE:LP:AF:SS:ID   -0.000917654:0.00414642:0.0836255:0.0987463:344729:rs10157329
1   759600  rs545998451 AGT A   .   PASS    AF=0.00648112   ES:SE:LP:AF:SS:ID   0.0110893:0.0160222:0.310812:0.00648112:344729:1_759600_AGT_A
1   759837  rs3115851   T   A   .   PASS    AF=0.874658 ES:SE:LP:AF:SS:ID   0.00202549:0.00361966:0.239754:0.874658:344729:rs3115851
1   761732  rs2286139   C   T   .   PASS    AF=0.864055 ES:SE:LP:AF:SS:ID   0.00150227:0.00354967:0.172541:0.864055:344729:rs2286139
1   761752  rs1057213   C   T   .   PASS    AF=0.869438 ES:SE:LP:AF:SS:ID   0.00113641:0.00358409:0.12425:0.869438:344729:rs1057213
1   762273  rs3115849   G   A   .   PASS    AF=0.866397 ES:SE:LP:AF:SS:ID   0.00152601:0.00358504:0.173695:0.866397:344729:rs3115849
1   762485  rs12095200  C   A   .   PASS    AF=0.0987143    ES:SE:LP:AF:SS:ID   0.000153157:0.00429309:0.0125389:0.0987143:344729:rs12095200
1   762589  rs3115848   G   C   .   PASS    AF=0.871574 ES:SE:LP:AF:SS:ID   0.0022705:0.00362571:0.274767:0.871574:344729:rs3115848
1   762592  rs3131950   C   G   .   PASS    AF=0.871574 ES:SE:LP:AF:SS:ID   0.00227084:0.00362571:0.274817:0.871574:344729:rs3131950
1   762601  rs3131949   T   C   .   PASS    AF=0.871574 ES:SE:LP:AF:SS:ID   0.00228833:0.00362578:0.277401:0.871574:344729:rs3131949
1   762632  rs3131948   T   A   .   PASS    AF=0.871945 ES:SE:LP:AF:SS:ID   0.00232934:0.00362784:0.283307:0.871945:344729:rs3131948
1   764191  rs7515915   T   G   .   PASS    AF=0.125545 ES:SE:LP:AF:SS:ID   -0.00259466:0.0036306:0.323474:0.125545:344729:rs7515915
1   766007  rs61768174  A   C   .   PASS    AF=0.105343 ES:SE:LP:AF:SS:ID   -2.16066e-05:0.00395363:0.00189766:0.105343:344729:rs61768174
1   766105  rs2519015   T   A   .   PASS    AF=0.855408 ES:SE:LP:AF:SS:ID   0.00110191:0.00354884:0.121373:0.855408:344729:rs2519015
1   767393  rs538667473 A   C   .   PASS    AF=0.00164172   ES:SE:LP:AF:SS:ID   0.00231838:0.0315892:0.026182:0.00164172:344729:rs538667473
1   768116  rs376645387 A   AGTTTT  .   PASS    AF=0.838258 ES:SE:LP:AF:SS:ID   -0.00427426:0.00349354:0.655313:0.838258:344729:rs376645387