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-1109,TotalVariants=2435413,VariantsNotRead=0,HarmonisedVariants=2435413,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-1109/ieu-a-1109_data.json --ref /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/QC/genomes/b37/human_g1k_v37.fasta; 1.1.1",
    "file_date": "2020-02-04T09:11:44.691888",
    "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-1109/ieu-a-1109.vcf.gz -O z /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-1109/ieu-a-1109_data.vcf.gz; Date=Tue Feb  4 16:42:34 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-1109/ieu-a-1109.vcf.gz; Date=Sun May 10 13:08:49 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-1109/ieu-a-1109.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-1109/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 08:59:34 2020
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-1109/ieu-a-1109.vcf.gz ...
Read summary statistics for 2435413 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, 1155101 SNPs remain.
After merging with regression SNP LD, 1155101 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0129 (0.0213)
Lambda GC: 1.0162
Mean Chi^2: 1.0257
Intercept: 1.0203 (0.0068)
Ratio: 0.789 (0.2628)
Analysis finished at Wed Feb  5 09:00:03 2020
Total time elapsed: 29.06s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9212,
    "inflation_factor": 1.0122,
    "mean_EFFECT": 0.0036,
    "n": 21185,
    "n_snps": 2435413,
    "n_clumped_hits": 2,
    "n_p_sig": 52,
    "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": 20502,
    "n_est": 20856.5935,
    "ratio_se_n": 0.9922,
    "mean_diff": -0.0026,
    "ratio_diff": 51.5247,
    "sd_y_est1": 3.4295,
    "sd_y_est2": 3.4028,
    "r2_sum1": 0.0464,
    "r2_sum2": 0.0039,
    "r2_sum3": 0.004,
    "r2_sum4": 0.0046,
    "ldsc_nsnp_merge_refpanel_ld": 1155101,
    "ldsc_nsnp_merge_regression_ld": 1155101,
    "ldsc_observed_scale_h2_beta": 0.0129,
    "ldsc_observed_scale_h2_se": 0.0213,
    "ldsc_intercept_beta": 1.0203,
    "ldsc_intercept_se": 0.0068,
    "ldsc_lambda_gc": 1.0162,
    "ldsc_mean_chisq": 1.0257,
    "ldsc_ratio": 0.7899
}

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 42 0 2435413 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 8.601999e+00 5.664878e+00 1.0000e+00 4.000000e+00 8.000000e+00 1.200000e+01 2.30000e+01 ▇▅▅▂▂
numeric POS 0 1.0000000 NA NA NA NA NA 7.876794e+07 5.569331e+07 1.1523e+04 3.253944e+07 7.015568e+07 1.143066e+08 2.49219e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA 3.645400e-03 5.785830e-02 -1.4429e+00 -2.750000e-02 2.100000e-03 3.260000e-02 1.36610e+00 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 5.051590e-02 2.768000e-02 3.0300e-02 3.440000e-02 4.000000e-02 5.430000e-02 7.12800e-01 ▇▁▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.975866e-01 2.895716e-01 0.0000e+00 2.459003e-01 4.974003e-01 7.480007e-01 1.00000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.975865e-01 2.895721e-01 0.0000e+00 2.459522e-01 4.974372e-01 7.480368e-01 1.00000e+00 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA 3.650276e-01 2.631140e-01 1.0600e-02 1.439000e-01 2.985000e-01 5.601000e-01 9.89300e-01 ▇▅▃▃▂
numeric AF_reference 20502 0.9915817 NA NA NA NA NA 3.635217e-01 2.547709e-01 1.9970e-04 1.493610e-01 3.025160e-01 5.475240e-01 1.00000e+00 ▇▆▅▃▂
numeric N 0 1.0000000 NA NA NA NA NA 2.118500e+04 0.000000e+00 2.1185e+04 2.118500e+04 2.118500e+04 2.118500e+04 2.11850e+04 ▁▁▇▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 721290 rs12565286 G C -0.0603 0.1481 0.6839998 0.6838924 0.0573 0.0371406 21185
1 723819 rs11804171 T A -0.3779 0.1815 0.0373396 0.0373339 0.0649 0.1345850 21185
1 723891 rs2977670 G C 0.3758 0.1810 0.0378399 0.0378715 0.9351 0.7799520 21185
1 752566 rs3094315 G A 0.1127 0.0659 0.0872107 0.0872350 0.8294 0.7182510 21185
1 754192 rs3131968 A G 0.1112 0.0968 0.2506998 0.2506548 0.8731 0.6785140 21185
1 768448 rs12562034 G A 0.0625 0.0714 0.3811000 0.3813834 0.0975 0.1918930 21185
1 775659 rs2905035 A G 0.1148 0.0992 0.2470000 0.2471669 0.8726 0.7450080 21185
1 776546 rs12124819 A G 0.0952 0.0671 0.1561000 0.1559638 0.2654 0.0756789 21185
1 777122 rs2980319 A T 0.1443 0.0865 0.0953103 0.0952744 0.8629 0.7472040 21185
1 779322 rs4040617 A G -0.1412 0.0870 0.1047999 0.1045919 0.1373 0.2264380 21185
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51216564 rs9616970 T C 0.0518 0.0913 0.5705005 0.5704694 0.1596 0.1563500 21185
22 51217134 rs117417021 A G -0.0230 0.0692 0.7390997 0.7396099 0.4441 0.2671730 21185
22 51222100 rs114553188 G T 0.0279 0.1063 0.7931001 0.7929632 0.0546 0.0880591 21185
22 51223637 rs375798137 G A 0.0282 0.1065 0.7910993 0.7911722 0.0546 0.0788738 21185
22 51229805 rs9616985 T C -0.0116 0.1322 0.9297999 0.9300787 0.1094 0.0730831 21185
23 35921591 rs2204667 C G 0.0440 0.0477 0.3563001 0.3563034 0.1568 NA 21185
23 51666786 rs14115 A G -0.0300 0.0699 0.6680993 0.6677889 0.0627 NA 21185
23 70163799 rs1626496 A C -0.0473 0.0630 0.4523004 0.4527769 0.0841 NA 21185
23 91415872 rs6562597 G A -0.0998 0.1219 0.4128003 0.4129554 0.0226 0.0021192 21185
23 118495837 rs12882977 G A 0.0052 0.0351 0.8820000 0.8822259 0.5005 0.2307280 21185

bcf preview

1   721290  rs12565286  G   C   .   PASS    AF=0.0573   ES:SE:LP:AF:SS:ID   -0.0603:0.1481:0.164944:0.0573:21185:rs12565286
1   723819  rs11804171  T   A   .   PASS    AF=0.0649   ES:SE:LP:AF:SS:ID   -0.3779:0.1815:1.42783:0.0649:21185:rs11804171
1   723891  rs2977670   G   C   .   PASS    AF=0.9351   ES:SE:LP:AF:SS:ID   0.3758:0.181:1.42205:0.9351:21185:rs2977670
1   752566  rs3094315   G   A   .   PASS    AF=0.8294   ES:SE:LP:AF:SS:ID   0.1127:0.0659:1.05943:0.8294:21185:rs3094315
1   754192  rs3131968   A   G   .   PASS    AF=0.8731   ES:SE:LP:AF:SS:ID   0.1112:0.0968:0.600846:0.8731:21185:rs3131968
1   768448  rs12562034  G   A   .   PASS    AF=0.0975   ES:SE:LP:AF:SS:ID   0.0625:0.0714:0.418961:0.0975:21185:rs12562034
1   775659  rs2905035   A   G   .   PASS    AF=0.8726   ES:SE:LP:AF:SS:ID   0.1148:0.0992:0.607303:0.8726:21185:rs2905035
1   776546  rs12124819  A   G   .   PASS    AF=0.2654   ES:SE:LP:AF:SS:ID   0.0952:0.0671:0.806597:0.2654:21185:rs12124819
1   777122  rs2980319   A   T   .   PASS    AF=0.8629   ES:SE:LP:AF:SS:ID   0.1443:0.0865:1.02086:0.8629:21185:rs2980319
1   779322  rs4040617   A   G   .   PASS    AF=0.1373   ES:SE:LP:AF:SS:ID   -0.1412:0.087:0.979639:0.1373:21185:rs4040617
1   780785  rs2977612   T   A   .   PASS    AF=0.8727   ES:SE:LP:AF:SS:ID   0.1287:0.1008:0.695725:0.8727:21185:rs2977612
1   785050  rs2905062   G   A   .   PASS    AF=0.8721   ES:SE:LP:AF:SS:ID   0.1365:0.1024:0.738261:0.8721:21185:rs2905062
1   785989  rs2980300   T   C   .   PASS    AF=0.8632   ES:SE:LP:AF:SS:ID   0.1488:0.0834:1.12802:0.8632:21185:rs2980300
1   798959  rs11240777  G   A   .   PASS    AF=0.2118   ES:SE:LP:AF:SS:ID   -0.0633:0.0777:0.381534:0.2118:21185:rs11240777
1   846864  rs950122    G   C   .   PASS    AF=0.1691   ES:SE:LP:AF:SS:ID   -0.0502:0.1663:0.117703:0.1691:21185:rs950122
1   882033  rs2272756   G   A   .   PASS    AF=0.2636   ES:SE:LP:AF:SS:ID   -0.0498:0.1175:0.172825:0.2636:21185:rs2272756
1   962210  rs3128126   A   G   .   PASS    AF=0.4368   ES:SE:LP:AF:SS:ID   -0.0294:0.0636:0.190844:0.4368:21185:rs3128126
1   990380  rs3121561   C   T   .   PASS    AF=0.2778   ES:SE:LP:AF:SS:ID   -0.0107:0.0548:0.0732975:0.2778:21185:rs3121561
1   998501  rs3813193   G   C   .   PASS    AF=0.1667   ES:SE:LP:AF:SS:ID   -0.0182:0.053:0.13543:0.1667:21185:rs3813193
1   1003629 rs4075116   C   T   .   PASS    AF=0.7398   ES:SE:LP:AF:SS:ID   -0.0031:0.0443:0.0247521:0.7398:21185:rs4075116
1   1005806 rs3934834   C   T   .   PASS    AF=0.1502   ES:SE:LP:AF:SS:ID   0.0118:0.0474:0.094744:0.1502:21185:rs3934834
1   1017170 rs3766193   C   G   .   PASS    AF=0.5525   ES:SE:LP:AF:SS:ID   0.0081:0.0369:0.0829148:0.5525:21185:rs3766193
1   1017197 rs3766192   C   T   .   PASS    AF=0.5628   ES:SE:LP:AF:SS:ID   0.006:0.0338:0.065552:0.5628:21185:rs3766192
1   1017587 rs3766191   C   T   .   PASS    AF=0.1434   ES:SE:LP:AF:SS:ID   0.0054:0.0497:0.0390063:0.1434:21185:rs3766191
1   1018562 rs9442371   C   T   .   PASS    AF=0.5716   ES:SE:LP:AF:SS:ID   0.0126:0.0351:0.142306:0.5716:21185:rs9442371
1   1018704 rs9442372   A   G   .   PASS    AF=0.572    ES:SE:LP:AF:SS:ID   0.0065:0.033:0.0734518:0.572:21185:rs9442372
1   1021346 rs10907177  A   G   .   PASS    AF=0.1445   ES:SE:LP:AF:SS:ID   0.0066:0.0503:0.0474982:0.1445:21185:rs10907177
1   1021415 rs3737728   A   G   .   PASS    AF=0.7228   ES:SE:LP:AF:SS:ID   0.0011:0.0369:0.010061:0.7228:21185:rs3737728
1   1021583 rs10907178  A   C   .   PASS    AF=0.1429   ES:SE:LP:AF:SS:ID   0.0079:0.0508:0.0576942:0.1429:21185:rs10907178
1   1021695 rs9442398   A   G   .   PASS    AF=0.7293   ES:SE:LP:AF:SS:ID   0.0123:0.0393:0.122801:0.7293:21185:rs9442398
1   1022037 rs6701114   C   T   .   PASS    AF=0.5548   ES:SE:LP:AF:SS:ID   -0.0022:0.0373:0.0208615:0.5548:21185:rs6701114
1   1025301 rs9442400   T   C   .   PASS    AF=0.9379   ES:SE:LP:AF:SS:ID   0.1218:0.1475:0.388489:0.9379:21185:rs9442400
1   1026707 rs4074137   C   A   .   PASS    AF=0.5993   ES:SE:LP:AF:SS:ID   -0.0244:0.0371:0.291494:0.5993:21185:rs4074137
1   1030565 rs6687776   C   T   .   PASS    AF=0.157    ES:SE:LP:AF:SS:ID   0.0625:0.0438:0.815593:0.157:21185:rs6687776
1   1030633 rs6678318   G   A   .   PASS    AF=0.1567   ES:SE:LP:AF:SS:ID   0.0516:0.0451:0.597223:0.1567:21185:rs6678318
1   1031540 rs9651273   A   G   .   PASS    AF=0.7341   ES:SE:LP:AF:SS:ID   0.0204:0.0388:0.222573:0.7341:21185:rs9651273
1   1036959 rs11579015  T   C   .   PASS    AF=0.1121   ES:SE:LP:AF:SS:ID   0.0844:0.0532:0.948847:0.1121:21185:rs11579015
1   1040026 rs6671356   T   C   .   PASS    AF=0.1432   ES:SE:LP:AF:SS:ID   0.0623:0.0471:0.73002:0.1432:21185:rs6671356
1   1046164 rs6666280   C   T   .   PASS    AF=0.137    ES:SE:LP:AF:SS:ID   0.0637:0.0494:0.705093:0.137:21185:rs6666280
1   1048955 rs4970405   A   G   .   PASS    AF=0.1064   ES:SE:LP:AF:SS:ID   0.0755:0.0541:0.788079:0.1064:21185:rs4970405
1   1049950 rs12726255  A   G   .   PASS    AF=0.1377   ES:SE:LP:AF:SS:ID   0.0479:0.0472:0.508498:0.1377:21185:rs12726255
1   1053452 rs4970409   G   A   .   PASS    AF=0.1077   ES:SE:LP:AF:SS:ID   0.0742:0.0543:0.764219:0.1077:21185:rs4970409
1   1060174 rs7548798   C   T   .   PASS    AF=0.3151   ES:SE:LP:AF:SS:ID   -0.0411:0.0416:0.489991:0.3151:21185:rs7548798
1   1060235 rs7540009   G   A   .   PASS    AF=0.0306   ES:SE:LP:AF:SS:ID   -0.0282:0.1171:0.0916222:0.0306:21185:rs7540009
1   1060608 rs17160824  G   A   .   PASS    AF=0.1174   ES:SE:LP:AF:SS:ID   0.0756:0.055:0.771856:0.1174:21185:rs17160824
1   1061115 rs17160826  T   C   .   PASS    AF=0.107    ES:SE:LP:AF:SS:ID   0.074:0.055:0.747875:0.107:21185:rs17160826
1   1061152 rs12748370  T   C   .   PASS    AF=0.1069   ES:SE:LP:AF:SS:ID   0.0743:0.055:0.753009:0.1069:21185:rs12748370
1   1061166 rs11807848  T   C   .   PASS    AF=0.4066   ES:SE:LP:AF:SS:ID   0.0032:0.0369:0.0313303:0.4066:21185:rs11807848
1   1062015 rs9659914   C   T   .   PASS    AF=0.03 ES:SE:LP:AF:SS:ID   -0.0347:0.1235:0.108463:0.03:21185:rs9659914
1   1062638 rs9442373   C   A   .   PASS    AF=0.5525   ES:SE:LP:AF:SS:ID   0.0068:0.0355:0.0715017:0.5525:21185:rs9442373