Summary

Summary {data-width=650}

Manhattan plot

manhattan_plot

manhattan_plot

QQ plot

qq_plot

qq_plot

AF plot

af_plot

af_plot

P-Z plot

pz_plot

pz_plot

beta_std 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-22614_1,TotalVariants=11359742,VariantsNotRead=0,HarmonisedVariants=11359742,VariantsNotHarmonised=0,SwitchedAlleles=222,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-22614_1/ukb-d-22614_1_data.json --ref /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/QC/genomes/b37/human_g1k_v37.fasta; 1.1.1",
    "file_date": "2019-11-25T15:11:43.720572",
    "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-22614_1/ukb-d-22614_1.vcf.gz -O z /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-22614_1/ukb-d-22614_1_data.vcf.gz; Date=Mon Nov 25 15:38:16 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-22614_1/ukb-d-22614_1.vcf.gz; Date=Sat May  9 15:28:10 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-22614_1/ukb-d-22614_1.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-22614_1/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 16:32:56 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-22614_1/ukb-d-22614_1.vcf.gz ...
Read summary statistics for 11359742 SNPs.
Dropped 9580 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, 1282450 SNPs remain.
After merging with regression SNP LD, 1282450 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0038 (0.0045)
Lambda GC: 1.0264
Mean Chi^2: 1.0165
Intercept: 1.01 (0.0057)
Ratio: 0.6101 (0.3454)
Analysis finished at Mon Nov 25 16:34:57 2019
Total time elapsed: 2.0m:1.74s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9471,
    "inflation_factor": 1.0267,
    "mean_EFFECT": 3.6264e-06,
    "n": 87998,
    "n_snps": 11359742,
    "n_clumped_hits": 0,
    "n_p_sig": 1,
    "n_mono": 0,
    "n_ns": 1155315,
    "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": 235816,
    "n_est": 88165.746,
    "ratio_se_n": 1.001,
    "mean_diff": 0,
    "ratio_diff": 9.3023,
    "sd_y_est1": 0.1882,
    "sd_y_est2": 0.1884,
    "r2_sum1": 0,
    "r2_sum2": 0,
    "r2_sum3": 0,
    "r2_sum4": 0,
    "ldsc_nsnp_merge_refpanel_ld": 1282450,
    "ldsc_nsnp_merge_regression_ld": 1282450,
    "ldsc_observed_scale_h2_beta": 0.0038,
    "ldsc_observed_scale_h2_se": 0.0045,
    "ldsc_intercept_beta": 1.01,
    "ldsc_intercept_se": 0.0057,
    "ldsc_lambda_gc": 1.0264,
    "ldsc_mean_chisq": 1.0165,
    "ldsc_ratio": 0.6061
}

Flags

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 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 numeric.mean numeric.sd numeric.p0 numeric.p25 numeric.p50 numeric.p75 numeric.p100 numeric.hist
character ID 0 1.0000000 3 94 0 11350759 0 NA NA NA NA NA NA NA NA
character REF 0 1.0000000 1 100 0 51941 0 NA NA NA NA NA NA NA NA
character ALT 0 1.0000000 1 342 0 31607 0 NA NA NA NA NA NA NA NA
numeric CHROM 0 1.0000000 NA NA NA NA NA 9.073903e+00 6.182617e+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 7.883509e+07 5.600438e+07 3.02000e+02 3.262630e+07 6.983279e+07 1.147284e+08 2.492309e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA 3.600000e-06 3.003600e-03 -2.92736e-02 -1.151000e-03 -7.900000e-06 1.123900e-03 4.135520e-02 ▁▃▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 2.388100e-03 1.819200e-03 7.41600e-04 1.016600e-03 1.528800e-03 3.232800e-03 1.072620e-02 ▇▂▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.962620e-01 2.892884e-01 0.00000e+00 2.446718e-01 4.943266e-01 7.470506e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.962602e-01 2.892895e-01 0.00000e+00 2.446691e-01 4.943246e-01 7.470490e-01 1.000000e+00 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA 2.261046e-01 2.610305e-01 3.69280e-03 2.061640e-02 1.086960e-01 3.614660e-01 9.963070e-01 ▇▂▁▁▁
numeric AF_reference 235816 0.9792411 NA NA NA NA NA 2.266436e-01 2.522373e-01 0.00000e+00 1.817090e-02 1.269970e-01 3.610220e-01 1.000000e+00 ▇▂▂▁▁
numeric N 0 1.0000000 NA NA NA NA NA 8.799800e+04 0.000000e+00 8.79980e+04 8.799800e+04 8.799800e+04 8.799800e+04 8.799800e+04 ▁▁▇▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 692794 rs530212009 CA C 0.0004880 0.0015676 0.7555618 0.7555607 0.1114960 0.1894970 87998
1 693731 rs12238997 A G 0.0016667 0.0014850 0.2617369 0.2617350 0.1165300 0.1417730 87998
1 707522 rs371890604 G C -0.0001638 0.0016690 0.9218191 0.9218186 0.0979575 0.1293930 87998
1 717587 rs144155419 G A 0.0027708 0.0039808 0.4864072 0.4864055 0.0157767 0.0045926 87998
1 730087 rs148120343 T C -0.0006313 0.0020596 0.7592031 0.7592029 0.0570081 0.0127796 87998
1 731718 rs142557973 T C 0.0011933 0.0014088 0.3969913 0.3969892 0.1224500 0.1543530 87998
1 732032 rs61770163 A C 0.0006713 0.0015028 0.6550976 0.6550968 0.1220280 0.1555510 87998
1 734349 rs141242758 T C 0.0012956 0.0014099 0.3581311 0.3581308 0.1216690 0.1525560 87998
1 740284 rs61770167 C T 0.0038849 0.0064477 0.5468245 0.5468225 0.0057907 0.0023962 87998
1 749963 rs529266287 T TAA -0.0009397 0.0013871 0.4981166 0.4981139 0.8688370 0.7641770 87998
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
23 154923311 rs141127553 C T 0.0010461 0.0016527 0.5267615 0.5267591 0.0551068 0.0309934 87998
23 154923374 rs111332691 T A -0.0004136 0.0017956 0.8178169 0.8178165 0.0448647 0.0116556 87998
23 154925045 rs509981 C T 0.0000106 0.0008652 0.9902150 0.9902148 0.2446380 0.3634440 87998
23 154925895 rs538470 C T -0.0000276 0.0008845 0.9751380 0.9751379 0.2411250 0.3634440 87998
23 154927581 rs644138 G A 0.0002807 0.0008140 0.7302154 0.7302149 0.3001550 0.4635760 87998
23 154929412 rs557132 C T -0.0000288 0.0008654 0.9734351 0.9734350 0.2444910 0.3568210 87998
23 154929637 rs35185538 CT C 0.0002926 0.0009038 0.7461274 0.7461263 0.2288010 0.3011920 87998
23 154929952 rs4012982 CAA C -0.0000164 0.0009106 0.9856050 0.9856045 0.2384500 0.3165560 87998
23 154930230 rs781880 A G 0.0000004 0.0008652 0.9996380 0.9996376 0.2449290 0.3618540 87998
23 154930487 rs781879 T A -0.0026477 0.0029233 0.3650816 0.3650805 0.0197684 0.1263580 87998

bcf preview

1   692794  rs530212009 CA  C   .   PASS    AF=0.111496 ES:SE:LP:AF:SS:ID   0.000488009:0.00156757:0.12173:0.111496:87998:1_692794_CA_C
1   693731  rs12238997  A   G   .   PASS    AF=0.11653  ES:SE:LP:AF:SS:ID   0.00166666:0.00148504:0.582135:0.11653:87998:rs12238997
1   707522  rs371890604 G   C   .   PASS    AF=0.0979575    ES:SE:LP:AF:SS:ID   -0.000163804:0.00166903:0.0353543:0.0979575:87998:rs371890604
1   717587  rs144155419 G   A   .   PASS    AF=0.0157767    ES:SE:LP:AF:SS:ID   0.00277082:0.00398085:0.313:0.0157767:87998:rs144155419
1   730087  rs148120343 T   C   .   PASS    AF=0.0570081    ES:SE:LP:AF:SS:ID   -0.000631309:0.00205955:0.119642:0.0570081:87998:rs148120343
1   731718  rs58276399  T   C   .   PASS    AF=0.12245  ES:SE:LP:AF:SS:ID   0.00119326:0.00140879:0.401219:0.12245:87998:rs58276399
1   732032  rs61770163  A   C   .   PASS    AF=0.122028 ES:SE:LP:AF:SS:ID   0.000671308:0.00150284:0.183694:0.122028:87998:rs61770163
1   734349  rs141242758 T   C   .   PASS    AF=0.121669 ES:SE:LP:AF:SS:ID   0.00129564:0.00140994:0.445958:0.121669:87998:rs141242758
1   740284  rs61770167  C   T   .   PASS    AF=0.00579073   ES:SE:LP:AF:SS:ID   0.00388494:0.00644773:0.262152:0.00579073:87998:rs61770167
1   749963  rs529266287 T   TAA .   PASS    AF=0.868837 ES:SE:LP:AF:SS:ID   -0.000939712:0.00138711:0.302669:0.868837:87998:rs529266287
1   751343  rs28544273  T   A   .   PASS    AF=0.123774 ES:SE:LP:AF:SS:ID   0.00106656:0.00137528:0.358492:0.123774:87998:rs28544273
1   751488  rs200141114 G   GA  .   PASS    AF=0.143283 ES:SE:LP:AF:SS:ID   0.00081886:0.00136123:0.26164:0.143283:87998:rs200141114
1   751756  rs28527770  T   C   .   PASS    AF=0.123911 ES:SE:LP:AF:SS:ID   0.00103995:0.00137326:0.347868:0.123911:87998:rs28527770
1   753405  rs3115860   C   A   .   PASS    AF=0.86982  ES:SE:LP:AF:SS:ID   -0.00126075:0.00133799:0.460852:0.86982:87998:rs3115860
1   753425  rs3131970   T   C   .   PASS    AF=0.874474 ES:SE:LP:AF:SS:ID   -0.000775855:0.00135989:0.245407:0.874474:87998:rs3131970
1   753541  rs2073813   G   A   .   PASS    AF=0.129597 ES:SE:LP:AF:SS:ID   0.00130157:0.00134216:0.478644:0.129597:87998:rs2073813
1   754105  rs12184325  C   T   .   PASS    AF=0.0357167    ES:SE:LP:AF:SS:ID   0.00885183:0.00245598:3.50405:0.0357167:87998:rs12184325
1   754182  rs3131969   A   G   .   PASS    AF=0.869462 ES:SE:LP:AF:SS:ID   -0.00129622:0.00133686:0.478538:0.869462:87998:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.869541 ES:SE:LP:AF:SS:ID   -0.00133033:0.00133745:0.49499:0.869541:87998:rs3131968
1   754334  rs3131967   T   C   .   PASS    AF=0.869458 ES:SE:LP:AF:SS:ID   -0.00130041:0.0013368:0.48061:0.869458:87998:rs3131967
1   754433  rs150578204 G   A   .   PASS    AF=0.00530476   ES:SE:LP:AF:SS:ID   0.00294264:0.00668863:0.180471:0.00530476:87998:rs150578204
1   754458  rs142682604 G   T   .   PASS    AF=0.00526955   ES:SE:LP:AF:SS:ID   0.00305445:0.00670549:0.187929:0.00526955:87998:rs142682604
1   755435  rs184270342 T   G   .   PASS    AF=0.00561078   ES:SE:LP:AF:SS:ID   -0.00137355:0.00661263:0.078079:0.00561078:87998:rs184270342
1   755890  rs3115858   A   T   .   PASS    AF=0.869456 ES:SE:LP:AF:SS:ID   -0.00121829:0.00133409:0.442323:0.869456:87998:rs3115858
1   756434  rs61768170  G   C   .   PASS    AF=0.126997 ES:SE:LP:AF:SS:ID   0.000941426:0.00136185:0.310346:0.126997:87998:rs61768170
1   756604  rs3131962   A   G   .   PASS    AF=0.86898  ES:SE:LP:AF:SS:ID   -0.0011234:0.00133061:0.399554:0.86898:87998:rs3131962
1   757640  rs3115853   G   A   .   PASS    AF=0.868353 ES:SE:LP:AF:SS:ID   -0.00109307:0.00132971:0.386097:0.868353:87998:rs3115853
1   757734  rs4951929   C   T   .   PASS    AF=0.869132 ES:SE:LP:AF:SS:ID   -0.00118998:0.00133183:0.429928:0.869132:87998:rs4951929
1   757936  rs4951862   C   A   .   PASS    AF=0.869137 ES:SE:LP:AF:SS:ID   -0.00119107:0.00133191:0.430405:0.869137:87998:rs4951862
1   758144  rs3131956   A   G   .   PASS    AF=0.86914  ES:SE:LP:AF:SS:ID   -0.0011931:0.00133193:0.431352:0.86914:87998:rs3131956
1   758626  rs3131954   C   T   .   PASS    AF=0.869616 ES:SE:LP:AF:SS:ID   -0.00126266:0.00133551:0.4629:0.869616:87998:rs3131954
1   759293  rs10157329  T   A   .   PASS    AF=0.099274 ES:SE:LP:AF:SS:ID   0.000373412:0.00155457:0.0914217:0.099274:87998:rs10157329
1   759600  rs545998451 AGT A   .   PASS    AF=0.00645507   ES:SE:LP:AF:SS:ID   -0.00114733:0.00602289:0.0711327:0.00645507:87998:1_759600_AGT_A
1   759837  rs3115851   T   A   .   PASS    AF=0.873585 ES:SE:LP:AF:SS:ID   -0.00109529:0.00135529:0.377786:0.873585:87998:rs3115851
1   761732  rs2286139   C   T   .   PASS    AF=0.862972 ES:SE:LP:AF:SS:ID   -0.0017391:0.00132936:0.719417:0.862972:87998:rs2286139
1   761752  rs1057213   C   T   .   PASS    AF=0.868391 ES:SE:LP:AF:SS:ID   -0.0013664:0.00134255:0.510334:0.868391:87998:rs1057213
1   762273  rs3115849   G   A   .   PASS    AF=0.865279 ES:SE:LP:AF:SS:ID   -0.00159735:0.00134272:0.630428:0.865279:87998:rs3115849
1   762485  rs12095200  C   A   .   PASS    AF=0.0995469    ES:SE:LP:AF:SS:ID   0.00200158:0.00160782:0.67127:0.0995469:87998:rs12095200
1   762589  rs3115848   G   C   .   PASS    AF=0.87056  ES:SE:LP:AF:SS:ID   -0.00118723:0.00135812:0.417905:0.87056:87998:rs3115848
1   762592  rs3131950   C   G   .   PASS    AF=0.87056  ES:SE:LP:AF:SS:ID   -0.00118742:0.00135812:0.417995:0.87056:87998:rs3131950
1   762601  rs3131949   T   C   .   PASS    AF=0.870557 ES:SE:LP:AF:SS:ID   -0.0011879:0.00135813:0.418208:0.870557:87998:rs3131949
1   762632  rs3131948   T   A   .   PASS    AF=0.870925 ES:SE:LP:AF:SS:ID   -0.00117335:0.00135877:0.411345:0.870925:87998:rs3131948
1   764191  rs7515915   T   G   .   PASS    AF=0.126601 ES:SE:LP:AF:SS:ID   0.00119202:0.00136026:0.419234:0.126601:87998:rs7515915
1   766007  rs61768174  A   C   .   PASS    AF=0.106143 ES:SE:LP:AF:SS:ID   0.00104707:0.00147858:0.319803:0.106143:87998:rs61768174
1   766105  rs2519015   T   A   .   PASS    AF=0.854323 ES:SE:LP:AF:SS:ID   -0.00115529:0.00132898:0.414896:0.854323:87998:rs2519015
1   768116  rs376645387 A   AGTTTT  .   PASS    AF=0.839279 ES:SE:LP:AF:SS:ID   -0.000886316:0.00131415:0.301001:0.839279:87998:rs376645387
1   768253  rs2977608   A   C   .   PASS    AF=0.76317  ES:SE:LP:AF:SS:ID   -0.000796459:0.00105605:0.346073:0.76317:87998:rs2977608
1   768448  rs12562034  G   A   .   PASS    AF=0.105042 ES:SE:LP:AF:SS:ID   0.000171049:0.00145616:0.0426365:0.105042:87998:rs12562034
1   768819  rs12562811  C   T   .   PASS    AF=0.00770606   ES:SE:LP:AF:SS:ID   -4.93485e-05:0.00539408:0.00318154:0.00770606:87998:rs12562811
1   769138  rs59306077  CAT C   .   PASS    AF=0.129977 ES:SE:LP:AF:SS:ID   0.00130612:0.00134123:0.481291:0.129977:87998:rs762168062