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-22617_4132,TotalVariants=9690721,VariantsNotRead=0,HarmonisedVariants=9690721,VariantsNotHarmonised=0,SwitchedAlleles=208,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-22617_4132/ukb-d-22617_4132_data.json --ref /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/QC/genomes/b37/human_g1k_v37.fasta; 1.1.1",
    "file_date": "2019-11-25T13:54:51.801864",
    "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-22617_4132/ukb-d-22617_4132.vcf.gz -O z /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-22617_4132/ukb-d-22617_4132_data.vcf.gz; Date=Mon Nov 25 14:41:25 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-22617_4132/ukb-d-22617_4132.vcf.gz; Date=Sun May 10 01:44:01 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-22617_4132/ukb-d-22617_4132.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-22617_4132/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 15:37:16 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-22617_4132/ukb-d-22617_4132.vcf.gz ...
Read summary statistics for 9690721 SNPs.
Dropped 7307 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, 1275455 SNPs remain.
After merging with regression SNP LD, 1275455 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0046 (0.0052)
Lambda GC: 1.0036
Mean Chi^2: 1.0087
Intercept: 1.0004 (0.0068)
Ratio: 0.045 (0.7811)
Analysis finished at Mon Nov 25 15:39:13 2019
Total time elapsed: 1.0m:56.56s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.94,
    "inflation_factor": 1.0047,
    "mean_EFFECT": -7.3056e-07,
    "n": 91149,
    "n_snps": 9690721,
    "n_clumped_hits": 1,
    "n_p_sig": 1,
    "n_mono": 0,
    "n_ns": 1063277,
    "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": 193001,
    "n_est": 91145.9567,
    "ratio_se_n": 1,
    "mean_diff": -5.9894e-06,
    "ratio_diff": 11.8374,
    "sd_y_est1": 0.1176,
    "sd_y_est2": 0.1176,
    "r2_sum1": 5.657e-06,
    "r2_sum2": 0.0004,
    "r2_sum3": 0.0004,
    "r2_sum4": 0.0004,
    "ldsc_nsnp_merge_refpanel_ld": 1275455,
    "ldsc_nsnp_merge_regression_ld": 1275455,
    "ldsc_observed_scale_h2_beta": 0.0046,
    "ldsc_observed_scale_h2_se": 0.0052,
    "ldsc_intercept_beta": 1.0004,
    "ldsc_intercept_se": 0.0068,
    "ldsc_lambda_gc": 1.0036,
    "ldsc_mean_chisq": 1.0087,
    "ldsc_ratio": 0.046
}

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 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 9683960 0 NA NA NA NA NA NA NA NA
character REF 0 1.0000000 1 98 0 47107 0 NA NA NA NA NA NA NA NA
character ALT 0 1.0000000 1 342 0 29699 0 NA NA NA NA NA NA NA NA
numeric CHROM 0 1.0000000 NA NA NA NA NA 9.079468e+00 6.175439e+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 7.874233e+07 5.611259e+07 3.02000e+02 3.243577e+07 6.963049e+07 1.147495e+08 2.492297e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA -7.000000e-07 1.243200e-03 -1.38101e-02 -5.996000e-04 -5.500000e-06 5.882000e-04 1.473670e-02 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 1.076700e-03 6.141000e-04 4.55000e-04 6.029000e-04 8.044000e-04 1.378600e-03 3.506900e-03 ▇▂▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.994205e-01 2.893283e-01 0.00000e+00 2.485009e-01 4.989982e-01 7.501014e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.994187e-01 2.893293e-01 0.00000e+00 2.484978e-01 4.989971e-01 7.501005e-01 9.999999e-01 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA 2.618408e-01 2.628724e-01 9.84250e-03 4.422030e-02 1.598390e-01 4.165300e-01 9.901570e-01 ▇▂▂▁▁
numeric AF_reference 193001 0.9800839 NA NA NA NA NA 2.613296e-01 2.536796e-01 0.00000e+00 5.031950e-02 1.749200e-01 4.121410e-01 1.000000e+00 ▇▃▂▁▁
numeric N 0 1.0000000 NA NA NA NA NA 9.114900e+04 0.000000e+00 9.11490e+04 9.114900e+04 9.114900e+04 9.114900e+04 9.114900e+04 ▁▁▇▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 692794 rs530212009 CA C -0.0006831 0.0009625 0.4778681 0.4778666 0.1114870 0.1894970 91149
1 693731 rs12238997 A G -0.0010564 0.0009116 0.2465069 0.2465029 0.1164590 0.1417730 91149
1 707522 rs371890604 G C -0.0007351 0.0010244 0.4730151 0.4730112 0.0978765 0.1293930 91149
1 717587 rs144155419 G A -0.0026306 0.0024419 0.2813520 0.2813499 0.0157837 0.0045926 91149
1 730087 rs148120343 T C -0.0007222 0.0012635 0.5676021 0.5676015 0.0569973 0.0127796 91149
1 731718 rs142557973 T C -0.0010064 0.0008650 0.2446352 0.2446315 0.1223590 0.1543530 91149
1 732032 rs61770163 A C -0.0010958 0.0009223 0.2347708 0.2347681 0.1220470 0.1555510 91149
1 734349 rs141242758 T C -0.0011064 0.0008657 0.2012162 0.2012132 0.1215880 0.1525560 91149
1 749963 rs529266287 T TAA 0.0008900 0.0008515 0.2959688 0.2959664 0.8689170 0.7641770 91149
1 751343 rs28544273 T A -0.0011646 0.0008442 0.1677571 0.1677536 0.1236990 0.2426120 91149
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
23 154923311 rs141127553 C T 0.0001811 0.0010126 0.8580540 0.8580536 0.0552869 0.0309934 91149
23 154923374 rs111332691 T A 0.0007211 0.0011020 0.5128567 0.5128551 0.0448387 0.0116556 91149
23 154925045 rs509981 C T -0.0008716 0.0005311 0.1007630 0.1007600 0.2444670 0.3634440 91149
23 154925895 rs538470 C T -0.0008753 0.0005429 0.1069331 0.1069292 0.2409490 0.3634440 91149
23 154927581 rs644138 G A -0.0007209 0.0004995 0.1489320 0.1489285 0.3001640 0.4635760 91149
23 154929412 rs557132 C T -0.0008655 0.0005312 0.1032640 0.1032612 0.2443160 0.3568210 91149
23 154929637 rs35185538 CT C -0.0010059 0.0005547 0.0697622 0.0697591 0.2286640 0.3011920 91149
23 154929952 rs4012982 CAA C -0.0008762 0.0005591 0.1170650 0.1170612 0.2382530 0.3165560 91149
23 154930230 rs781880 A G -0.0008864 0.0005310 0.0950692 0.0950667 0.2447660 0.3618540 91149
23 154930487 rs781879 T A 0.0004590 0.0018010 0.7988400 0.7988396 0.0196632 0.1263580 91149

bcf preview

1   692794  rs530212009 CA  C   .   PASS    AF=0.111487 ES:SE:LP:AF:SS:ID   -0.000683103:0.000962472:0.320692:0.111487:91149:1_692794_CA_C
1   693731  rs12238997  A   G   .   PASS    AF=0.116459 ES:SE:LP:AF:SS:ID   -0.00105639:0.000911557:0.608171:0.116459:91149:rs12238997
1   707522  rs371890604 G   C   .   PASS    AF=0.0978765    ES:SE:LP:AF:SS:ID   -0.000735083:0.00102438:0.325125:0.0978765:91149:rs371890604
1   717587  rs144155419 G   A   .   PASS    AF=0.0157837    ES:SE:LP:AF:SS:ID   -0.00263065:0.00244191:0.55075:0.0157837:91149:rs144155419
1   730087  rs148120343 T   C   .   PASS    AF=0.0569973    ES:SE:LP:AF:SS:ID   -0.000722195:0.00126349:0.245956:0.0569973:91149:rs148120343
1   731718  rs58276399  T   C   .   PASS    AF=0.122359 ES:SE:LP:AF:SS:ID   -0.00100643:0.000865011:0.611481:0.122359:91149:rs58276399
1   732032  rs61770163  A   C   .   PASS    AF=0.122047 ES:SE:LP:AF:SS:ID   -0.00109585:0.000922304:0.629356:0.122047:91149:rs61770163
1   734349  rs141242758 T   C   .   PASS    AF=0.121588 ES:SE:LP:AF:SS:ID   -0.00110641:0.000865666:0.696337:0.121588:91149:rs141242758
1   749963  rs529266287 T   TAA .   PASS    AF=0.868917 ES:SE:LP:AF:SS:ID   0.000889952:0.000851529:0.528754:0.868917:91149:rs529266287
1   751343  rs28544273  T   A   .   PASS    AF=0.123699 ES:SE:LP:AF:SS:ID   -0.00116457:0.000844223:0.775319:0.123699:91149:rs28544273
1   751488  rs200141114 G   GA  .   PASS    AF=0.143202 ES:SE:LP:AF:SS:ID   -0.000887965:0.000835791:0.540538:0.143202:91149:rs200141114
1   751756  rs28527770  T   C   .   PASS    AF=0.123834 ES:SE:LP:AF:SS:ID   -0.00116544:0.000843002:0.777744:0.123834:91149:rs28527770
1   753405  rs3115860   C   A   .   PASS    AF=0.869892 ES:SE:LP:AF:SS:ID   0.00111504:0.000821424:0.757851:0.869892:91149:rs3115860
1   753425  rs3131970   T   C   .   PASS    AF=0.874553 ES:SE:LP:AF:SS:ID   0.00109031:0.000834746:0.717829:0.874553:91149:rs3131970
1   753541  rs2073813   G   A   .   PASS    AF=0.129529 ES:SE:LP:AF:SS:ID   -0.00118723:0.000824:0.824949:0.129529:91149:rs2073813
1   754105  rs12184325  C   T   .   PASS    AF=0.0358205    ES:SE:LP:AF:SS:ID   0.00219583:0.00150536:0.839655:0.0358205:91149:rs12184325
1   754182  rs3131969   A   G   .   PASS    AF=0.869539 ES:SE:LP:AF:SS:ID   0.00114285:0.000820737:0.785726:0.869539:91149:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.869616 ES:SE:LP:AF:SS:ID   0.00113216:0.000821096:0.774825:0.869616:91149:rs3131968
1   754334  rs3131967   T   C   .   PASS    AF=0.869535 ES:SE:LP:AF:SS:ID   0.00114281:0.000820703:0.785737:0.869535:91149:rs3131967
1   755890  rs3115858   A   T   .   PASS    AF=0.86952  ES:SE:LP:AF:SS:ID   0.00114718:0.000819012:0.792336:0.86952:91149:rs3115858
1   756434  rs61768170  G   C   .   PASS    AF=0.126911 ES:SE:LP:AF:SS:ID   -0.00113474:0.000836068:0.757685:0.126911:91149:rs61768170
1   756604  rs3131962   A   G   .   PASS    AF=0.86905  ES:SE:LP:AF:SS:ID   0.00108358:0.000816893:0.733561:0.86905:91149:rs3131962
1   757640  rs3115853   G   A   .   PASS    AF=0.868436 ES:SE:LP:AF:SS:ID   0.00116661:0.000816374:0.815303:0.868436:91149:rs3115853
1   757734  rs4951929   C   T   .   PASS    AF=0.869199 ES:SE:LP:AF:SS:ID   0.00115046:0.000817632:0.797482:0.869199:91149:rs4951929
1   757936  rs4951862   C   A   .   PASS    AF=0.869205 ES:SE:LP:AF:SS:ID   0.00115142:0.000817685:0.798354:0.869205:91149:rs4951862
1   758144  rs3131956   A   G   .   PASS    AF=0.869207 ES:SE:LP:AF:SS:ID   0.00115026:0.000817692:0.797196:0.869207:91149:rs3131956
1   758626  rs3131954   C   T   .   PASS    AF=0.869687 ES:SE:LP:AF:SS:ID   0.00113458:0.000819881:0.778818:0.869687:91149:rs3131954
1   759293  rs10157329  T   A   .   PASS    AF=0.0991787    ES:SE:LP:AF:SS:ID   -0.000730529:0.000954148:0.352719:0.0991787:91149:rs10157329
1   759837  rs3115851   T   A   .   PASS    AF=0.873682 ES:SE:LP:AF:SS:ID   0.00115587:0.000832023:0.783127:0.873682:91149:rs3115851
1   761732  rs2286139   C   T   .   PASS    AF=0.863058 ES:SE:LP:AF:SS:ID   0.00117871:0.000816147:0.827762:0.863058:91149:rs2286139
1   761752  rs1057213   C   T   .   PASS    AF=0.868472 ES:SE:LP:AF:SS:ID   0.00117507:0.000824245:0.812547:0.868472:91149:rs1057213
1   762273  rs3115849   G   A   .   PASS    AF=0.865369 ES:SE:LP:AF:SS:ID   0.0011429:0.0008244:0.780816:0.865369:91149:rs3115849
1   762485  rs12095200  C   A   .   PASS    AF=0.0995228    ES:SE:LP:AF:SS:ID   -0.00119538:0.000986654:0.646488:0.0995228:91149:rs12095200
1   762589  rs3115848   G   C   .   PASS    AF=0.870657 ES:SE:LP:AF:SS:ID   0.00112628:0.000833792:0.752599:0.870657:91149:rs3115848
1   762592  rs3131950   C   G   .   PASS    AF=0.870657 ES:SE:LP:AF:SS:ID   0.00112629:0.000833792:0.752609:0.870657:91149:rs3131950
1   762601  rs3131949   T   C   .   PASS    AF=0.870654 ES:SE:LP:AF:SS:ID   0.00112606:0.000833795:0.752397:0.870654:91149:rs3131949
1   762632  rs3131948   T   A   .   PASS    AF=0.871019 ES:SE:LP:AF:SS:ID   0.00119581:0.000834181:0.818974:0.871019:91149:rs3131948
1   764191  rs7515915   T   G   .   PASS    AF=0.126515 ES:SE:LP:AF:SS:ID   -0.00117703:0.000835109:0.799393:0.126515:91149:rs7515915
1   766007  rs61768174  A   C   .   PASS    AF=0.106037 ES:SE:LP:AF:SS:ID   -0.000924008:0.000907774:0.510413:0.106037:91149:rs61768174
1   766105  rs2519015   T   A   .   PASS    AF=0.85438  ES:SE:LP:AF:SS:ID   0.00113484:0.000815836:0.784561:0.85438:91149:rs2519015
1   768116  rs376645387 A   AGTTTT  .   PASS    AF=0.839153 ES:SE:LP:AF:SS:ID   0.00106355:0.000806082:0.728068:0.839153:91149:rs376645387
1   768253  rs2977608   A   C   .   PASS    AF=0.763195 ES:SE:LP:AF:SS:ID   0.000921061:0.000648131:0.808856:0.763195:91149:rs2977608
1   768448  rs12562034  G   A   .   PASS    AF=0.105092 ES:SE:LP:AF:SS:ID   -0.000418317:0.00089314:0.194143:0.105092:91149:rs12562034
1   769138  rs59306077  CAT C   .   PASS    AF=0.129904 ES:SE:LP:AF:SS:ID   -0.00106294:0.000823446:0.706059:0.129904:91149:rs762168062
1   769223  rs60320384  C   G   .   PASS    AF=0.129636 ES:SE:LP:AF:SS:ID   -0.00117471:0.000822361:0.814846:0.129636:91149:rs60320384
1   769963  rs7518545   G   A   .   PASS    AF=0.104365 ES:SE:LP:AF:SS:ID   -0.000452131:0.000900074:0.210815:0.104365:91149:rs7518545
1   770886  rs371458725 G   A   .   PASS    AF=0.103379 ES:SE:LP:AF:SS:ID   -0.000371575:0.000907858:0.166006:0.103379:91149:rs371458725
1   771410  rs2519006   C   T   .   PASS    AF=0.829291 ES:SE:LP:AF:SS:ID   0.00155892:0.000802308:1.28388:0.829291:91149:rs2519006
1   771823  rs2977605   T   C   .   PASS    AF=0.869067 ES:SE:LP:AF:SS:ID   0.00105704:0.000818399:0.70664:0.869067:91149:rs2977605
1   771967  rs59066358  G   A   .   PASS    AF=0.129741 ES:SE:LP:AF:SS:ID   -0.00112752:0.000821912:0.769245:0.129741:91149:rs59066358