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-30650_raw,TotalVariants=13586008,VariantsNotRead=0,HarmonisedVariants=13586008,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-30650_raw/ukb-d-30650_raw_data.json --ref /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/QC/genomes/b37/human_g1k_v37.fasta; 1.1.1",
    "file_date": "2019-11-25T13:29:31.387501",
    "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-30650_raw/ukb-d-30650_raw.vcf.gz -O z /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-30650_raw/ukb-d-30650_raw_data.vcf.gz; Date=Mon Nov 25 14:22:25 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-30650_raw/ukb-d-30650_raw.vcf.gz; Date=Sun May 10 12:55:19 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-30650_raw/ukb-d-30650_raw.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-30650_raw/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 14:56:15 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-30650_raw/ukb-d-30650_raw.vcf.gz ...
Read summary statistics for 13586008 SNPs.
Dropped 12709 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: 0.0562 (0.0049)
Lambda GC: 1.225
Mean Chi^2: 1.4064
Intercept: 1.0249 (0.0116)
Ratio: 0.0613 (0.0285)
Analysis finished at Mon Nov 25 14:58:19 2019
Total time elapsed: 2.0m:4.46s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9521,
    "inflation_factor": 1.1388,
    "mean_EFFECT": -0,
    "n": 342990,
    "n_snps": 13586008,
    "n_clumped_hits": 87,
    "n_p_sig": 17213,
    "n_mono": 0,
    "n_ns": 1251783,
    "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": 569151,
    "n_est": 344313.2421,
    "ratio_se_n": 1.0019,
    "mean_diff": 0,
    "ratio_diff": 30.4643,
    "sd_y_est1": 10.4547,
    "sd_y_est2": 10.4749,
    "r2_sum1": 1.9482,
    "r2_sum2": 0.0178,
    "r2_sum3": 0.0178,
    "r2_sum4": 0.0178,
    "ldsc_nsnp_merge_refpanel_ld": 1283504,
    "ldsc_nsnp_merge_regression_ld": 1283504,
    "ldsc_observed_scale_h2_beta": 0.0562,
    "ldsc_observed_scale_h2_se": 0.0049,
    "ldsc_intercept_beta": 1.0249,
    "ldsc_intercept_se": 0.0116,
    "ldsc_lambda_gc": 1.225,
    "ldsc_mean_chisq": 1.4064,
    "ldsc_ratio": 0.0613
}

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 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 TRUE
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 13573963 0 NA NA NA NA NA NA NA NA
character REF 0 1.0000000 1 100 0 57081 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 9.051252e+00 6.184978e+00 1.0000e+00 4.000000e+00 8.000000e+00 1.300000e+01 2.300000e+01 ▇▅▅▂▂
numeric POS 0 1.0000000 NA NA NA NA NA 7.902572e+07 5.591523e+07 3.0200e+02 3.293103e+07 7.013951e+07 1.148603e+08 2.492309e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA -4.240000e-05 1.504514e-01 -2.9069e+00 -4.426800e-02 -1.056600e-03 4.099300e-02 2.823300e+00 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 1.060704e-01 1.023167e-01 2.0754e-02 3.020000e-02 5.565100e-02 1.524300e-01 5.169400e-01 ▇▂▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.779580e-01 2.963408e-01 0.0000e+00 2.162898e-01 4.716697e-01 7.348793e-01 1.000000e+00 ▇▇▆▆▆
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.779576e-01 2.963411e-01 0.0000e+00 2.162859e-01 4.716678e-01 7.348800e-01 9.999998e-01 ▇▇▆▆▆
numeric AF 0 1.0000000 NA NA NA NA NA 1.908097e-01 2.544045e-01 1.0000e-03 7.431700e-03 6.004100e-02 2.953200e-01 9.990000e-01 ▇▂▁▁▁
numeric AF_reference 569151 0.9581076 NA NA NA NA NA 1.963389e-01 2.471025e-01 0.0000e+00 5.591000e-03 8.426520e-02 3.081070e-01 1.000000e+00 ▇▂▁▁▁
numeric N 0 1.0000000 NA NA NA NA NA 3.429900e+05 0.000000e+00 3.4299e+05 3.429900e+05 3.429900e+05 3.429900e+05 3.429900e+05 ▁▁▇▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 692794 rs530212009 CA C -0.0161230 0.044207 0.7153194 0.7153234 0.1105500 0.1894970 342990
1 693731 rs12238997 A G -0.0034667 0.041750 0.9338201 0.9338239 0.1158500 0.1417730 342990
1 707522 rs371890604 G C 0.0072918 0.046962 0.8766100 0.8766083 0.0972770 0.1293930 342990
1 717587 rs144155419 G A -0.1053400 0.112080 0.3472802 0.3472871 0.0156720 0.0045926 342990
1 723329 rs189787166 A T -0.5902300 0.330000 0.0736835 0.0736832 0.0017395 0.0003994 342990
1 730087 rs148120343 T C 0.0034634 0.058183 0.9525301 0.9525332 0.0564430 0.0127796 342990
1 731718 rs142557973 T C -0.0007583 0.039597 0.9847200 0.9847213 0.1217400 0.1543530 342990
1 732032 rs61770163 A C 0.0002134 0.042253 0.9959700 0.9959705 0.1211400 0.1555510 342990
1 734349 rs141242758 T C -0.0001671 0.039619 0.9966300 0.9966348 0.1209600 0.1525560 342990
1 740284 rs61770167 C T -0.1475700 0.181700 0.4167101 0.4166982 0.0057593 0.0023962 342990
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
23 154923311 rs141127553 C T 0.022605 0.045756 0.6212695 0.6212825 0.056215 0.0309934 342990
23 154923374 rs111332691 T A 0.020956 0.050235 0.6765595 0.6765619 0.044874 0.0116556 342990
23 154925045 rs509981 C T 0.029824 0.024200 0.2178101 0.2178009 0.245670 0.3634440 342990
23 154925895 rs538470 C T 0.030192 0.024755 0.2225999 0.2226043 0.242010 0.3634440 342990
23 154927581 rs644138 G A 0.031902 0.022759 0.1609900 0.1609955 0.302270 0.4635760 342990
23 154929412 rs557132 C T 0.029817 0.024207 0.2180399 0.2180421 0.245530 0.3568210 342990
23 154929637 rs35185538 CT C 0.019390 0.025265 0.4428096 0.4428052 0.229800 0.3011920 342990
23 154929952 rs4012982 CAA C 0.025061 0.025458 0.3249197 0.3249161 0.239520 0.3165560 342990
23 154930230 rs781880 A G 0.028784 0.024203 0.2343398 0.2343318 0.245930 0.3618540 342990
23 154930487 rs781879 T A -0.111460 0.083018 0.1793899 0.1794014 0.019548 0.1263580 342990

bcf preview

1   692794  rs530212009 CA  C   .   PASS    AF=0.11055  ES:SE:LP:AF:SS:ID   -0.016123:0.044207:0.1455:0.11055:342990:1_692794_CA_C
1   693731  rs12238997  A   G   .   PASS    AF=0.11585  ES:SE:LP:AF:SS:ID   -0.0034667:0.04175:0.0297368:0.11585:342990:rs12238997
1   707522  rs371890604 G   C   .   PASS    AF=0.097277 ES:SE:LP:AF:SS:ID   0.0072918:0.046962:0.0571936:0.097277:342990:rs371890604
1   717587  rs144155419 G   A   .   PASS    AF=0.015672 ES:SE:LP:AF:SS:ID   -0.10534:0.11208:0.45932:0.015672:342990:rs144155419
1   723329  rs189787166 A   T   .   PASS    AF=0.0017395    ES:SE:LP:AF:SS:ID   -0.59023:0.33:1.13263:0.0017395:342990:rs189787166
1   730087  rs148120343 T   C   .   PASS    AF=0.056443 ES:SE:LP:AF:SS:ID   0.0034634:0.058183:0.0211213:0.056443:342990:rs148120343
1   731718  rs58276399  T   C   .   PASS    AF=0.12174  ES:SE:LP:AF:SS:ID   -0.00075829:0.039597:0.00668724:0.12174:342990:rs58276399
1   732032  rs61770163  A   C   .   PASS    AF=0.12114  ES:SE:LP:AF:SS:ID   0.00021339:0.042253:0.00175374:0.12114:342990:rs61770163
1   734349  rs141242758 T   C   .   PASS    AF=0.12096  ES:SE:LP:AF:SS:ID   -0.0001671:0.039619:0.00146604:0.12096:342990:rs141242758
1   740284  rs61770167  C   T   .   PASS    AF=0.0057593    ES:SE:LP:AF:SS:ID   -0.14757:0.1817:0.380166:0.0057593:342990:rs61770167
1   742813  rs112573343 C   T   .   PASS    AF=0.0018588    ES:SE:LP:AF:SS:ID   0.068099:0.34491:0.0739252:0.0018588:342990:rs112573343
1   749963  rs529266287 T   TAA .   PASS    AF=0.86976  ES:SE:LP:AF:SS:ID   -0.0029733:0.039061:0.0271864:0.86976:342990:rs529266287
1   750230  rs190826124 G   C   .   PASS    AF=0.0015222    ES:SE:LP:AF:SS:ID   -0.4082:0.35478:0.602216:0.0015222:342990:rs190826124
1   751343  rs28544273  T   A   .   PASS    AF=0.12292  ES:SE:LP:AF:SS:ID   0.0029393:0.03868:0.0271356:0.12292:342990:rs28544273
1   751488  rs200141114 G   GA  .   PASS    AF=0.14274  ES:SE:LP:AF:SS:ID   -0.0072407:0.038229:0.0706935:0.14274:342990:rs200141114
1   751756  rs28527770  T   C   .   PASS    AF=0.12304  ES:SE:LP:AF:SS:ID   0.0030528:0.038626:0.0282558:0.12304:342990:rs28527770
1   753405  rs3115860   C   A   .   PASS    AF=0.87093  ES:SE:LP:AF:SS:ID   -0.0089364:0.037648:0.0902461:0.87093:342990:rs3115860
1   753425  rs3131970   T   C   .   PASS    AF=0.87548  ES:SE:LP:AF:SS:ID   -0.006444:0.038266:0.0623467:0.87548:342990:rs3131970
1   753541  rs2073813   G   A   .   PASS    AF=0.12861  ES:SE:LP:AF:SS:ID   0.0095022:0.03774:0.0962536:0.12861:342990:rs2073813
1   754105  rs12184325  C   T   .   PASS    AF=0.036317 ES:SE:LP:AF:SS:ID   0.11741:0.068532:1.0621:0.036317:342990:rs12184325
1   754182  rs3131969   A   G   .   PASS    AF=0.87052  ES:SE:LP:AF:SS:ID   -0.0081788:0.037608:0.0820536:0.87052:342990:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.87062  ES:SE:LP:AF:SS:ID   -0.0088165:0.037626:0.0889863:0.87062:342990:rs3131968
1   754334  rs3131967   T   C   .   PASS    AF=0.87052  ES:SE:LP:AF:SS:ID   -0.0082536:0.037607:0.0828728:0.87052:342990:rs3131967
1   754433  rs150578204 G   A   .   PASS    AF=0.0050449    ES:SE:LP:AF:SS:ID   0.071947:0.19302:0.149152:0.0050449:342990:rs150578204
1   754458  rs142682604 G   T   .   PASS    AF=0.0050118    ES:SE:LP:AF:SS:ID   0.076489:0.19353:0.159474:0.0050118:342990:rs142682604
1   755435  rs184270342 T   G   .   PASS    AF=0.0055444    ES:SE:LP:AF:SS:ID   0.015092:0.18777:0.028752:0.0055444:342990:rs184270342
1   755890  rs3115858   A   T   .   PASS    AF=0.87061  ES:SE:LP:AF:SS:ID   -0.0095179:0.037542:0.096986:0.87061:342990:rs3115858
1   756434  rs61768170  G   C   .   PASS    AF=0.12595  ES:SE:LP:AF:SS:ID   0.010433:0.038304:0.104948:0.12595:342990:rs61768170
1   756604  rs3131962   A   G   .   PASS    AF=0.87018  ES:SE:LP:AF:SS:ID   -0.017576:0.037453:0.194587:0.87018:342990:rs3131962
1   757640  rs3115853   G   A   .   PASS    AF=0.86945  ES:SE:LP:AF:SS:ID   -0.0088399:0.037419:0.0897813:0.86945:342990:rs3115853
1   757734  rs4951929   C   T   .   PASS    AF=0.87032  ES:SE:LP:AF:SS:ID   -0.0095351:0.037484:0.0973391:0.87032:342990:rs4951929
1   757936  rs4951862   C   A   .   PASS    AF=0.87033  ES:SE:LP:AF:SS:ID   -0.0095862:0.037487:0.0979046:0.87033:342990:rs4951862
1   758144  rs3131956   A   G   .   PASS    AF=0.87034  ES:SE:LP:AF:SS:ID   -0.0094732:0.037488:0.0966387:0.87034:342990:rs3131956
1   758626  rs3131954   C   T   .   PASS    AF=0.87078  ES:SE:LP:AF:SS:ID   -0.0092828:0.037583:0.0942527:0.87078:342990:rs3131954
1   759293  rs10157329  T   A   .   PASS    AF=0.098823 ES:SE:LP:AF:SS:ID   0.017812:0.043679:0.165312:0.098823:342990:rs10157329
1   759600  rs545998451 AGT A   .   PASS    AF=0.0064308    ES:SE:LP:AF:SS:ID   -0.063752:0.16963:0.150556:0.0064308:342990:1_759600_AGT_A
1   759837  rs3115851   T   A   .   PASS    AF=0.87466  ES:SE:LP:AF:SS:ID   -0.0054408:0.038139:0.0522919:0.87466:342990:rs3115851
1   761732  rs2286139   C   T   .   PASS    AF=0.86408  ES:SE:LP:AF:SS:ID   -0.016655:0.037409:0.182977:0.86408:342990:rs2286139
1   761752  rs1057213   C   T   .   PASS    AF=0.86946  ES:SE:LP:AF:SS:ID   -0.0090069:0.037766:0.0907115:0.86946:342990:rs1057213
1   762273  rs3115849   G   A   .   PASS    AF=0.8664   ES:SE:LP:AF:SS:ID   -0.0010485:0.037774:0.00972332:0.8664:342990:rs3115849
1   762485  rs12095200  C   A   .   PASS    AF=0.098771 ES:SE:LP:AF:SS:ID   0.0057866:0.045219:0.0466415:0.098771:342990:rs12095200
1   762589  rs3115848   G   C   .   PASS    AF=0.87158  ES:SE:LP:AF:SS:ID   -0.0054967:0.038205:0.0527624:0.87158:342990:rs3115848
1   762592  rs3131950   C   G   .   PASS    AF=0.87158  ES:SE:LP:AF:SS:ID   -0.0054986:0.038205:0.052782:0.87158:342990:rs3131950
1   762601  rs3131949   T   C   .   PASS    AF=0.87158  ES:SE:LP:AF:SS:ID   -0.00564:0.038206:0.0542164:0.87158:342990:rs3131949
1   762632  rs3131948   T   A   .   PASS    AF=0.87195  ES:SE:LP:AF:SS:ID   -0.0063049:0.038227:0.0609802:0.87195:342990:rs3131948
1   764191  rs7515915   T   G   .   PASS    AF=0.12555  ES:SE:LP:AF:SS:ID   0.0075755:0.038253:0.0741621:0.12555:342990:rs7515915
1   766007  rs61768174  A   C   .   PASS    AF=0.10542  ES:SE:LP:AF:SS:ID   0.020087:0.041653:0.200908:0.10542:342990:rs61768174
1   766105  rs2519015   T   A   .   PASS    AF=0.85542  ES:SE:LP:AF:SS:ID   -0.0038416:0.037393:0.0370769:0.85542:342990:rs2519015
1   767393  rs538667473 A   C   .   PASS    AF=0.001658 ES:SE:LP:AF:SS:ID   -0.5894:0.33083:1.12599:0.001658:342990:rs538667473
1   768116  rs376645387 A   AGTTTT  .   PASS    AF=0.83825  ES:SE:LP:AF:SS:ID   -0.023557:0.036827:0.281997:0.83825:342990:rs376645387