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-1124,TotalVariants=15409386,VariantsNotRead=447,HarmonisedVariants=15408939,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-1124/ieu-a-1124_data.json --ref /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/QC/genomes/b37/human_g1k_v37.fasta; 1.1.1",
    "file_date": "2020-02-04T10:18:37.120636",
    "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-1124/ieu-a-1124.vcf.gz -O z /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-1124/ieu-a-1124_data.vcf.gz; Date=Tue Feb  4 16:12:15 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-1124/ieu-a-1124.vcf.gz; Date=Sun May 10 23:26:08 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-1124/ieu-a-1124.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-1124/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 08:28:44 2020
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-1124/ieu-a-1124.vcf.gz ...
Read summary statistics for 15408939 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, 1218946 SNPs remain.
After merging with regression SNP LD, 1218946 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0195 (0.0111)
Lambda GC: 1.0196
Mean Chi^2: 1.0245
Intercept: 1.0084 (0.0061)
Ratio: 0.3429 (0.2495)
Analysis finished at Wed Feb  5 08:31:18 2020
Total time elapsed: 2.0m:34.03s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9603,
    "inflation_factor": 1.0193,
    "mean_EFFECT": -1.0539,
    "n": 42307,
    "n_snps": 15408939,
    "n_clumped_hits": 1,
    "n_p_sig": 5,
    "n_mono": 0,
    "n_ns": 779184,
    "n_mac": 294044,
    "is_snpid_unique": false,
    "n_miss_EFFECT": 0,
    "n_miss_SE": 0,
    "n_miss_PVAL": 0,
    "n_miss_AF": 1462,
    "n_miss_AF_reference": 160771,
    "n_est": 40816.8553,
    "ratio_se_n": 0.9822,
    "mean_diff": 1.0479,
    "ratio_diff": 6.5306,
    "sd_y_est1": 6.4315,
    "sd_y_est2": 6.3172,
    "r2_sum1": 0.0273,
    "r2_sum2": 0.0007,
    "r2_sum3": 0.0007,
    "r2_sum4": 0.0008,
    "ldsc_nsnp_merge_refpanel_ld": 1218946,
    "ldsc_nsnp_merge_regression_ld": 1218946,
    "ldsc_observed_scale_h2_beta": 0.0195,
    "ldsc_observed_scale_h2_se": 0.0111,
    "ldsc_intercept_beta": 1.0084,
    "ldsc_intercept_se": 0.0061,
    "ldsc_lambda_gc": 1.0196,
    "ldsc_mean_chisq": 1.0245,
    "ldsc_ratio": 0.3429
}

Flags

name value
af_correlation FALSE
inflation_factor FALSE
n FALSE
is_snpid_non_unique TRUE
mean_EFFECT_nonfinite FALSE
mean_EFFECT_05 TRUE
mean_EFFECT_01 TRUE
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 47 0 15408937 0 NA NA NA NA NA NA NA NA
character REF 0 1.0000000 1 101 0 37510 0 NA NA NA NA NA NA NA NA
character ALT 0 1.0000000 1 105 0 18062 0 NA NA NA NA NA NA NA NA
numeric CHROM 0 1.0000000 NA NA NA NA NA 8.893860e+00 6.253752e+00 1.0000e+00 4.000000e+00 7.000000e+00 1.400000e+01 2.400000e+01 ▇▆▂▃▂
numeric POS 0 1.0000000 NA NA NA NA NA 7.931363e+07 5.682710e+07 5.6000e+01 3.251458e+07 6.963991e+07 1.158380e+08 2.492402e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA -1.053851e+00 4.327412e+00 -2.0370e+01 -1.197000e-01 -4.455000e-03 8.415000e-02 2.042000e+01 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 2.942088e+00 1.765263e+01 8.7600e-05 5.585000e-02 1.595000e-01 6.361000e-01 2.212000e+03 ▇▁▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.971523e-01 2.887379e-01 0.0000e+00 2.471001e-01 4.958999e-01 7.471005e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.972707e-01 2.886859e-01 0.0000e+00 2.473155e-01 4.960101e-01 7.471320e-01 1.000000e+00 ▇▇▇▇▇
numeric AF 1462 0.9999051 NA NA NA NA NA 1.553931e-01 2.457435e-01 0.0000e+00 2.176000e-03 2.120000e-02 2.109000e-01 9.999890e-01 ▇▁▁▁▁
numeric AF_reference 160771 0.9895664 NA NA NA NA NA 1.551530e-01 2.331800e-01 0.0000e+00 2.795500e-03 3.254790e-02 2.166530e-01 1.000000e+00 ▇▁▁▁▁
numeric N 0 1.0000000 NA NA NA NA NA 4.230700e+04 0.000000e+00 4.2307e+04 4.230700e+04 4.230700e+04 4.230700e+04 4.230700e+04 ▁▁▇▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 10616 rs376342519 CCGCCGTTGCAAAGGCGCGCCG C -0.13060 0.27890 0.6395007 0.6395928 0.991000 0.9930110 42307
1 14933 rs199856693 G A 0.07263 0.17950 0.6856998 0.6857539 0.047970 0.0283546 42307
1 15774 rs374029747 G A 0.73990 0.38750 0.0561798 0.0562080 0.006579 0.0119808 42307
1 16949 rs199745162 A C -0.21920 0.25930 0.3978002 0.3979138 0.016750 0.0139776 42307
1 51479 rs116400033 T A -0.09142 0.08008 0.2535999 0.2536168 0.232100 0.1281950 42307
1 52185 rs201374420 TTAA T -1.12000 2.90200 0.6994006 0.6995406 0.005882 0.0053914 42307
1 54353 rs140052487 C A -2.45200 1.56200 0.1165000 0.1164658 0.001339 0.0089856 42307
1 54490 rs141149254 G A -0.05759 0.09482 0.5435994 0.5436112 0.166100 0.0960463 42307
1 55164 rs3091274 C A -0.19990 0.25670 0.4360999 0.4361388 0.980700 0.9233230 42307
1 55326 rs3107975 T C 0.68800 0.48540 0.1564001 0.1563696 0.028260 0.0459265 42307
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
23 154925045 rs509981 C T -0.013810 0.05180 0.7897998 0.7897754 0.250000 0.3634440 42307
23 154925895 rs538470 C T -0.024810 0.05377 0.6445996 0.6445047 0.252700 0.3634440 42307
23 154926376 rs116490668 C T -1.009000 1.07200 0.3466004 0.3465863 0.001859 0.0349669 42307
23 154927185 rs185685661 T C 0.058720 0.08925 0.5106002 0.5105849 0.139300 0.1796030 42307
23 154927199 rs645904 C T -0.013510 0.05188 0.7946001 0.7945486 0.248000 0.3674170 42307
23 154927581 rs644138 G A -0.005728 0.05059 0.9097999 0.9098530 0.299900 0.4635760 42307
23 154929412 rs557132 C T -0.010620 0.05192 0.8379000 0.8379273 0.250400 0.3568210 42307
23 154929952 rs4012982 CAA C -0.012530 0.05198 0.8095001 0.8095131 0.250900 0.3165560 42307
23 154930230 rs781880 A G -0.016410 0.05228 0.7537008 0.7536070 0.249000 0.3618540 42307
24 13537468 rs7203107 A G -0.220800 0.27020 0.4137005 0.4138299 0.985590 NA 42307

bcf preview

1   10616   rs376342519 CCGCCGTTGCAAAGGCGCGCCG  C   .   PASS    AF=0.991    ES:SE:LP:AF:SS:ID   -0.1306:0.2789:0.194159:0.991:42307:rs376342519
1   14933   rs199856693 G   A   .   PASS    AF=0.04797  ES:SE:LP:AF:SS:ID   0.07263:0.1795:0.163866:0.04797:42307:rs199856693
1   15774   rs374029747 G   A   .   PASS    AF=0.006579 ES:SE:LP:AF:SS:ID   0.7399:0.3875:1.25042:0.006579:42307:rs374029747
1   16949   rs199745162 A   C   .   PASS    AF=0.01675  ES:SE:LP:AF:SS:ID   -0.2192:0.2593:0.400335:0.01675:42307:rs199745162
1   51479   rs116400033 T   A   .   PASS    AF=0.2321   ES:SE:LP:AF:SS:ID   -0.09142:0.08008:0.595851:0.2321:42307:rs116400033
1   52185   rs201374420 TTAA    T   .   PASS    AF=0.005882 ES:SE:LP:AF:SS:ID   -1.12:2.902:0.155274:0.005882:42307:rs201374420
1   54353   rs140052487 C   A   .   PASS    AF=0.001339 ES:SE:LP:AF:SS:ID   -2.452:1.562:0.933674:0.001339:42307:rs140052487
1   54490   rs141149254 G   A   .   PASS    AF=0.1661   ES:SE:LP:AF:SS:ID   -0.05759:0.09482:0.264721:0.1661:42307:rs141149254
1   55164   rs3091274   C   A   .   PASS    AF=0.9807   ES:SE:LP:AF:SS:ID   -0.1999:0.2567:0.360414:0.9807:42307:rs3091274
1   55326   rs3107975   T   C   .   PASS    AF=0.02826  ES:SE:LP:AF:SS:ID   0.688:0.4854:0.805763:0.02826:42307:rs3107975
1   55545   rs28396308  C   T   .   PASS    AF=0.2248   ES:SE:LP:AF:SS:ID   -0.07953:0.08682:0.44406:0.2248:42307:rs28396308
1   57183   rs368339209 A   G   .   PASS    AF=0.0007041    ES:SE:LP:AF:SS:ID   -1.221:1.867:0.289713:0.0007041:42307:rs368339209
1   57292   rs201418760 C   T   .   PASS    AF=0.02393  ES:SE:LP:AF:SS:ID   0.5308:0.4904:0.55424:0.02393:42307:rs201418760
1   58814   rs114420996 G   A   .   PASS    AF=0.1003   ES:SE:LP:AF:SS:ID   -0.1992:0.127:0.932929:0.1003:42307:rs114420996
1   61543   rs201849102 T   C   .   PASS    AF=0.0003079    ES:SE:LP:AF:SS:ID   -20.19:11.96:1.03839:0.0003079:42307:rs201849102
1   61743   rs184286948 G   C   .   PASS    AF=0.009155 ES:SE:LP:AF:SS:ID   -0.7362:0.4343:1.04542:0.009155:42307:rs184286948
1   61920   rs62637820  G   A   .   PASS    AF=0.02945  ES:SE:LP:AF:SS:ID   -0.1176:0.2167:0.23114:0.02945:42307:rs62637820
1   63093   rs200092917 G   A   .   PASS    AF=0.0207   ES:SE:LP:AF:SS:ID   0.131:0.2716:0.201004:0.0207:42307:rs200092917
1   64649   rs181431124 A   C   .   PASS    AF=0.02715  ES:SE:LP:AF:SS:ID   -0.009702:0.2314:0.0147532:0.02715:42307:rs181431124
1   66219   rs181028663 A   T   .   PASS    AF=0.01624  ES:SE:LP:AF:SS:ID   0.6418:0.2483:2.01149:0.01624:42307:rs181028663
1   68082   rs367789441 T   C   .   PASS    AF=0.06526  ES:SE:LP:AF:SS:ID   0.06779:0.1342:0.212256:0.06526:42307:rs367789441
1   68596   rs372212855 T   G   .   PASS    AF=0.003797 ES:SE:LP:AF:SS:ID   0.2608:0.4966:0.222283:0.003797:42307:rs372212855
1   69428   rs140739101 T   G   .   PASS    AF=0.04215  ES:SE:LP:AF:SS:ID   0.3047:0.1573:1.27819:0.04215:42307:rs140739101
1   69534   rs190717287 T   C   .   PASS    AF=0.0003164    ES:SE:LP:AF:SS:ID   0.5289:1.38:0.154034:0.0003164:42307:rs190717287
1   69761   rs200505207 A   T   .   PASS    AF=0.06821  ES:SE:LP:AF:SS:ID   0.08096:0.1298:0.273436:0.06821:42307:rs200505207
1   69897   rs200676709 T   C   .   PASS    AF=0.7661   ES:SE:LP:AF:SS:ID   -0.1388:0.08359:1.01359:0.7661:42307:rs200676709
1   72297   rs200651397 G   GTAT    .   PASS    AF=0.006341 ES:SE:LP:AF:SS:ID   -0.1492:0.5029:0.115375:0.006341:42307:rs200651397
1   74790   rs13328700  C   G   .   PASS    AF=0.03421  ES:SE:LP:AF:SS:ID   0.2221:0.1691:0.723538:0.03421:42307:rs13328700
1   74792   rs13328684  G   A   .   PASS    AF=0.03421  ES:SE:LP:AF:SS:ID   0.2221:0.1691:0.723538:0.03421:42307:rs13328684
1   76854   rs367666799 A   G   .   PASS    AF=0.06856  ES:SE:LP:AF:SS:ID   0.0001374:0.1447:0.000347575:0.06856:42307:rs367666799
1   78942   rs372315362 C   G   .   PASS    AF=0.01116  ES:SE:LP:AF:SS:ID   -4.703:4.071:0.605548:0.01116:42307:rs372315362
1   80454   rs144226842 G   C   .   PASS    AF=0.0004404    ES:SE:LP:AF:SS:ID   -20.05:57.62:0.137928:0.0004404:42307:rs144226842
1   81590   rs202072409 AC  A   .   PASS    AF=0.004955 ES:SE:LP:AF:SS:ID   -20.03:31.65:0.278354:0.004955:42307:rs202072409
1   82163   rs139113303 G   A   .   PASS    AF=0.06791  ES:SE:LP:AF:SS:ID   -0.002873:0.1461:0.00687251:0.06791:42307:rs139113303
1   82609   rs149189449 C   G   .   PASS    AF=0.06818  ES:SE:LP:AF:SS:ID   -0.005419:0.1457:0.013094:0.06818:42307:rs149189449
1   83514   rs201754587 C   T   .   PASS    AF=0.3501   ES:SE:LP:AF:SS:ID   -0.004514:0.07785:0.0205427:0.3501:42307:rs201754587
1   84139   rs183605470 A   T   .   PASS    AF=0.02132  ES:SE:LP:AF:SS:ID   -0.04947:0.2871:0.0638886:0.02132:42307:rs183605470
1   86028   rs114608975 T   C   .   PASS    AF=0.04742  ES:SE:LP:AF:SS:ID   -0.2722:0.1784:0.896196:0.04742:42307:rs114608975
1   86065   rs116504101 G   C   .   PASS    AF=0.06995  ES:SE:LP:AF:SS:ID   0.02634:0.1443:0.0679831:0.06995:42307:rs116504101
1   86331   rs115209712 A   G   .   PASS    AF=0.1018   ES:SE:LP:AF:SS:ID   -0.04172:0.1223:0.134896:0.1018:42307:rs115209712
1   87021   rs188486692 T   C   .   PASS    AF=0.00763  ES:SE:LP:AF:SS:ID   0.3894:0.3723:0.529442:0.00763:42307:rs188486692
1   87360   rs180907504 C   T   .   PASS    AF=0.01853  ES:SE:LP:AF:SS:ID   0.09414:0.2525:0.14917:0.01853:42307:rs180907504
1   87409   rs139490478 C   T   .   PASS    AF=0.07088  ES:SE:LP:AF:SS:ID   0.0292:0.1425:0.0769115:0.07088:42307:rs139490478
1   88169   rs940550    C   T   .   PASS    AF=0.2022   ES:SE:LP:AF:SS:ID   0.02552:0.08251:0.120847:0.2022:42307:rs940550
1   88172   rs940551    G   A   .   PASS    AF=0.06423  ES:SE:LP:AF:SS:ID   0.0233:0.137:0.0629839:0.06423:42307:rs940551
1   88177   rs143215837 G   C   .   PASS    AF=0.06377  ES:SE:LP:AF:SS:ID   0.04629:0.1373:0.133122:0.06377:42307:rs143215837
1   88188   rs148331237 C   A   .   PASS    AF=0.007142 ES:SE:LP:AF:SS:ID   -0.3513:0.419:0.39599:0.007142:42307:rs148331237
1   88236   rs186918018 C   T   .   PASS    AF=0.01279  ES:SE:LP:AF:SS:ID   -0.772:0.8706:0.425737:0.01279:42307:rs186918018
1   88316   rs113759966 G   A   .   PASS    AF=0.06376  ES:SE:LP:AF:SS:ID   0.03231:0.1382:0.0887358:0.06376:42307:rs113759966
1   88338   rs55700207  G   A   .   PASS    AF=0.08209  ES:SE:LP:AF:SS:ID   -0.2869:0.1426:1.35389:0.08209:42307:rs55700207