Summary

Summary {data-width=650}

Manhattan plot

manhattan_plot

manhattan_plot

QQ plot

qq_plot

qq_plot

AF plot

af_plot

af_plot

P-Z plot

pz_plot

pz_plot

beta_std plot

beta_std_plot

beta_std_plot

Metadata

{
    "fileformat": "VCFv4.2",
    "FILTER": "<ID=PASS,Description=\"All filters passed\">",
    "INFO": "<ID=AF,Number=A,Type=Float,Description=\"Allele Frequency\">",
    "FORMAT": "<ID=ES,Number=A,Type=Float,Description=\"Effect size estimate relative to the alternative allele\">",
    "FORMAT.1": "<ID=SE,Number=A,Type=Float,Description=\"Standard error of effect size estimate\">",
    "FORMAT.2": "<ID=LP,Number=A,Type=Float,Description=\"-log10 p-value for effect estimate\">",
    "FORMAT.3": "<ID=AF,Number=A,Type=Float,Description=\"Alternate allele frequency in the association study\">",
    "FORMAT.4": "<ID=SS,Number=A,Type=Float,Description=\"Sample size used to estimate genetic effect\">",
    "FORMAT.5": "<ID=EZ,Number=A,Type=Float,Description=\"Z-score provided if it was used to derive the EFFECT and SE fields\">",
    "FORMAT.6": "<ID=SI,Number=A,Type=Float,Description=\"Accuracy score of summary data imputation\">",
    "FORMAT.7": "<ID=NC,Number=A,Type=Float,Description=\"Number of cases used to estimate genetic effect\">",
    "FORMAT.8": "<ID=ID,Number=1,Type=String,Description=\"Study variant identifier\">",
    "META": "<ID=TotalVariants,Number=1,Type=Integer,Description=\"Total number of variants in input\">",
    "META.1": "<ID=VariantsNotRead,Number=1,Type=Integer,Description=\"Number of variants that could not be read\">",
    "META.2": "<ID=HarmonisedVariants,Number=1,Type=Integer,Description=\"Total number of harmonised variants\">",
    "META.3": "<ID=VariantsNotHarmonised,Number=1,Type=Integer,Description=\"Total number of variants that could not be harmonised\">",
    "META.4": "<ID=SwitchedAlleles,Number=1,Type=Integer,Description=\"Total number of variants strand switched\">",
    "META.5": "<ID=TotalControls,Number=1,Type=Integer,Description=\"Total number of controls in the association study\">",
    "META.6": "<ID=TotalCases,Number=1,Type=Integer,Description=\"Total number of cases in the association study\">",
    "META.7": "<ID=StudyType,Number=1,Type=String,Description=\"Type of GWAS study [Continuous or CaseControl]\">",
    "SAMPLE": "<ID=ukb-d-2654_9,TotalVariants=12587824,VariantsNotRead=0,HarmonisedVariants=12587824,VariantsNotHarmonised=0,SwitchedAlleles=227,StudyType=Continuous>",
    "contig": "<ID=1,length=249250621,assembly=HG19/GRCh37>",
    "contig.1": "<ID=2,length=243199373,assembly=HG19/GRCh37>",
    "contig.2": "<ID=3,length=198022430,assembly=HG19/GRCh37>",
    "contig.3": "<ID=4,length=191154276,assembly=HG19/GRCh37>",
    "contig.4": "<ID=5,length=180915260,assembly=HG19/GRCh37>",
    "contig.5": "<ID=6,length=171115067,assembly=HG19/GRCh37>",
    "contig.6": "<ID=7,length=159138663,assembly=HG19/GRCh37>",
    "contig.7": "<ID=8,length=146364022,assembly=HG19/GRCh37>",
    "contig.8": "<ID=9,length=141213431,assembly=HG19/GRCh37>",
    "contig.9": "<ID=10,length=135534747,assembly=HG19/GRCh37>",
    "contig.10": "<ID=11,length=135006516,assembly=HG19/GRCh37>",
    "contig.11": "<ID=12,length=133851895,assembly=HG19/GRCh37>",
    "contig.12": "<ID=13,length=115169878,assembly=HG19/GRCh37>",
    "contig.13": "<ID=14,length=107349540,assembly=HG19/GRCh37>",
    "contig.14": "<ID=15,length=102531392,assembly=HG19/GRCh37>",
    "contig.15": "<ID=16,length=90354753,assembly=HG19/GRCh37>",
    "contig.16": "<ID=17,length=81195210,assembly=HG19/GRCh37>",
    "contig.17": "<ID=18,length=78077248,assembly=HG19/GRCh37>",
    "contig.18": "<ID=19,length=59128983,assembly=HG19/GRCh37>",
    "contig.19": "<ID=20,length=63025520,assembly=HG19/GRCh37>",
    "contig.20": "<ID=21,length=48129895,assembly=HG19/GRCh37>",
    "contig.21": "<ID=22,length=51304566,assembly=HG19/GRCh37>",
    "contig.22": "<ID=X,length=155270560,assembly=HG19/GRCh37>",
    "contig.23": "<ID=Y,length=59373566,assembly=HG19/GRCh37>",
    "contig.24": "<ID=MT,length=16569,assembly=HG19/GRCh37>",
    "contig.25": "<ID=GL000207.1,length=4262,assembly=HG19/GRCh37>",
    "contig.26": "<ID=GL000226.1,length=15008,assembly=HG19/GRCh37>",
    "contig.27": "<ID=GL000229.1,length=19913,assembly=HG19/GRCh37>",
    "contig.28": "<ID=GL000231.1,length=27386,assembly=HG19/GRCh37>",
    "contig.29": "<ID=GL000210.1,length=27682,assembly=HG19/GRCh37>",
    "contig.30": "<ID=GL000239.1,length=33824,assembly=HG19/GRCh37>",
    "contig.31": "<ID=GL000235.1,length=34474,assembly=HG19/GRCh37>",
    "contig.32": "<ID=GL000201.1,length=36148,assembly=HG19/GRCh37>",
    "contig.33": "<ID=GL000247.1,length=36422,assembly=HG19/GRCh37>",
    "contig.34": "<ID=GL000245.1,length=36651,assembly=HG19/GRCh37>",
    "contig.35": "<ID=GL000197.1,length=37175,assembly=HG19/GRCh37>",
    "contig.36": "<ID=GL000203.1,length=37498,assembly=HG19/GRCh37>",
    "contig.37": "<ID=GL000246.1,length=38154,assembly=HG19/GRCh37>",
    "contig.38": "<ID=GL000249.1,length=38502,assembly=HG19/GRCh37>",
    "contig.39": "<ID=GL000196.1,length=38914,assembly=HG19/GRCh37>",
    "contig.40": "<ID=GL000248.1,length=39786,assembly=HG19/GRCh37>",
    "contig.41": "<ID=GL000244.1,length=39929,assembly=HG19/GRCh37>",
    "contig.42": "<ID=GL000238.1,length=39939,assembly=HG19/GRCh37>",
    "contig.43": "<ID=GL000202.1,length=40103,assembly=HG19/GRCh37>",
    "contig.44": "<ID=GL000234.1,length=40531,assembly=HG19/GRCh37>",
    "contig.45": "<ID=GL000232.1,length=40652,assembly=HG19/GRCh37>",
    "contig.46": "<ID=GL000206.1,length=41001,assembly=HG19/GRCh37>",
    "contig.47": "<ID=GL000240.1,length=41933,assembly=HG19/GRCh37>",
    "contig.48": "<ID=GL000236.1,length=41934,assembly=HG19/GRCh37>",
    "contig.49": "<ID=GL000241.1,length=42152,assembly=HG19/GRCh37>",
    "contig.50": "<ID=GL000243.1,length=43341,assembly=HG19/GRCh37>",
    "contig.51": "<ID=GL000242.1,length=43523,assembly=HG19/GRCh37>",
    "contig.52": "<ID=GL000230.1,length=43691,assembly=HG19/GRCh37>",
    "contig.53": "<ID=GL000237.1,length=45867,assembly=HG19/GRCh37>",
    "contig.54": "<ID=GL000233.1,length=45941,assembly=HG19/GRCh37>",
    "contig.55": "<ID=GL000204.1,length=81310,assembly=HG19/GRCh37>",
    "contig.56": "<ID=GL000198.1,length=90085,assembly=HG19/GRCh37>",
    "contig.57": "<ID=GL000208.1,length=92689,assembly=HG19/GRCh37>",
    "contig.58": "<ID=GL000191.1,length=106433,assembly=HG19/GRCh37>",
    "contig.59": "<ID=GL000227.1,length=128374,assembly=HG19/GRCh37>",
    "contig.60": "<ID=GL000228.1,length=129120,assembly=HG19/GRCh37>",
    "contig.61": "<ID=GL000214.1,length=137718,assembly=HG19/GRCh37>",
    "contig.62": "<ID=GL000221.1,length=155397,assembly=HG19/GRCh37>",
    "contig.63": "<ID=GL000209.1,length=159169,assembly=HG19/GRCh37>",
    "contig.64": "<ID=GL000218.1,length=161147,assembly=HG19/GRCh37>",
    "contig.65": "<ID=GL000220.1,length=161802,assembly=HG19/GRCh37>",
    "contig.66": "<ID=GL000213.1,length=164239,assembly=HG19/GRCh37>",
    "contig.67": "<ID=GL000211.1,length=166566,assembly=HG19/GRCh37>",
    "contig.68": "<ID=GL000199.1,length=169874,assembly=HG19/GRCh37>",
    "contig.69": "<ID=GL000217.1,length=172149,assembly=HG19/GRCh37>",
    "contig.70": "<ID=GL000216.1,length=172294,assembly=HG19/GRCh37>",
    "contig.71": "<ID=GL000215.1,length=172545,assembly=HG19/GRCh37>",
    "contig.72": "<ID=GL000205.1,length=174588,assembly=HG19/GRCh37>",
    "contig.73": "<ID=GL000219.1,length=179198,assembly=HG19/GRCh37>",
    "contig.74": "<ID=GL000224.1,length=179693,assembly=HG19/GRCh37>",
    "contig.75": "<ID=GL000223.1,length=180455,assembly=HG19/GRCh37>",
    "contig.76": "<ID=GL000195.1,length=182896,assembly=HG19/GRCh37>",
    "contig.77": "<ID=GL000212.1,length=186858,assembly=HG19/GRCh37>",
    "contig.78": "<ID=GL000222.1,length=186861,assembly=HG19/GRCh37>",
    "contig.79": "<ID=GL000200.1,length=187035,assembly=HG19/GRCh37>",
    "contig.80": "<ID=GL000193.1,length=189789,assembly=HG19/GRCh37>",
    "contig.81": "<ID=GL000194.1,length=191469,assembly=HG19/GRCh37>",
    "contig.82": "<ID=GL000225.1,length=211173,assembly=HG19/GRCh37>",
    "contig.83": "<ID=GL000192.1,length=547496,assembly=HG19/GRCh37>",
    "gwas_harmonisation_command": "--json /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-2654_9/ukb-d-2654_9_data.json --ref /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/QC/genomes/b37/human_g1k_v37.fasta; 1.1.1",
    "file_date": "2019-11-25T15:18:23.937771",
    "bcftools_annotateVersion": "1.9-74-g6af271c+htslib-1.9-64-g226b4a8",
    "bcftools_annotateCommand": "annotate -a /mnt/storage/home/gh13047/mr-eve/vcf-reference-datasets/dbsnp/dbsnp.v153.b37.vcf.gz -c ID -o /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-2654_9/ukb-d-2654_9.vcf.gz -O z /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-2654_9/ukb-d-2654_9_data.vcf.gz; Date=Mon Nov 25 16:01:06 2019",
    "bcftools_viewVersion": "1.9-74-g6af271c+htslib-1.9-64-g226b4a8",
    "bcftools_viewCommand": "view -h /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukb-d-2654_9/ukb-d-2654_9.vcf.gz; Date=Sun May 10 23:21:35 2020"
}

LDSC

*********************************************************************
* LD Score Regression (LDSC)
* Version 1.0.1
* (C) 2014-2019 Brendan Bulik-Sullivan and Hilary Finucane
* Broad Institute of MIT and Harvard / MIT Department of Mathematics
* GNU General Public License v3
*********************************************************************
Call: 
./ldsc.py \
--h2 /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-2654_9/ukb-d-2654_9.vcf.gz \
--ref-ld-chr /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-2654_9/ldsc.txt \
--w-ld-chr /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/reference/eur_w_ld_chr/ 

Beginning analysis at Mon Nov 25 16:44:25 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-2654_9/ukb-d-2654_9.vcf.gz ...
Read summary statistics for 12587824 SNPs.
Dropped 11286 SNPs with duplicated rs numbers.
Reading reference panel LD Score from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/reference/eur_w_ld_chr/[1-22] ...
Read reference panel LD Scores for 1290028 SNPs.
Removing partitioned LD Scores with zero variance.
Reading regression weight LD Score from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/reference/eur_w_ld_chr/[1-22] ...
Read regression weight LD Scores for 1290028 SNPs.
After merging with reference panel LD, 1283274 SNPs remain.
After merging with regression SNP LD, 1283274 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: -0.0008 (0.0026)
Lambda GC: 1.0136
Mean Chi^2: 1.0157
Intercept: 1.0186 (0.0062)
Ratio: 1.1868 (0.3935)
Analysis finished at Mon Nov 25 16:46:30 2019
Total time elapsed: 2.0m:5.6s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9503,
    "inflation_factor": 1.0053,
    "mean_EFFECT": -1.0416e-06,
    "n": 190094,
    "n_snps": 12587824,
    "n_clumped_hits": 0,
    "n_p_sig": 2,
    "n_mono": 0,
    "n_ns": 1210629,
    "n_mac": 0,
    "is_snpid_unique": false,
    "n_miss_EFFECT": 0,
    "n_miss_SE": 0,
    "n_miss_PVAL": 0,
    "n_miss_AF": 0,
    "n_miss_AF_reference": 358175,
    "n_est": 190809.6135,
    "ratio_se_n": 1.0019,
    "mean_diff": -2.6862e-06,
    "ratio_diff": 1.4443,
    "sd_y_est1": 0.1861,
    "sd_y_est2": 0.1864,
    "r2_sum1": 0,
    "r2_sum2": 0,
    "r2_sum3": 0,
    "r2_sum4": 0,
    "ldsc_nsnp_merge_refpanel_ld": 1283274,
    "ldsc_nsnp_merge_regression_ld": 1283274,
    "ldsc_observed_scale_h2_beta": "NA",
    "ldsc_observed_scale_h2_se": "NA",
    "ldsc_intercept_beta": 1.0186,
    "ldsc_intercept_se": 0.0062,
    "ldsc_lambda_gc": 1.0136,
    "ldsc_mean_chisq": 1.0157,
    "ldsc_ratio": 1.1847
}

Flags

name value
af_correlation FALSE
inflation_factor FALSE
n FALSE
is_snpid_non_unique TRUE
mean_EFFECT_nonfinite FALSE
mean_EFFECT_05 FALSE
mean_EFFECT_01 FALSE
mean_chisq FALSE
n_p_sig FALSE
miss_EFFECT FALSE
miss_SE FALSE
miss_PVAL FALSE
ldsc_ratio 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 94 0 12577175 0 NA NA NA NA NA NA NA NA
character REF 0 1.0000000 1 100 0 54814 0 NA NA NA NA NA NA NA NA
character ALT 0 1.0000000 1 342 0 32636 0 NA NA NA NA NA NA NA NA
numeric CHROM 0 1.0000000 NA NA NA NA NA 9.061283e+00 6.184868e+00 1.00000e+00 4.000000e+00 8.000000e+00 1.300000e+01 2.300000e+01 ▇▅▅▂▂
numeric POS 0 1.0000000 NA NA NA NA NA 7.895172e+07 5.595817e+07 3.02000e+02 3.278838e+07 7.000414e+07 1.148077e+08 2.492309e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA -1.000000e-06 2.742600e-03 -2.92840e-02 -8.603000e-04 -6.900000e-06 8.373000e-04 3.914160e-02 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 2.057700e-03 1.813500e-03 4.89600e-04 7.038000e-04 1.177800e-03 2.887200e-03 1.049480e-02 ▇▂▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.992572e-01 2.887905e-01 0.00000e+00 2.492298e-01 4.988707e-01 7.493488e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.992563e-01 2.887910e-01 0.00000e+00 2.492284e-01 4.988703e-01 7.493486e-01 1.000000e+00 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA 2.051363e-01 2.576319e-01 1.83550e-03 1.170490e-02 7.908530e-02 3.235452e-01 9.981640e-01 ▇▂▁▁▁
numeric AF_reference 358175 0.9715459 NA NA NA NA NA 2.076929e-01 2.494640e-01 0.00000e+00 8.586300e-03 1.002400e-01 3.290730e-01 1.000000e+00 ▇▂▁▁▁
numeric N 0 1.0000000 NA NA NA NA NA 1.900940e+05 0.000000e+00 1.90094e+05 1.900940e+05 1.900940e+05 1.900940e+05 1.900940e+05 ▁▁▇▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 692794 rs530212009 CA C 0.0004806 0.0010586 0.6498573 0.6498563 0.1105380 0.1894970 190094
1 693731 rs12238997 A G 0.0008145 0.0009988 0.4148232 0.4148223 0.1158410 0.1417730 190094
1 707522 rs371890604 G C 0.0001253 0.0011234 0.9111729 0.9111724 0.0972978 0.1293930 190094
1 717587 rs144155419 G A 0.0010303 0.0026980 0.7025706 0.7025700 0.0155305 0.0045926 190094
1 730087 rs148120343 T C -0.0013015 0.0013912 0.3495047 0.3495044 0.0565146 0.0127796 190094
1 731718 rs142557973 T C 0.0005051 0.0009477 0.5940555 0.5940545 0.1216850 0.1543530 190094
1 732032 rs61770163 A C 0.0005716 0.0010116 0.5720869 0.5720856 0.1210600 0.1555510 190094
1 734349 rs141242758 T C 0.0005946 0.0009483 0.5306461 0.5306452 0.1209220 0.1525560 190094
1 740284 rs61770167 C T 0.0064692 0.0043328 0.1354160 0.1354146 0.0058053 0.0023962 190094
1 742813 rs112573343 C T -0.0014837 0.0080066 0.8529850 0.8529851 0.0019615 0.1030350 190094
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
23 154923311 rs141127553 C T 0.0008495 0.0010820 0.4323635 0.4323625 0.0559986 0.0309934 190094
23 154923374 rs111332691 T A -0.0000362 0.0011922 0.9757791 0.9757786 0.0444754 0.0116556 190094
23 154925045 rs509981 C T -0.0009257 0.0005721 0.1056701 0.1056684 0.2448880 0.3634440 190094
23 154925895 rs538470 C T -0.0010431 0.0005850 0.0745847 0.0745820 0.2413400 0.3634440 190094
23 154927581 rs644138 G A -0.0005821 0.0005378 0.2791072 0.2791055 0.3012450 0.4635760 190094
23 154929412 rs557132 C T -0.0009351 0.0005723 0.1022659 0.1022642 0.2447450 0.3568210 190094
23 154929637 rs35185538 CT C -0.0008653 0.0005973 0.1474260 0.1474245 0.2287730 0.3011920 190094
23 154929952 rs4012982 CAA C -0.0009515 0.0006016 0.1136999 0.1136981 0.2390160 0.3165560 190094
23 154930230 rs781880 A G -0.0009349 0.0005721 0.1022471 0.1022454 0.2451860 0.3618540 190094
23 154930487 rs781879 T A 0.0038950 0.0019546 0.0462924 0.0462916 0.0196401 0.1263580 190094

bcf preview

1   692794  rs530212009 CA  C   .   PASS    AF=0.110538 ES:SE:LP:AF:SS:ID   0.000480564:0.0010586:0.187182:0.110538:190094:1_692794_CA_C
1   693731  rs12238997  A   G   .   PASS    AF=0.115841 ES:SE:LP:AF:SS:ID   0.00081446:0.000998802:0.382137:0.115841:190094:rs12238997
1   707522  rs371890604 G   C   .   PASS    AF=0.0972978    ES:SE:LP:AF:SS:ID   0.000125323:0.00112337:0.0403992:0.0972978:190094:rs371890604
1   717587  rs144155419 G   A   .   PASS    AF=0.0155305    ES:SE:LP:AF:SS:ID   0.00103026:0.00269805:0.15331:0.0155305:190094:rs144155419
1   730087  rs148120343 T   C   .   PASS    AF=0.0565146    ES:SE:LP:AF:SS:ID   -0.00130152:0.00139118:0.456547:0.0565146:190094:rs148120343
1   731718  rs58276399  T   C   .   PASS    AF=0.121685 ES:SE:LP:AF:SS:ID   0.00050512:0.000947746:0.226173:0.121685:190094:rs58276399
1   732032  rs61770163  A   C   .   PASS    AF=0.12106  ES:SE:LP:AF:SS:ID   0.000571559:0.00101164:0.242538:0.12106:190094:rs61770163
1   734349  rs141242758 T   C   .   PASS    AF=0.120922 ES:SE:LP:AF:SS:ID   0.000594605:0.000948301:0.275195:0.120922:190094:rs141242758
1   740284  rs61770167  C   T   .   PASS    AF=0.00580529   ES:SE:LP:AF:SS:ID   0.00646917:0.00433275:0.86833:0.00580529:190094:rs61770167
1   742813  rs112573343 C   T   .   PASS    AF=0.00196152   ES:SE:LP:AF:SS:ID   -0.00148372:0.00800665:0.0690586:0.00196152:190094:rs112573343
1   749963  rs529266287 T   TAA .   PASS    AF=0.869749 ES:SE:LP:AF:SS:ID   4.43069e-05:0.000934327:0.0167446:0.869749:190094:rs529266287
1   751343  rs28544273  T   A   .   PASS    AF=0.122867 ES:SE:LP:AF:SS:ID   0.000218914:0.000925849:0.0898635:0.122867:190094:rs28544273
1   751488  rs200141114 G   GA  .   PASS    AF=0.142766 ES:SE:LP:AF:SS:ID   0.000217867:0.000914453:0.0906103:0.142766:190094:rs200141114
1   751756  rs28527770  T   C   .   PASS    AF=0.122958 ES:SE:LP:AF:SS:ID   0.000201911:0.000924644:0.0824189:0.122958:190094:rs28527770
1   753405  rs3115860   C   A   .   PASS    AF=0.870967 ES:SE:LP:AF:SS:ID   -0.000131759:0.000901024:0.0536765:0.870967:190094:rs3115860
1   753425  rs3131970   T   C   .   PASS    AF=0.875573 ES:SE:LP:AF:SS:ID   -8.42763e-05:0.000916087:0.0330604:0.875573:190094:rs3131970
1   753541  rs2073813   G   A   .   PASS    AF=0.128534 ES:SE:LP:AF:SS:ID   0.000141842:0.000903352:0.0578768:0.128534:190094:rs2073813
1   754105  rs12184325  C   T   .   PASS    AF=0.0363057    ES:SE:LP:AF:SS:ID   -0.00240293:0.00163997:0.845086:0.0363057:190094:rs12184325
1   754182  rs3131969   A   G   .   PASS    AF=0.870568 ES:SE:LP:AF:SS:ID   -0.000113366:0.000900094:0.0458675:0.870568:190094:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.870672 ES:SE:LP:AF:SS:ID   -0.000117846:0.00090054:0.0477477:0.870672:190094:rs3131968
1   754334  rs3131967   T   C   .   PASS    AF=0.870565 ES:SE:LP:AF:SS:ID   -0.000112053:0.000900072:0.0453114:0.870565:190094:rs3131967
1   754433  rs150578204 G   A   .   PASS    AF=0.00503531   ES:SE:LP:AF:SS:ID   -0.00556879:0.00462066:0.641816:0.00503531:190094:rs150578204
1   754458  rs142682604 G   T   .   PASS    AF=0.00500306   ES:SE:LP:AF:SS:ID   -0.00548687:0.00463314:0.626518:0.00500306:190094:rs142682604
1   755435  rs184270342 T   G   .   PASS    AF=0.00567154   ES:SE:LP:AF:SS:ID   0.0084817:0.00443145:1.25474:0.00567154:190094:rs184270342
1   755890  rs3115858   A   T   .   PASS    AF=0.870656 ES:SE:LP:AF:SS:ID   -0.000116981:0.000898441:0.0474957:0.870656:190094:rs3115858
1   756434  rs61768170  G   C   .   PASS    AF=0.125912 ES:SE:LP:AF:SS:ID   6.7092e-05:0.000916811:0.0261045:0.125912:190094:rs61768170
1   756604  rs3131962   A   G   .   PASS    AF=0.870227 ES:SE:LP:AF:SS:ID   -6.27195e-05:0.000896239:0.0249319:0.870227:190094:rs3131962
1   757640  rs3115853   G   A   .   PASS    AF=0.869481 ES:SE:LP:AF:SS:ID   -5.91255e-05:0.000895414:0.0234882:0.869481:190094:rs3115853
1   757734  rs4951929   C   T   .   PASS    AF=0.870368 ES:SE:LP:AF:SS:ID   -0.000117778:0.00089701:0.047916:0.870368:190094:rs4951929
1   757936  rs4951862   C   A   .   PASS    AF=0.870374 ES:SE:LP:AF:SS:ID   -0.000116799:0.000897076:0.0474943:0.870374:190094:rs4951862
1   758144  rs3131956   A   G   .   PASS    AF=0.870381 ES:SE:LP:AF:SS:ID   -0.000117753:0.000897101:0.0479005:0.870381:190094:rs3131956
1   758626  rs3131954   C   T   .   PASS    AF=0.870831 ES:SE:LP:AF:SS:ID   -0.000104406:0.000899491:0.0421079:0.870831:190094:rs3131954
1   759293  rs10157329  T   A   .   PASS    AF=0.0989106    ES:SE:LP:AF:SS:ID   6.62979e-05:0.00104455:0.0225544:0.0989106:190094:rs10157329
1   759600  rs545998451 AGT A   .   PASS    AF=0.00651227   ES:SE:LP:AF:SS:ID   0.00521316:0.00403167:0.707755:0.00651227:190094:1_759600_AGT_A
1   759837  rs3115851   T   A   .   PASS    AF=0.87474  ES:SE:LP:AF:SS:ID   -0.000135072:0.000912955:0.0543434:0.87474:190094:rs3115851
1   761732  rs2286139   C   T   .   PASS    AF=0.864063 ES:SE:LP:AF:SS:ID   -0.00014591:0.000895016:0.0602317:0.864063:190094:rs2286139
1   761752  rs1057213   C   T   .   PASS    AF=0.869532 ES:SE:LP:AF:SS:ID   -0.000243566:0.000903992:0.103696:0.869532:190094:rs1057213
1   762273  rs3115849   G   A   .   PASS    AF=0.866506 ES:SE:LP:AF:SS:ID   -0.000138441:0.000903864:0.0563734:0.866506:190094:rs3115849
1   762485  rs12095200  C   A   .   PASS    AF=0.0985314    ES:SE:LP:AF:SS:ID   0.000563418:0.00108408:0.219496:0.0985314:190094:rs12095200
1   762589  rs3115848   G   C   .   PASS    AF=0.871615 ES:SE:LP:AF:SS:ID   -4.65197e-05:0.00091406:0.0179958:0.871615:190094:rs3115848
1   762592  rs3131950   C   G   .   PASS    AF=0.871615 ES:SE:LP:AF:SS:ID   -4.6496e-05:0.00091406:0.0179863:0.871615:190094:rs3131950
1   762601  rs3131949   T   C   .   PASS    AF=0.871616 ES:SE:LP:AF:SS:ID   -4.72073e-05:0.00091409:0.0182665:0.871616:190094:rs3131949
1   762632  rs3131948   T   A   .   PASS    AF=0.872007 ES:SE:LP:AF:SS:ID   -2.37723e-05:0.000914726:0.00909888:0.872007:190094:rs3131948
1   764191  rs7515915   T   G   .   PASS    AF=0.125446 ES:SE:LP:AF:SS:ID   0.00024116:0.000915863:0.101105:0.125446:190094:rs7515915
1   766007  rs61768174  A   C   .   PASS    AF=0.10548  ES:SE:LP:AF:SS:ID   0.000173567:0.000995897:0.0646721:0.10548:190094:rs61768174
1   766105  rs2519015   T   A   .   PASS    AF=0.855514 ES:SE:LP:AF:SS:ID   -0.000340878:0.000895255:0.152809:0.855514:190094:rs2519015
1   768116  rs376645387 A   AGTTTT  .   PASS    AF=0.838708 ES:SE:LP:AF:SS:ID   -0.00126353:0.000882656:0.817343:0.838708:190094:rs376645387
1   768253  rs2977608   A   C   .   PASS    AF=0.763462 ES:SE:LP:AF:SS:ID   -0.000758464:0.000709012:0.545561:0.763462:190094:rs2977608
1   768448  rs12562034  G   A   .   PASS    AF=0.105863 ES:SE:LP:AF:SS:ID   0.00120879:0.000977696:0.664897:0.105863:190094:rs12562034
1   768819  rs12562811  C   T   .   PASS    AF=0.00775589   ES:SE:LP:AF:SS:ID   -0.000779527:0.00361407:0.081326:0.00775589:190094:rs12562811