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=ieu-a-965,TotalVariants=8763362,VariantsNotRead=0,HarmonisedVariants=8763362,VariantsNotHarmonised=0,SwitchedAlleles=0,StudyType=Continuous>",
    "contig": "<ID=1,length=249250621,assembly=HG19/GRCh37>",
    "contig.1": "<ID=2,length=243199373,assembly=HG19/GRCh37>",
    "contig.2": "<ID=3,length=198022430,assembly=HG19/GRCh37>",
    "contig.3": "<ID=4,length=191154276,assembly=HG19/GRCh37>",
    "contig.4": "<ID=5,length=180915260,assembly=HG19/GRCh37>",
    "contig.5": "<ID=6,length=171115067,assembly=HG19/GRCh37>",
    "contig.6": "<ID=7,length=159138663,assembly=HG19/GRCh37>",
    "contig.7": "<ID=8,length=146364022,assembly=HG19/GRCh37>",
    "contig.8": "<ID=9,length=141213431,assembly=HG19/GRCh37>",
    "contig.9": "<ID=10,length=135534747,assembly=HG19/GRCh37>",
    "contig.10": "<ID=11,length=135006516,assembly=HG19/GRCh37>",
    "contig.11": "<ID=12,length=133851895,assembly=HG19/GRCh37>",
    "contig.12": "<ID=13,length=115169878,assembly=HG19/GRCh37>",
    "contig.13": "<ID=14,length=107349540,assembly=HG19/GRCh37>",
    "contig.14": "<ID=15,length=102531392,assembly=HG19/GRCh37>",
    "contig.15": "<ID=16,length=90354753,assembly=HG19/GRCh37>",
    "contig.16": "<ID=17,length=81195210,assembly=HG19/GRCh37>",
    "contig.17": "<ID=18,length=78077248,assembly=HG19/GRCh37>",
    "contig.18": "<ID=19,length=59128983,assembly=HG19/GRCh37>",
    "contig.19": "<ID=20,length=63025520,assembly=HG19/GRCh37>",
    "contig.20": "<ID=21,length=48129895,assembly=HG19/GRCh37>",
    "contig.21": "<ID=22,length=51304566,assembly=HG19/GRCh37>",
    "contig.22": "<ID=X,length=155270560,assembly=HG19/GRCh37>",
    "contig.23": "<ID=Y,length=59373566,assembly=HG19/GRCh37>",
    "contig.24": "<ID=MT,length=16569,assembly=HG19/GRCh37>",
    "contig.25": "<ID=GL000207.1,length=4262,assembly=HG19/GRCh37>",
    "contig.26": "<ID=GL000226.1,length=15008,assembly=HG19/GRCh37>",
    "contig.27": "<ID=GL000229.1,length=19913,assembly=HG19/GRCh37>",
    "contig.28": "<ID=GL000231.1,length=27386,assembly=HG19/GRCh37>",
    "contig.29": "<ID=GL000210.1,length=27682,assembly=HG19/GRCh37>",
    "contig.30": "<ID=GL000239.1,length=33824,assembly=HG19/GRCh37>",
    "contig.31": "<ID=GL000235.1,length=34474,assembly=HG19/GRCh37>",
    "contig.32": "<ID=GL000201.1,length=36148,assembly=HG19/GRCh37>",
    "contig.33": "<ID=GL000247.1,length=36422,assembly=HG19/GRCh37>",
    "contig.34": "<ID=GL000245.1,length=36651,assembly=HG19/GRCh37>",
    "contig.35": "<ID=GL000197.1,length=37175,assembly=HG19/GRCh37>",
    "contig.36": "<ID=GL000203.1,length=37498,assembly=HG19/GRCh37>",
    "contig.37": "<ID=GL000246.1,length=38154,assembly=HG19/GRCh37>",
    "contig.38": "<ID=GL000249.1,length=38502,assembly=HG19/GRCh37>",
    "contig.39": "<ID=GL000196.1,length=38914,assembly=HG19/GRCh37>",
    "contig.40": "<ID=GL000248.1,length=39786,assembly=HG19/GRCh37>",
    "contig.41": "<ID=GL000244.1,length=39929,assembly=HG19/GRCh37>",
    "contig.42": "<ID=GL000238.1,length=39939,assembly=HG19/GRCh37>",
    "contig.43": "<ID=GL000202.1,length=40103,assembly=HG19/GRCh37>",
    "contig.44": "<ID=GL000234.1,length=40531,assembly=HG19/GRCh37>",
    "contig.45": "<ID=GL000232.1,length=40652,assembly=HG19/GRCh37>",
    "contig.46": "<ID=GL000206.1,length=41001,assembly=HG19/GRCh37>",
    "contig.47": "<ID=GL000240.1,length=41933,assembly=HG19/GRCh37>",
    "contig.48": "<ID=GL000236.1,length=41934,assembly=HG19/GRCh37>",
    "contig.49": "<ID=GL000241.1,length=42152,assembly=HG19/GRCh37>",
    "contig.50": "<ID=GL000243.1,length=43341,assembly=HG19/GRCh37>",
    "contig.51": "<ID=GL000242.1,length=43523,assembly=HG19/GRCh37>",
    "contig.52": "<ID=GL000230.1,length=43691,assembly=HG19/GRCh37>",
    "contig.53": "<ID=GL000237.1,length=45867,assembly=HG19/GRCh37>",
    "contig.54": "<ID=GL000233.1,length=45941,assembly=HG19/GRCh37>",
    "contig.55": "<ID=GL000204.1,length=81310,assembly=HG19/GRCh37>",
    "contig.56": "<ID=GL000198.1,length=90085,assembly=HG19/GRCh37>",
    "contig.57": "<ID=GL000208.1,length=92689,assembly=HG19/GRCh37>",
    "contig.58": "<ID=GL000191.1,length=106433,assembly=HG19/GRCh37>",
    "contig.59": "<ID=GL000227.1,length=128374,assembly=HG19/GRCh37>",
    "contig.60": "<ID=GL000228.1,length=129120,assembly=HG19/GRCh37>",
    "contig.61": "<ID=GL000214.1,length=137718,assembly=HG19/GRCh37>",
    "contig.62": "<ID=GL000221.1,length=155397,assembly=HG19/GRCh37>",
    "contig.63": "<ID=GL000209.1,length=159169,assembly=HG19/GRCh37>",
    "contig.64": "<ID=GL000218.1,length=161147,assembly=HG19/GRCh37>",
    "contig.65": "<ID=GL000220.1,length=161802,assembly=HG19/GRCh37>",
    "contig.66": "<ID=GL000213.1,length=164239,assembly=HG19/GRCh37>",
    "contig.67": "<ID=GL000211.1,length=166566,assembly=HG19/GRCh37>",
    "contig.68": "<ID=GL000199.1,length=169874,assembly=HG19/GRCh37>",
    "contig.69": "<ID=GL000217.1,length=172149,assembly=HG19/GRCh37>",
    "contig.70": "<ID=GL000216.1,length=172294,assembly=HG19/GRCh37>",
    "contig.71": "<ID=GL000215.1,length=172545,assembly=HG19/GRCh37>",
    "contig.72": "<ID=GL000205.1,length=174588,assembly=HG19/GRCh37>",
    "contig.73": "<ID=GL000219.1,length=179198,assembly=HG19/GRCh37>",
    "contig.74": "<ID=GL000224.1,length=179693,assembly=HG19/GRCh37>",
    "contig.75": "<ID=GL000223.1,length=180455,assembly=HG19/GRCh37>",
    "contig.76": "<ID=GL000195.1,length=182896,assembly=HG19/GRCh37>",
    "contig.77": "<ID=GL000212.1,length=186858,assembly=HG19/GRCh37>",
    "contig.78": "<ID=GL000222.1,length=186861,assembly=HG19/GRCh37>",
    "contig.79": "<ID=GL000200.1,length=187035,assembly=HG19/GRCh37>",
    "contig.80": "<ID=GL000193.1,length=189789,assembly=HG19/GRCh37>",
    "contig.81": "<ID=GL000194.1,length=191469,assembly=HG19/GRCh37>",
    "contig.82": "<ID=GL000225.1,length=211173,assembly=HG19/GRCh37>",
    "contig.83": "<ID=GL000192.1,length=547496,assembly=HG19/GRCh37>",
    "gwas_harmonisation_command": "--json /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-965/ieu-a-965_data.json --ref /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/QC/genomes/b37/human_g1k_v37.fasta; 1.1.1",
    "file_date": "2020-02-04T08:07:47.524488",
    "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/ieu-a-import/processed/ieu-a-965/ieu-a-965.vcf.gz -O z /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-965/ieu-a-965_data.vcf.gz; Date=Tue Feb  4 17:00:02 2020",
    "bcftools_viewVersion": "1.9-74-g6af271c+htslib-1.9-64-g226b4a8",
    "bcftools_viewCommand": "view -h /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ieu-a-965/ieu-a-965.vcf.gz; Date=Sat May  9 18:58:49 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/ieu-a-import/processed/ieu-a-965/ieu-a-965.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/ieu-a-import/processed/ieu-a-965/ldsc.txt \
--w-ld-chr /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/reference/eur_w_ld_chr/ 

Beginning analysis at Wed Feb  5 08:52:54 2020
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-965/ieu-a-965.vcf.gz ...
Read summary statistics for 8763362 SNPs.
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, 1236976 SNPs remain.
After merging with regression SNP LD, 1236976 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: -0.0651 (0.0294)
Lambda GC: 1.1102
Mean Chi^2: 1.1298
Intercept: 1.1535 (0.0075)
Ratio: 1.1826 (0.058)
Analysis finished at Wed Feb  5 08:54:20 2020
Total time elapsed: 1.0m:26.04s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9503,
    "inflation_factor": 1.0175,
    "mean_EFFECT": 0.0066,
    "n": 18336,
    "n_snps": 8763362,
    "n_clumped_hits": 2,
    "n_p_sig": 236,
    "n_mono": 0,
    "n_ns": 0,
    "n_mac": 234,
    "is_snpid_unique": true,
    "n_miss_EFFECT": 0,
    "n_miss_SE": 0,
    "n_miss_PVAL": 0,
    "n_miss_AF": 0,
    "n_miss_AF_reference": 171724,
    "n_est": 18143.3486,
    "ratio_se_n": 0.9947,
    "mean_diff": -0.0128,
    "ratio_diff": 1.4702,
    "sd_y_est1": 2.6387,
    "sd_y_est2": 2.6248,
    "r2_sum1": 0.0672,
    "r2_sum2": 0.0096,
    "r2_sum3": 0.0097,
    "r2_sum4": 0.0087,
    "ldsc_nsnp_merge_refpanel_ld": 1236976,
    "ldsc_nsnp_merge_regression_ld": 1236976,
    "ldsc_observed_scale_h2_beta": "NA",
    "ldsc_observed_scale_h2_se": "NA",
    "ldsc_intercept_beta": 1.1535,
    "ldsc_intercept_se": 0.0075,
    "ldsc_lambda_gc": 1.1102,
    "ldsc_mean_chisq": 1.1298,
    "ldsc_ratio": 1.1826
}

Flags

name value
af_correlation FALSE
inflation_factor FALSE
n FALSE
is_snpid_non_unique FALSE
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 58 0 8763362 0 NA NA NA NA NA NA NA NA
character REF 0 1.0000000 1 1 0 4 0 NA NA NA NA NA NA NA NA
character ALT 0 1.0000000 1 1 0 4 0 NA NA NA NA NA NA NA NA
numeric CHROM 0 1.0000000 NA NA NA NA NA 8.544449e+00 5.697802e+00 1.00000e+00 4.000000e+00 8.000000e+00 1.200000e+01 2.300000e+01 ▇▅▅▂▂
numeric POS 0 1.0000000 NA NA NA NA NA 7.948926e+07 5.584624e+07 1.31330e+04 3.365770e+07 7.066895e+07 1.147680e+08 2.492183e+08 ▇▇▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA 6.600000e-03 1.466147e-01 -3.63826e+00 -3.561360e-02 1.322100e-03 3.967060e-02 6.241480e+00 ▁▇▁▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 8.465440e-02 2.952423e-01 2.18920e-02 3.192500e-02 4.715400e-02 9.906500e-02 2.549200e+02 ▇▁▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.971337e-01 2.898923e-01 0.00000e+00 2.452009e-01 4.962768e-01 7.485227e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.733176e-01 2.943088e-01 0.00000e+00 2.157170e-01 4.618391e-01 7.271057e-01 1.000000e+00 ▇▇▆▆▆
numeric AF 0 1.0000000 NA NA NA NA NA 2.210875e-01 2.592634e-01 5.03000e-05 2.035300e-02 1.065600e-01 3.404790e-01 9.998630e-01 ▇▂▁▁▁
numeric AF_reference 171724 0.9804043 NA NA NA NA NA 2.249555e-01 2.517448e-01 0.00000e+00 2.416130e-02 1.240020e-01 3.474440e-01 1.000000e+00 ▇▂▁▁▁
numeric N 0 1.0000000 NA NA NA NA NA 1.833600e+04 0.000000e+00 1.83360e+04 1.833600e+04 1.833600e+04 1.833600e+04 1.833600e+04 ▁▁▇▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 996248 rs28479311 C T -0.0681546 0.040878 0.1363139 0.0954610 0.152990 0.106629 18336
1 998501 rs3813193 G C -0.0735669 0.037500 0.0802047 0.0497876 0.167842 0.206669 18336
1 1002387 rs74048003 A G -0.0706682 0.036531 0.0832243 0.0530551 0.231358 0.244609 18336
1 1002539 rs60442576 G A -0.0784546 0.036150 0.0537997 0.0299878 0.236100 0.343051 18336
1 1004957 rs4073176 G A 0.0547783 0.029687 0.0905357 0.0650092 0.574465 0.550319 18336
1 1004980 rs4073177 G A 0.0547413 0.029683 0.0907027 0.0651544 0.574083 0.550319 18336
1 1005806 rs3934834 C T -0.0568328 0.033947 0.1271780 0.0940986 0.161461 0.223442 18336
1 1006223 rs9442394 G A 0.0538144 0.029351 0.0921531 0.0667316 0.570742 0.547125 18336
1 1006990 rs4326571 G A 0.0136599 0.033597 0.6983884 0.6843158 0.715920 0.816294 18336
1 1007203 rs4633229 A G 0.0265904 0.038082 0.5134380 0.4850267 0.769638 0.841254 18336
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51178607 rs6010067 G C -0.0943305 0.093530 0.4111545 0.3131863 0.0239111 0.0814696 18336
22 51178756 rs141844965 A T 0.1744560 0.187699 0.3548967 0.3526582 0.0082341 0.0059904 18336
22 51179000 rs2283675 C A -0.0137207 0.036209 0.7187387 0.7047394 0.3108630 0.5127800 18336
22 51179770 rs2283676 G A -0.0067628 0.040446 0.8733600 0.8672078 0.2447270 0.3945690 18336
22 51180501 rs5770999 T C 0.0141872 0.037159 0.7171252 0.7026118 0.6889610 0.6369810 18336
22 51180878 rs6010069 A G 0.0757269 0.056344 0.1693640 0.1789452 0.1396220 0.1589460 18336
22 51180934 rs9616824 C T -0.0075323 0.051423 0.8903240 0.8835446 0.1280690 0.1689300 18336
22 51180959 rs6010070 A G 0.0418797 0.056046 0.4608908 0.4549199 0.1353370 0.2056710 18336
22 51182399 rs56238942 A G -0.0375503 0.060768 0.5771810 0.5366222 0.0758708 0.0992412 18336
23 51866774 rs150899468 C A -0.0792279 0.259245 0.8064380 0.7599015 0.9974540 0.9965560 18336

bcf preview

1   996248  rs28479311  C   T   .   PASS    AF=0.15299  ES:SE:LP:AF:SS:ID   -0.0681546:0.040878:0.86546:0.15299:18336:rs28479311
1   998501  rs3813193   G   C   .   PASS    AF=0.167842 ES:SE:LP:AF:SS:ID   -0.0735669:0.0375:1.0958:0.167842:18336:rs3813193
1   1002387 rs74048003  A   G   .   PASS    AF=0.231358 ES:SE:LP:AF:SS:ID   -0.0706682:0.036531:1.07975:0.231358:18336:rs74048003
1   1002539 rs60442576  G   A   .   PASS    AF=0.2361   ES:SE:LP:AF:SS:ID   -0.0784546:0.03615:1.26922:0.2361:18336:rs60442576
1   1004957 rs4073176   G   A   .   PASS    AF=0.574465 ES:SE:LP:AF:SS:ID   0.0547783:0.029687:1.04318:0.574465:18336:rs4073176
1   1004980 rs4073177   G   A   .   PASS    AF=0.574083 ES:SE:LP:AF:SS:ID   0.0547413:0.029683:1.04238:0.574083:18336:rs4073177
1   1005806 rs3934834   C   T   .   PASS    AF=0.161461 ES:SE:LP:AF:SS:ID   -0.0568328:0.033947:0.895588:0.161461:18336:rs3934834
1   1006223 rs9442394   G   A   .   PASS    AF=0.570742 ES:SE:LP:AF:SS:ID   0.0538144:0.029351:1.03549:0.570742:18336:rs9442394
1   1006990 rs4326571   G   A   .   PASS    AF=0.71592  ES:SE:LP:AF:SS:ID   0.0136599:0.033597:0.155903:0.71592:18336:rs4326571
1   1007203 rs4633229   A   G   .   PASS    AF=0.769638 ES:SE:LP:AF:SS:ID   0.0265904:0.038082:0.289512:0.769638:18336:rs4633229
1   1007222 rs71628928  G   T   .   PASS    AF=0.171459 ES:SE:LP:AF:SS:ID   -0.0504337:0.035735:0.706883:0.171459:18336:rs71628928
1   1007432 rs4333796   G   A   .   PASS    AF=0.551232 ES:SE:LP:AF:SS:ID   0.0556565:0.028711:1.12298:0.551232:18336:rs4333796
1   1009234 rs9442366   T   C   .   PASS    AF=0.551281 ES:SE:LP:AF:SS:ID   0.0487901:0.028712:0.934073:0.551281:18336:rs9442366
1   1009478 rs9442367   G   C   .   PASS    AF=0.716226 ES:SE:LP:AF:SS:ID   0.0132605:0.033591:0.150815:0.716226:18336:rs9442367
1   1009823 rs12752391  G   A   .   PASS    AF=0.16581  ES:SE:LP:AF:SS:ID   -0.0507555:0.03486:0.739156:0.16581:18336:rs12752391
1   1010717 rs9442368   C   T   .   PASS    AF=0.557013 ES:SE:LP:AF:SS:ID   0.0502549:0.028664:0.975707:0.557013:18336:rs9442368
1   1012706 rs78632925  T   C   .   PASS    AF=0.444399 ES:SE:LP:AF:SS:ID   -0.0619329:0.033702:1.01892:0.444399:18336:rs78632925
1   1014836 rs12401605  A   G   .   PASS    AF=0.525042 ES:SE:LP:AF:SS:ID   0.0308263:0.028949:0.499858:0.525042:18336:rs12401605
1   1015126 rs36027499  A   G   .   PASS    AF=0.54399  ES:SE:LP:AF:SS:ID   0.0386369:0.028146:0.699694:0.54399:18336:rs36027499
1   1015257 rs9442369   A   G   .   PASS    AF=0.541094 ES:SE:LP:AF:SS:ID   0.0364576:0.028418:0.638712:0.541094:18336:rs9442369
1   1015551 rs9442370   C   T   .   PASS    AF=0.533098 ES:SE:LP:AF:SS:ID   0.0327815:0.02896:0.540976:0.533098:18336:rs9442370
1   1015716 rs61290587  G   A   .   PASS    AF=0.174158 ES:SE:LP:AF:SS:ID   -0.0391494:0.036636:0.491087:0.174158:18336:rs61290587
1   1015817 rs12746483  G   A   .   PASS    AF=0.706403 ES:SE:LP:AF:SS:ID   0.0103645:0.03132:0.124321:0.706403:18336:rs12746483
1   1017197 rs3766192   C   T   .   PASS    AF=0.533784 ES:SE:LP:AF:SS:ID   0.0375669:0.027776:0.686789:0.533784:18336:rs3766192
1   1017341 rs1133647   G   T   .   PASS    AF=0.707623 ES:SE:LP:AF:SS:ID   0.00410843:0.030694:0.0471301:0.707623:18336:rs1133647
1   1017587 rs3766191   C   T   .   PASS    AF=0.160858 ES:SE:LP:AF:SS:ID   -0.0598137:0.035715:0.889498:0.160858:18336:rs3766191
1   1018144 rs9442395   T   C   .   PASS    AF=0.544707 ES:SE:LP:AF:SS:ID   0.0386296:0.027353:0.728991:0.544707:18336:rs9442395
1   1018562 rs9442371   C   T   .   PASS    AF=0.544339 ES:SE:LP:AF:SS:ID   0.0381734:0.02736:0.717138:0.544339:18336:rs9442371
1   1018704 rs9442372   A   G   .   PASS    AF=0.545963 ES:SE:LP:AF:SS:ID   0.0386109:0.027293:0.730833:0.545963:18336:rs9442372
1   1019175 rs2298215   C   G   .   PASS    AF=0.704808 ES:SE:LP:AF:SS:ID   0.0208519:0.030178:0.290895:0.704808:18336:rs2298215
1   1019180 rs9442396   T   C   .   PASS    AF=0.554512 ES:SE:LP:AF:SS:ID   0.0431142:0.027606:0.835189:0.554512:18336:rs9442396
1   1020406 rs9442397   T   C   .   PASS    AF=0.708703 ES:SE:LP:AF:SS:ID   0.0238092:0.029832:0.346979:0.708703:18336:rs9442397
1   1021346 rs10907177  A   G   .   PASS    AF=0.169213 ES:SE:LP:AF:SS:ID   -0.0377538:0.0375:0.454259:0.169213:18336:rs10907177
1   1021415 rs3737728   A   G   .   PASS    AF=0.712207 ES:SE:LP:AF:SS:ID   0.0114463:0.029508:0.148871:0.712207:18336:rs3737728
1   1021583 rs10907178  A   C   .   PASS    AF=0.163341 ES:SE:LP:AF:SS:ID   -0.0438589:0.03722:0.555599:0.163341:18336:rs10907178
1   1021695 rs9442398   A   G   .   PASS    AF=0.706606 ES:SE:LP:AF:SS:ID   0.0222221:0.029921:0.317659:0.706606:18336:rs9442398
1   1022037 rs6701114   C   T   .   PASS    AF=0.550023 ES:SE:LP:AF:SS:ID   0.0405991:0.027753:0.763455:0.550023:18336:rs6701114
1   1023145 rs3737727   G   A   .   PASS    AF=0.153517 ES:SE:LP:AF:SS:ID   -0.0568296:0.037433:0.774078:0.153517:18336:rs3737727
1   1023310 rs11260589  T   C   .   PASS    AF=0.159764 ES:SE:LP:AF:SS:ID   -0.0419768:0.039123:0.49003:0.159764:18336:rs11260589
1   1023788 rs12132100  C   T   .   PASS    AF=0.152599 ES:SE:LP:AF:SS:ID   -0.0461068:0.03868:0.561293:0.152599:18336:rs12132100
1   1026707 rs4074137   C   A   .   PASS    AF=0.599227 ES:SE:LP:AF:SS:ID   0.00979885:0.029725:0.1241:0.599227:18336:rs4074137
1   1026801 rs4562563   T   A   .   PASS    AF=0.6128   ES:SE:LP:AF:SS:ID   -0.00316299:0.030197:0.0367951:0.6128:18336:rs4562563
1   1027070 rs11260590  G   A   .   PASS    AF=0.109617 ES:SE:LP:AF:SS:ID   -0.0031941:0.04809:0.022403:0.109617:18336:rs11260590
1   1027845 rs74048006  T   G   .   PASS    AF=0.161964 ES:SE:LP:AF:SS:ID   -0.0496315:0.034999:0.713256:0.161964:18336:rs74048006
1   1027846 rs76994018  T   C   .   PASS    AF=0.161964 ES:SE:LP:AF:SS:ID   -0.0495779:0.035001:0.712196:0.161964:18336:rs76994018
1   1028259 rs12077244  C   T   .   PASS    AF=0.109206 ES:SE:LP:AF:SS:ID   -0.00808863:0.046774:0.0604233:0.109206:18336:rs12077244
1   1029805 rs6689308   A   G   .   PASS    AF=0.164072 ES:SE:LP:AF:SS:ID   -0.0468023:0.034531:0.67287:0.164072:18336:rs6689308
1   1030374 rs12731175  G   A   .   PASS    AF=0.0535093    ES:SE:LP:AF:SS:ID   -0.159316:0.056576:1.6018:0.0535093:18336:rs12731175
1   1030565 rs6687776   C   T   .   PASS    AF=0.164139 ES:SE:LP:AF:SS:ID   -0.0474418:0.034411:0.68852:0.164139:18336:rs6687776
1   1030633 rs6678318   G   A   .   PASS    AF=0.164027 ES:SE:LP:AF:SS:ID   -0.0477207:0.034445:0.692906:0.164027:18336:rs6678318