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-963,TotalVariants=2455460,VariantsNotRead=0,HarmonisedVariants=2455460,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-963/ieu-a-963_data.json --ref /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/QC/genomes/b37/human_g1k_v37.fasta; 1.1.1",
    "file_date": "2020-02-04T11:26:10.725074",
    "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-963/ieu-a-963.vcf.gz -O z /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-963/ieu-a-963_data.vcf.gz; Date=Tue Feb  4 18:29:09 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-963/ieu-a-963.vcf.gz; Date=Sat May  9 21:27:54 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-963/ieu-a-963.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-963/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 09:45:33 2020
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-963/ieu-a-963.vcf.gz ...
Read summary statistics for 2455460 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, 1158474 SNPs remain.
After merging with regression SNP LD, 1158474 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0381 (0.0061)
Lambda GC: 1.0486
Mean Chi^2: 1.0507
Intercept: 0.9985 (0.0064)
Ratio < 0 (usually indicates GC correction).
Analysis finished at Wed Feb  5 09:46:01 2020
Total time elapsed: 28.08s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9265,
    "inflation_factor": 1.0508,
    "mean_EFFECT": 0.0004,
    "n": 70675,
    "n_snps": 2455460,
    "n_clumped_hits": 0,
    "n_p_sig": 0,
    "n_mono": 0,
    "n_ns": 0,
    "n_mac": 0,
    "is_snpid_unique": true,
    "n_miss_EFFECT": 0,
    "n_miss_SE": 0,
    "n_miss_PVAL": 0,
    "n_miss_AF": 0,
    "n_miss_AF_reference": 20334,
    "n_est": 65212.5231,
    "ratio_se_n": 0.9606,
    "mean_diff": -0.0002,
    "ratio_diff": 111.9615,
    "sd_y_est1": 3.1775,
    "sd_y_est2": 3.0522,
    "r2_sum1": 0,
    "r2_sum2": 0,
    "r2_sum3": 0,
    "r2_sum4": 0,
    "ldsc_nsnp_merge_refpanel_ld": 1158474,
    "ldsc_nsnp_merge_regression_ld": 1158474,
    "ldsc_observed_scale_h2_beta": 0.0381,
    "ldsc_observed_scale_h2_se": 0.0061,
    "ldsc_intercept_beta": 0.9985,
    "ldsc_intercept_se": 0.0064,
    "ldsc_lambda_gc": 1.0486,
    "ldsc_mean_chisq": 1.0507,
    "ldsc_ratio": -0.0296
}

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 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 42 0 2455460 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 8.593282e+00 5.661076e+00 1.00000e+00 4.000000e+00 8.000000e+00 1.200000e+01 2.30000e+01 ▇▅▅▂▂
numeric POS 0 1.0000000 NA NA NA NA NA 7.882105e+07 5.567206e+07 1.15230e+04 3.266042e+07 7.023120e+07 1.142944e+08 2.49219e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA 3.649000e-04 9.637920e-02 -1.08218e+01 -1.550000e-02 3.000000e-04 1.620000e-02 3.58646e+01 ▁▇▁▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 3.266970e-02 2.232931e-01 1.55000e-02 1.720000e-02 2.050000e-02 2.890000e-02 1.06482e+02 ▇▁▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.918746e-01 2.905770e-01 1.00000e-07 2.387998e-01 4.892998e-01 7.430003e-01 1.00000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.918755e-01 2.905798e-01 1.00000e-07 2.388308e-01 4.893103e-01 7.430797e-01 1.00000e+00 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA 3.588522e-01 2.708192e-01 1.00000e-02 1.250000e-01 2.944000e-01 5.558000e-01 9.90000e-01 ▇▅▃▂▂
numeric AF_reference 20334 0.9917189 NA NA NA NA NA 3.614093e-01 2.554940e-01 0.00000e+00 1.461660e-01 2.991210e-01 5.455270e-01 1.00000e+00 ▇▆▃▃▂
numeric N 0 1.0000000 NA NA NA NA NA 7.067500e+04 0.000000e+00 7.06750e+04 7.067500e+04 7.067500e+04 7.067500e+04 7.06750e+04 ▁▁▇▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 721290 rs12565286 G C 0.0533 0.0934 0.5679996 0.5682276 0.0457 0.0371406 70675
1 723819 rs11804171 T A 0.0553 0.0937 0.5546998 0.5550690 0.0457 0.1345850 70675
1 752566 rs3094315 G A -0.0479 0.0316 0.1300999 0.1295642 0.8238 0.7182510 70675
1 754192 rs3131968 A G -0.0912 0.0529 0.0847696 0.0847065 0.8654 0.6785140 70675
1 768448 rs12562034 G A -0.0503 0.0725 0.4878002 0.4878120 0.1115 0.1918930 70675
1 775659 rs2905035 A G -0.0595 0.0370 0.1074999 0.1078115 0.8617 0.7450080 70675
1 776546 rs12124819 A G -0.0699 0.0968 0.4706001 0.4702284 0.2406 0.0756789 70675
1 777122 rs2980319 A T -0.0578 0.0367 0.1152001 0.1152722 0.8618 0.7472040 70675
1 779322 rs4040617 A G 0.0553 0.0366 0.1313999 0.1308066 0.1380 0.2264380 70675
1 780785 rs2977612 T A -0.0551 0.0366 0.1328000 0.1322047 0.8616 0.6693290 70675
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51171693 rs756638 G A -0.0014 0.0241 0.9526001 0.9536759 0.2720 0.3049120 70675
22 51175626 rs3810648 A G 0.0092 0.0347 0.7915001 0.7909096 0.0594 0.1084270 70675
22 51178090 rs2285395 G A 0.0135 0.0353 0.7019998 0.7021378 0.0576 0.0666933 70675
22 51196164 rs8136603 A T -0.0330 0.0794 0.6773997 0.6776902 0.0578 0.1427720 70675
22 51212875 rs2238837 A C 0.0117 0.0329 0.7213001 0.7221228 0.3542 0.3724040 70675
23 35921591 rs2204667 C G -0.0349 0.0218 0.1086000 0.1093952 0.1624 NA 70675
23 51666786 rs14115 A G 0.0488 0.0350 0.1634000 0.1632313 0.0590 NA 70675
23 70163799 rs1626496 A C 0.0258 0.0314 0.4107003 0.4112727 0.0787 NA 70675
23 91415872 rs6562597 G A 0.0328 0.0612 0.5918995 0.5919947 0.0225 0.0021192 70675
23 118495837 rs12882977 G A -0.0071 0.0160 0.6583002 0.6572233 0.4887 0.2307280 70675

bcf preview

1   721290  rs12565286  G   C   .   PASS    AF=0.0457   ES:SE:LP:AF:SS:ID   0.0533:0.0934:0.245652:0.0457:70675:rs12565286
1   723819  rs11804171  T   A   .   PASS    AF=0.0457   ES:SE:LP:AF:SS:ID   0.0553:0.0937:0.255942:0.0457:70675:rs11804171
1   752566  rs3094315   G   A   .   PASS    AF=0.8238   ES:SE:LP:AF:SS:ID   -0.0479:0.0316:0.885723:0.8238:70675:rs3094315
1   754192  rs3131968   A   G   .   PASS    AF=0.8654   ES:SE:LP:AF:SS:ID   -0.0912:0.0529:1.07176:0.8654:70675:rs3131968
1   768448  rs12562034  G   A   .   PASS    AF=0.1115   ES:SE:LP:AF:SS:ID   -0.0503:0.0725:0.311758:0.1115:70675:rs12562034
1   775659  rs2905035   A   G   .   PASS    AF=0.8617   ES:SE:LP:AF:SS:ID   -0.0595:0.037:0.968592:0.8617:70675:rs2905035
1   776546  rs12124819  A   G   .   PASS    AF=0.2406   ES:SE:LP:AF:SS:ID   -0.0699:0.0968:0.327348:0.2406:70675:rs12124819
1   777122  rs2980319   A   T   .   PASS    AF=0.8618   ES:SE:LP:AF:SS:ID   -0.0578:0.0367:0.938547:0.8618:70675:rs2980319
1   779322  rs4040617   A   G   .   PASS    AF=0.138    ES:SE:LP:AF:SS:ID   0.0553:0.0366:0.881405:0.138:70675:rs4040617
1   780785  rs2977612   T   A   .   PASS    AF=0.8616   ES:SE:LP:AF:SS:ID   -0.0551:0.0366:0.876802:0.8616:70675:rs2977612
1   785050  rs2905062   G   A   .   PASS    AF=0.859    ES:SE:LP:AF:SS:ID   -0.0566:0.0366:0.913284:0.859:70675:rs2905062
1   785989  rs2980300   T   C   .   PASS    AF=0.8586   ES:SE:LP:AF:SS:ID   -0.0577:0.0366:0.940815:0.8586:70675:rs2980300
1   798026  rs4951864   C   T   .   PASS    AF=0.9162   ES:SE:LP:AF:SS:ID   -0.1101:0.1235:0.428874:0.9162:70675:rs4951864
1   798801  rs12132517  G   A   .   PASS    AF=0.1092   ES:SE:LP:AF:SS:ID   0.0864:0.1135:0.350179:0.1092:70675:rs12132517
1   798959  rs11240777  G   A   .   PASS    AF=0.2148   ES:SE:LP:AF:SS:ID   0.0095:0.0346:0.106294:0.2148:70675:rs11240777
1   998501  rs3813193   G   C   .   PASS    AF=0.1741   ES:SE:LP:AF:SS:ID   0.0247:0.0453:0.231954:0.1741:70675:rs3813193
1   1003629 rs4075116   C   T   .   PASS    AF=0.7281   ES:SE:LP:AF:SS:ID   0.0273:0.032:0.405166:0.7281:70675:rs4075116
1   1005806 rs3934834   C   T   .   PASS    AF=0.1456   ES:SE:LP:AF:SS:ID   -0.0142:0.0348:0.165452:0.1456:70675:rs3934834
1   1017170 rs3766193   C   G   .   PASS    AF=0.5347   ES:SE:LP:AF:SS:ID   0.054:0.0291:1.1986:0.5347:70675:rs3766193
1   1017197 rs3766192   C   T   .   PASS    AF=0.5579   ES:SE:LP:AF:SS:ID   0.0514:0.0212:1.80967:0.5579:70675:rs3766192
1   1017587 rs3766191   C   T   .   PASS    AF=0.1416   ES:SE:LP:AF:SS:ID   -0.0189:0.0342:0.237096:0.1416:70675:rs3766191
1   1018562 rs9442371   C   T   .   PASS    AF=0.565    ES:SE:LP:AF:SS:ID   0.0508:0.0207:1.8514:0.565:70675:rs9442371
1   1018704 rs9442372   A   G   .   PASS    AF=0.5644   ES:SE:LP:AF:SS:ID   0.0515:0.0206:1.91151:0.5644:70675:rs9442372
1   1021346 rs10907177  A   G   .   PASS    AF=0.1477   ES:SE:LP:AF:SS:ID   0.0044:0.0382:0.0415795:0.1477:70675:rs10907177
1   1021415 rs3737728   A   G   .   PASS    AF=0.7263   ES:SE:LP:AF:SS:ID   0.0092:0.0234:0.159141:0.7263:70675:rs3737728
1   1021583 rs10907178  A   C   .   PASS    AF=0.1456   ES:SE:LP:AF:SS:ID   0.0049:0.0389:0.0459988:0.1456:70675:rs10907178
1   1021695 rs9442398   A   G   .   PASS    AF=0.7354   ES:SE:LP:AF:SS:ID   0.0125:0.0253:0.207118:0.7354:70675:rs9442398
1   1022037 rs6701114   C   T   .   PASS    AF=0.5605   ES:SE:LP:AF:SS:ID   0.0314:0.0268:0.618704:0.5605:70675:rs6701114
1   1026707 rs4074137   C   A   .   PASS    AF=0.6114   ES:SE:LP:AF:SS:ID   0.0112:0.0238:0.195861:0.6114:70675:rs4074137
1   1030565 rs6687776   C   T   .   PASS    AF=0.1585   ES:SE:LP:AF:SS:ID   -0.0013:0.0283:0.0158779:0.1585:70675:rs6687776
1   1030633 rs6678318   G   A   .   PASS    AF=0.1616   ES:SE:LP:AF:SS:ID   -0.0069:0.041:0.0625824:0.1616:70675:rs6678318
1   1031540 rs9651273   A   G   .   PASS    AF=0.7304   ES:SE:LP:AF:SS:ID   0.0056:0.0243:0.0872998:0.7304:70675:rs9651273
1   1036959 rs11579015  T   C   .   PASS    AF=0.1067   ES:SE:LP:AF:SS:ID   0.0115:0.0348:0.130475:0.1067:70675:rs11579015
1   1040026 rs6671356   T   C   .   PASS    AF=0.1418   ES:SE:LP:AF:SS:ID   0.0251:0.0308:0.38122:0.1418:70675:rs6671356
1   1046164 rs6666280   C   T   .   PASS    AF=0.1358   ES:SE:LP:AF:SS:ID   0.0256:0.0304:0.398809:0.1358:70675:rs6666280
1   1048955 rs4970405   A   G   .   PASS    AF=0.1067   ES:SE:LP:AF:SS:ID   0.0133:0.0341:0.157266:0.1067:70675:rs4970405
1   1049950 rs12726255  A   G   .   PASS    AF=0.1379   ES:SE:LP:AF:SS:ID   0.0288:0.0297:0.479516:0.1379:70675:rs12726255
1   1053452 rs4970409   G   A   .   PASS    AF=0.1081   ES:SE:LP:AF:SS:ID   0.0179:0.0344:0.219611:0.1081:70675:rs4970409
1   1060174 rs7548798   C   T   .   PASS    AF=0.3224   ES:SE:LP:AF:SS:ID   -0.0431:0.0593:0.33059:0.3224:70675:rs7548798
1   1060235 rs7540009   G   A   .   PASS    AF=0.0328   ES:SE:LP:AF:SS:ID   0.0548:0.0686:0.372737:0.0328:70675:rs7540009
1   1060608 rs17160824  G   A   .   PASS    AF=0.1156   ES:SE:LP:AF:SS:ID   0.0252:0.036:0.315514:0.1156:70675:rs17160824
1   1061115 rs17160826  T   C   .   PASS    AF=0.1068   ES:SE:LP:AF:SS:ID   0.0182:0.0351:0.219107:0.1068:70675:rs17160826
1   1061152 rs12748370  T   C   .   PASS    AF=0.1066   ES:SE:LP:AF:SS:ID   0.0182:0.0352:0.218029:0.1066:70675:rs12748370
1   1061166 rs11807848  T   C   .   PASS    AF=0.4124   ES:SE:LP:AF:SS:ID   0.0151:0.0446:0.133713:0.4124:70675:rs11807848
1   1062015 rs9659914   C   T   .   PASS    AF=0.0304   ES:SE:LP:AF:SS:ID   0.0625:0.0747:0.394911:0.0304:70675:rs9659914
1   1062638 rs9442373   C   A   .   PASS    AF=0.5476   ES:SE:LP:AF:SS:ID   -0.0288:0.0439:0.290985:0.5476:70675:rs9442373
1   1064979 rs2298217   C   T   .   PASS    AF=0.1472   ES:SE:LP:AF:SS:ID   0.0253:0.0314:0.376647:0.1472:70675:rs2298217
1   1066029 rs12145826  G   A   .   PASS    AF=0.0896   ES:SE:LP:AF:SS:ID   0.1036:0.0797:0.713544:0.0896:70675:rs12145826
1   1066403 rs10907182  T   C   .   PASS    AF=0.6272   ES:SE:LP:AF:SS:ID   -0.0393:0.0973:0.163803:0.6272:70675:rs10907182
1   1071118 rs10907183  G   C   .   PASS    AF=0.6272   ES:SE:LP:AF:SS:ID   -0.0232:0.1455:0.0588863:0.6272:70675:rs10907183