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-30630_raw,TotalVariants=13585233,VariantsNotRead=0,HarmonisedVariants=13585233,VariantsNotHarmonised=0,SwitchedAlleles=229,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-30630_raw/ukb-d-30630_raw_data.json --ref /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/QC/genomes/b37/human_g1k_v37.fasta; 1.1.1",
    "file_date": "2019-11-25T13:11:28.650181",
    "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-30630_raw/ukb-d-30630_raw.vcf.gz -O z /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-30630_raw/ukb-d-30630_raw_data.vcf.gz; Date=Mon Nov 25 14:13:53 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-30630_raw/ukb-d-30630_raw.vcf.gz; Date=Sat May  9 18:07:32 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-30630_raw/ukb-d-30630_raw.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-30630_raw/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 14:53:39 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-30630_raw/ukb-d-30630_raw.vcf.gz ...
Read summary statistics for 13585233 SNPs.
Dropped 12711 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, 1283501 SNPs remain.
After merging with regression SNP LD, 1283501 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.2115 (0.0352)
Lambda GC: 1.5929
Mean Chi^2: 2.3197
Intercept: 1.1259 (0.0169)
Ratio: 0.0954 (0.0128)
Analysis finished at Mon Nov 25 14:55:58 2019
Total time elapsed: 2.0m:19.01s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9521,
    "inflation_factor": 1.359,
    "mean_EFFECT": 4.4223e-06,
    "n": 313387,
    "n_snps": 13585233,
    "n_clumped_hits": 248,
    "n_p_sig": 49158,
    "n_mono": 0,
    "n_ns": 1251736,
    "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": 568956,
    "n_est": 314615.7118,
    "ratio_se_n": 1.002,
    "mean_diff": 0,
    "ratio_diff": 6.9283,
    "sd_y_est1": 0.2494,
    "sd_y_est2": 0.2499,
    "r2_sum1": 0.0063,
    "r2_sum2": 0.1011,
    "r2_sum3": 0.1007,
    "r2_sum4": 0.1007,
    "ldsc_nsnp_merge_refpanel_ld": 1283501,
    "ldsc_nsnp_merge_regression_ld": 1283501,
    "ldsc_observed_scale_h2_beta": 0.2115,
    "ldsc_observed_scale_h2_se": 0.0352,
    "ldsc_intercept_beta": 1.1259,
    "ldsc_intercept_se": 0.0169,
    "ldsc_lambda_gc": 1.5929,
    "ldsc_mean_chisq": 2.3197,
    "ldsc_ratio": 0.0954
}

Flags

name value
af_correlation FALSE
inflation_factor TRUE
n FALSE
is_snpid_non_unique TRUE
mean_EFFECT_nonfinite FALSE
mean_EFFECT_05 FALSE
mean_EFFECT_01 FALSE
mean_chisq TRUE
n_p_sig TRUE
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 94 0 13573186 0 NA NA NA NA NA NA NA NA
character REF 0 1.0000000 1 100 0 57079 0 NA NA NA NA NA NA NA NA
character ALT 0 1.0000000 1 342 0 33335 0 NA NA NA NA NA NA NA NA
numeric CHROM 0 1.0000000 NA NA NA NA NA 9.051232e+00 6.184941e+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 7.902532e+07 5.591514e+07 3.02000e+02 3.293044e+07 7.013909e+07 1.148601e+08 2.492309e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA 4.400000e-06 3.916800e-03 -1.29810e-01 -1.188500e-03 5.200000e-06 1.193000e-03 2.244300e-01 ▁▇▁▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 2.646600e-03 2.552900e-03 5.17000e-04 7.536000e-04 1.388600e-03 3.803100e-03 1.289200e-02 ▇▂▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.490373e-01 3.031995e-01 0.00000e+00 1.735601e-01 4.317000e-01 7.117099e-01 1.000000e+00 ▇▆▅▅▅
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.490368e-01 3.031997e-01 0.00000e+00 1.735642e-01 4.317011e-01 7.117085e-01 1.000000e+00 ▇▆▅▅▅
numeric AF 0 1.0000000 NA NA NA NA NA 1.908207e-01 2.544081e-01 1.00000e-03 7.434400e-03 6.004800e-02 2.953300e-01 9.990000e-01 ▇▂▁▁▁
numeric AF_reference 568956 0.9581195 NA NA NA NA NA 1.963469e-01 2.471052e-01 0.00000e+00 5.591000e-03 8.426520e-02 3.081070e-01 1.000000e+00 ▇▂▁▁▁
numeric N 0 1.0000000 NA NA NA NA NA 3.133870e+05 0.000000e+00 3.13387e+05 3.133870e+05 3.133870e+05 3.133870e+05 3.133870e+05 ▁▁▇▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 692794 rs530212009 CA C 0.0005702 0.0011034 0.6052893 0.6052940 0.1105400 0.1894970 313387
1 693731 rs12238997 A G 0.0009297 0.0010423 0.3723703 0.3723886 0.1158700 0.1417730 313387
1 707522 rs371890604 G C 0.0015800 0.0011729 0.1779299 0.1779518 0.0972180 0.1293930 313387
1 717587 rs144155419 G A 0.0001576 0.0027929 0.9549899 0.9549888 0.0157040 0.0045926 313387
1 723329 rs189787166 A T 0.0084233 0.0082359 0.3064298 0.3064242 0.0017383 0.0003994 313387
1 730087 rs148120343 T C 0.0018235 0.0014521 0.2091900 0.2092003 0.0564720 0.0127796 313387
1 731718 rs142557973 T C 0.0006168 0.0009886 0.5327004 0.5326974 0.1217500 0.1543530 313387
1 732032 rs61770163 A C 0.0008370 0.0010552 0.4276495 0.4276473 0.1210900 0.1555510 313387
1 734349 rs141242758 T C 0.0006448 0.0009892 0.5144699 0.5144744 0.1209700 0.1525560 313387
1 740284 rs61770167 C T 0.0027278 0.0045347 0.5474797 0.5474809 0.0057566 0.0023962 313387
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
23 154923311 rs141127553 C T 0.0006848 0.0011408 0.5482896 0.5483018 0.056109 0.0309934 313387
23 154923374 rs111332691 T A 0.0010375 0.0012487 0.4060598 0.4060504 0.045003 0.0116556 313387
23 154925045 rs509981 C T 0.0027651 0.0006028 0.0000045 0.0000045 0.245750 0.3634440 313387
23 154925895 rs538470 C T 0.0026911 0.0006166 0.0000127 0.0000127 0.242040 0.3634440 313387
23 154927581 rs644138 G A 0.0026058 0.0005669 0.0000043 0.0000043 0.302240 0.4635760 313387
23 154929412 rs557132 C T 0.0027645 0.0006029 0.0000045 0.0000045 0.245600 0.3568210 313387
23 154929637 rs35185538 CT C 0.0032046 0.0006292 0.0000004 0.0000004 0.229990 0.3011920 313387
23 154929952 rs4012982 CAA C 0.0028074 0.0006341 0.0000095 0.0000095 0.239540 0.3165560 313387
23 154930230 rs781880 A G 0.0027218 0.0006029 0.0000063 0.0000063 0.245980 0.3618540 313387
23 154930487 rs781879 T A 0.0011771 0.0020712 0.5698296 0.5698191 0.019483 0.1263580 313387

bcf preview

1   692794  rs530212009 CA  C   .   PASS    AF=0.11054  ES:SE:LP:AF:SS:ID   0.00057024:0.0011034:0.218037:0.11054:313387:1_692794_CA_C
1   693731  rs12238997  A   G   .   PASS    AF=0.11587  ES:SE:LP:AF:SS:ID   0.00092974:0.0010423:0.429025:0.11587:313387:rs12238997
1   707522  rs371890604 G   C   .   PASS    AF=0.097218 ES:SE:LP:AF:SS:ID   0.00158:0.0011729:0.749751:0.097218:313387:rs371890604
1   717587  rs144155419 G   A   .   PASS    AF=0.015704 ES:SE:LP:AF:SS:ID   0.00015764:0.0027929:0.0200012:0.015704:313387:rs144155419
1   723329  rs189787166 A   T   .   PASS    AF=0.0017383    ES:SE:LP:AF:SS:ID   0.0084233:0.0082359:0.513669:0.0017383:313387:rs189787166
1   730087  rs148120343 T   C   .   PASS    AF=0.056472 ES:SE:LP:AF:SS:ID   0.0018235:0.0014521:0.679459:0.056472:313387:rs148120343
1   731718  rs58276399  T   C   .   PASS    AF=0.12175  ES:SE:LP:AF:SS:ID   0.0006168:0.00098863:0.273517:0.12175:313387:rs58276399
1   732032  rs61770163  A   C   .   PASS    AF=0.12109  ES:SE:LP:AF:SS:ID   0.00083701:0.0010552:0.368912:0.12109:313387:rs61770163
1   734349  rs141242758 T   C   .   PASS    AF=0.12097  ES:SE:LP:AF:SS:ID   0.00064482:0.00098916:0.28864:0.12097:313387:rs141242758
1   740284  rs61770167  C   T   .   PASS    AF=0.0057566    ES:SE:LP:AF:SS:ID   0.0027278:0.0045347:0.261632:0.0057566:313387:rs61770167
1   742813  rs112573343 C   T   .   PASS    AF=0.0018544    ES:SE:LP:AF:SS:ID   0.0059525:0.0086136:0.310221:0.0018544:313387:rs112573343
1   749963  rs529266287 T   TAA .   PASS    AF=0.86971  ES:SE:LP:AF:SS:ID   -0.00057221:0.00097515:0.25388:0.86971:313387:rs529266287
1   750230  rs190826124 G   C   .   PASS    AF=0.0015215    ES:SE:LP:AF:SS:ID   -0.01021:0.0088534:0.60408:0.0015215:313387:rs190826124
1   751343  rs28544273  T   A   .   PASS    AF=0.12294  ES:SE:LP:AF:SS:ID   0.00062391:0.00096583:0.285427:0.12294:313387:rs28544273
1   751488  rs200141114 G   GA  .   PASS    AF=0.14275  ES:SE:LP:AF:SS:ID   0.00030344:0.00095448:0.12462:0.14275:313387:rs200141114
1   751756  rs28527770  T   C   .   PASS    AF=0.12306  ES:SE:LP:AF:SS:ID   0.00059558:0.00096447:0.270115:0.12306:313387:rs28527770
1   753405  rs3115860   C   A   .   PASS    AF=0.87094  ES:SE:LP:AF:SS:ID   -0.0007507:0.00094008:0.372061:0.87094:313387:rs3115860
1   753425  rs3131970   T   C   .   PASS    AF=0.87547  ES:SE:LP:AF:SS:ID   -0.00060174:0.00095544:0.276684:0.87547:313387:rs3131970
1   753541  rs2073813   G   A   .   PASS    AF=0.12862  ES:SE:LP:AF:SS:ID   0.00069315:0.00094234:0.335358:0.12862:313387:rs2073813
1   754105  rs12184325  C   T   .   PASS    AF=0.036319 ES:SE:LP:AF:SS:ID   -0.0022666:0.0017103:0.732664:0.036319:313387:rs12184325
1   754182  rs3131969   A   G   .   PASS    AF=0.87053  ES:SE:LP:AF:SS:ID   -0.00075141:0.00093907:0.373024:0.87053:313387:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.87064  ES:SE:LP:AF:SS:ID   -0.00083232:0.00093952:0.425193:0.87064:313387:rs3131968
1   754334  rs3131967   T   C   .   PASS    AF=0.87053  ES:SE:LP:AF:SS:ID   -0.00074397:0.00093904:0.368353:0.87053:313387:rs3131967
1   754433  rs150578204 G   A   .   PASS    AF=0.0050421    ES:SE:LP:AF:SS:ID   0.0016279:0.004816:0.133506:0.0050421:313387:rs150578204
1   754458  rs142682604 G   T   .   PASS    AF=0.0050087    ES:SE:LP:AF:SS:ID   0.0017925:0.0048289:0.148442:0.0050087:313387:rs142682604
1   755435  rs184270342 T   G   .   PASS    AF=0.00552  ES:SE:LP:AF:SS:ID   -0.00023847:0.0046956:0.017955:0.00552:313387:rs184270342
1   755890  rs3115858   A   T   .   PASS    AF=0.87062  ES:SE:LP:AF:SS:ID   -0.00081193:0.00093747:0.412918:0.87062:313387:rs3115858
1   756434  rs61768170  G   C   .   PASS    AF=0.12595  ES:SE:LP:AF:SS:ID   0.00081997:0.00095642:0.407535:0.12595:313387:rs61768170
1   756604  rs3131962   A   G   .   PASS    AF=0.87018  ES:SE:LP:AF:SS:ID   -0.00090955:0.00093522:0.480461:0.87018:313387:rs3131962
1   757640  rs3115853   G   A   .   PASS    AF=0.86946  ES:SE:LP:AF:SS:ID   -0.00076587:0.00093439:0.38466:0.86946:313387:rs3115853
1   757734  rs4951929   C   T   .   PASS    AF=0.87033  ES:SE:LP:AF:SS:ID   -0.00086315:0.00093602:0.448001:0.87033:313387:rs4951929
1   757936  rs4951862   C   A   .   PASS    AF=0.87034  ES:SE:LP:AF:SS:ID   -0.00086833:0.00093608:0.451475:0.87034:313387:rs4951862
1   758144  rs3131956   A   G   .   PASS    AF=0.87035  ES:SE:LP:AF:SS:ID   -0.00087002:0.00093611:0.452619:0.87035:313387:rs3131956
1   758626  rs3131954   C   T   .   PASS    AF=0.87079  ES:SE:LP:AF:SS:ID   -0.00082789:0.0009385:0.422853:0.87079:313387:rs3131954
1   759293  rs10157329  T   A   .   PASS    AF=0.098835 ES:SE:LP:AF:SS:ID   0.0011859:0.0010907:0.557677:0.098835:313387:rs10157329
1   759600  rs545998451 AGT A   .   PASS    AF=0.0064046    ES:SE:LP:AF:SS:ID   -0.00081308:0.0042427:0.0715939:0.0064046:313387:1_759600_AGT_A
1   759837  rs3115851   T   A   .   PASS    AF=0.87464  ES:SE:LP:AF:SS:ID   -0.00081266:0.00095226:0.405121:0.87464:313387:rs3115851
1   761732  rs2286139   C   T   .   PASS    AF=0.86407  ES:SE:LP:AF:SS:ID   -0.00070099:0.00093411:0.343911:0.86407:313387:rs2286139
1   761752  rs1057213   C   T   .   PASS    AF=0.86946  ES:SE:LP:AF:SS:ID   -0.00086404:0.00094298:0.444289:0.86946:313387:rs1057213
1   762273  rs3115849   G   A   .   PASS    AF=0.86641  ES:SE:LP:AF:SS:ID   -0.00067363:0.00094318:0.323215:0.86641:313387:rs3115849
1   762485  rs12095200  C   A   .   PASS    AF=0.098823 ES:SE:LP:AF:SS:ID   0.00043567:0.0011286:0.155225:0.098823:313387:rs12095200
1   762589  rs3115848   G   C   .   PASS    AF=0.87158  ES:SE:LP:AF:SS:ID   -0.00080464:0.00095389:0.399103:0.87158:313387:rs3115848
1   762592  rs3131950   C   G   .   PASS    AF=0.87158  ES:SE:LP:AF:SS:ID   -0.00080473:0.00095389:0.399169:0.87158:313387:rs3131950
1   762601  rs3131949   T   C   .   PASS    AF=0.87158  ES:SE:LP:AF:SS:ID   -0.00080728:0.00095391:0.400783:0.87158:313387:rs3131949
1   762632  rs3131948   T   A   .   PASS    AF=0.87194  ES:SE:LP:AF:SS:ID   -0.00079553:0.00095443:0.393028:0.87194:313387:rs3131948
1   764191  rs7515915   T   G   .   PASS    AF=0.12557  ES:SE:LP:AF:SS:ID   0.0007869:0.00095511:0.387206:0.12557:313387:rs7515915
1   766007  rs61768174  A   C   .   PASS    AF=0.1054   ES:SE:LP:AF:SS:ID   0.0012004:0.0010403:0.604569:0.1054:313387:rs61768174
1   766105  rs2519015   T   A   .   PASS    AF=0.85541  ES:SE:LP:AF:SS:ID   -0.0011531:0.0009337:0.663901:0.85541:313387:rs2519015
1   767393  rs538667473 A   C   .   PASS    AF=0.001657 ES:SE:LP:AF:SS:ID   0.0099844:0.0082554:0.644951:0.001657:313387:rs538667473
1   768116  rs376645387 A   AGTTTT  .   PASS    AF=0.83824  ES:SE:LP:AF:SS:ID   0.00081335:0.00091857:0.424916:0.83824:313387:rs376645387