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-22606_0,TotalVariants=13566930,VariantsNotRead=0,HarmonisedVariants=13566930,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-22606_0/ukb-d-22606_0_data.json --ref /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/QC/genomes/b37/human_g1k_v37.fasta; 1.1.1",
    "file_date": "2019-11-25T15:14:37.859231",
    "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-22606_0/ukb-d-22606_0.vcf.gz -O z /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-22606_0/ukb-d-22606_0_data.vcf.gz; Date=Mon Nov 25 15:51:04 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-22606_0/ukb-d-22606_0.vcf.gz; Date=Sat May  9 18:59:16 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-22606_0/ukb-d-22606_0.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-22606_0/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 16:38:16 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-22606_0/ukb-d-22606_0.vcf.gz ...
Read summary statistics for 13566930 SNPs.
Dropped 12681 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, 1283504 SNPs remain.
After merging with regression SNP LD, 1283504 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.027 (0.0054)
Lambda GC: 1.0407
Mean Chi^2: 1.0503
Intercept: 1.0031 (0.0058)
Ratio: 0.0613 (0.1162)
Analysis finished at Mon Nov 25 16:40:32 2019
Total time elapsed: 2.0m:15.93s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9521,
    "inflation_factor": 1.0317,
    "mean_EFFECT": -0,
    "n": 90617,
    "n_snps": 13566930,
    "n_clumped_hits": 0,
    "n_p_sig": 1,
    "n_mono": 0,
    "n_ns": 1251240,
    "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": 563198,
    "n_est": 90939.5631,
    "ratio_se_n": 1.0018,
    "mean_diff": -0,
    "ratio_diff": 21.9083,
    "sd_y_est1": 0.4259,
    "sd_y_est2": 0.4267,
    "r2_sum1": 0,
    "r2_sum2": 0,
    "r2_sum3": 0,
    "r2_sum4": 0,
    "ldsc_nsnp_merge_refpanel_ld": 1283504,
    "ldsc_nsnp_merge_regression_ld": 1283504,
    "ldsc_observed_scale_h2_beta": 0.027,
    "ldsc_observed_scale_h2_se": 0.0054,
    "ldsc_intercept_beta": 1.0031,
    "ldsc_intercept_se": 0.0058,
    "ldsc_lambda_gc": 1.0407,
    "ldsc_mean_chisq": 1.0503,
    "ldsc_ratio": 0.0616
}

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 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 13554913 0 NA NA NA NA NA NA NA NA
character REF 0 1.0000000 1 100 0 57048 0 NA NA NA NA NA NA NA NA
character ALT 0 1.0000000 1 342 0 33333 0 NA NA NA NA NA NA NA NA
numeric CHROM 0 1.0000000 NA NA NA NA NA 9.051348e+00 6.184958e+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 7.902470e+07 5.591654e+07 3.02000e+02 3.292786e+07 7.013474e+07 1.148620e+08 2.492309e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA -1.640000e-05 1.169500e-02 -1.55196e-01 -3.117100e-03 4.600000e-06 3.154600e-03 1.328350e-01 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 8.374100e-03 8.070100e-03 1.65170e-03 2.392600e-03 4.400900e-03 1.202480e-02 4.058850e-02 ▇▂▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.947110e-01 2.902451e-01 0.00000e+00 2.421040e-01 4.932772e-01 7.459917e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.947092e-01 2.902461e-01 0.00000e+00 2.421012e-01 4.932753e-01 7.459903e-01 1.000000e+00 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA 1.910661e-01 2.544735e-01 1.00000e-03 7.499200e-03 6.029850e-02 2.957758e-01 9.990000e-01 ▇▂▁▁▁
numeric AF_reference 563198 0.9584874 NA NA NA NA NA 1.965231e-01 2.471450e-01 0.00000e+00 5.790700e-03 8.446490e-02 3.085060e-01 1.000000e+00 ▇▂▁▁▁
numeric N 0 1.0000000 NA NA NA NA NA 9.061700e+04 0.000000e+00 9.06170e+04 9.061700e+04 9.061700e+04 9.061700e+04 9.061700e+04 ▁▁▇▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 692794 rs530212009 CA C -0.0039648 0.0034953 0.2566540 0.2566511 0.1113950 0.1894970 90617
1 693731 rs12238997 A G -0.0021710 0.0033101 0.5119046 0.5119030 0.1163860 0.1417730 90617
1 707522 rs371890604 G C -0.0002022 0.0037190 0.9566481 0.9566479 0.0978590 0.1293930 90617
1 717587 rs144155419 G A -0.0140304 0.0088759 0.1139449 0.1139402 0.0157467 0.0045926 90617
1 723329 rs189787166 A T 0.0180278 0.0258648 0.4858028 0.4858020 0.0017779 0.0003994 90617
1 730087 rs148120343 T C -0.0014151 0.0045878 0.7577396 0.7577401 0.0569496 0.0127796 90617
1 731718 rs142557973 T C -0.0019601 0.0031410 0.5326145 0.5326127 0.1222710 0.1543530 90617
1 732032 rs61770163 A C -0.0018508 0.0033492 0.5805224 0.5805226 0.1219580 0.1555510 90617
1 734349 rs141242758 T C -0.0022752 0.0031435 0.4692032 0.4692015 0.1215020 0.1525560 90617
1 740284 rs61770167 C T 0.0199956 0.0144240 0.1656659 0.1656636 0.0057474 0.0023962 90617
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
23 154923311 rs141127553 C T 0.0072522 0.0036740 0.0483894 0.0483869 0.0553245 0.0309934 90617
23 154923374 rs111332691 T A -0.0050485 0.0040004 0.2069512 0.2069477 0.0448150 0.0116556 90617
23 154925045 rs509981 C T 0.0007896 0.0019273 0.6820434 0.6820419 0.2445590 0.3634440 90617
23 154925895 rs538470 C T 0.0013980 0.0019703 0.4779902 0.4779867 0.2410610 0.3634440 90617
23 154927581 rs644138 G A 0.0024528 0.0018128 0.1760492 0.1760459 0.3002870 0.4635760 90617
23 154929412 rs557132 C T 0.0008626 0.0019278 0.6545442 0.6545429 0.2444160 0.3568210 90617
23 154929637 rs35185538 CT C 0.0013172 0.0020130 0.5128850 0.5128840 0.2287530 0.3011920 90617
23 154929952 rs4012982 CAA C 0.0010128 0.0020290 0.6176679 0.6176669 0.2383300 0.3165560 90617
23 154930230 rs781880 A G 0.0008571 0.0019272 0.6565155 0.6565144 0.2448690 0.3618540 90617
23 154930487 rs781879 T A -0.0060916 0.0065352 0.3512780 0.3512760 0.0196492 0.1263580 90617

bcf preview

1   692794  rs530212009 CA  C   .   PASS    AF=0.111395 ES:SE:LP:AF:SS:ID   -0.00396482:0.00349526:0.590652:0.111395:90617:1_692794_CA_C
1   693731  rs12238997  A   G   .   PASS    AF=0.116386 ES:SE:LP:AF:SS:ID   -0.00217102:0.0033101:0.290811:0.116386:90617:rs12238997
1   707522  rs371890604 G   C   .   PASS    AF=0.097859 ES:SE:LP:AF:SS:ID   -0.000202168:0.00371902:0.0192478:0.097859:90617:rs371890604
1   717587  rs144155419 G   A   .   PASS    AF=0.0157467    ES:SE:LP:AF:SS:ID   -0.0140304:0.00887591:0.943305:0.0157467:90617:rs144155419
1   723329  rs189787166 A   T   .   PASS    AF=0.0017779    ES:SE:LP:AF:SS:ID   0.0180278:0.0258648:0.31354:0.0017779:90617:rs189787166
1   730087  rs148120343 T   C   .   PASS    AF=0.0569496    ES:SE:LP:AF:SS:ID   -0.0014151:0.00458778:0.12048:0.0569496:90617:rs148120343
1   731718  rs58276399  T   C   .   PASS    AF=0.122271 ES:SE:LP:AF:SS:ID   -0.00196008:0.00314104:0.273587:0.122271:90617:rs58276399
1   732032  rs61770163  A   C   .   PASS    AF=0.121958 ES:SE:LP:AF:SS:ID   -0.00185084:0.0033492:0.236181:0.121958:90617:rs61770163
1   734349  rs141242758 T   C   .   PASS    AF=0.121502 ES:SE:LP:AF:SS:ID   -0.00227517:0.00314346:0.328639:0.121502:90617:rs141242758
1   740284  rs61770167  C   T   .   PASS    AF=0.00574737   ES:SE:LP:AF:SS:ID   0.0199956:0.014424:0.780767:0.00574737:90617:rs61770167
1   742813  rs112573343 C   T   .   PASS    AF=0.00181683   ES:SE:LP:AF:SS:ID   4.11369e-05:0.0276516:0.000515814:0.00181683:90617:rs112573343
1   749963  rs529266287 T   TAA .   PASS    AF=0.869026 ES:SE:LP:AF:SS:ID   0.00220319:0.00309234:0.322231:0.869026:90617:rs529266287
1   750230  rs190826124 G   C   .   PASS    AF=0.00160564   ES:SE:LP:AF:SS:ID   0.0309746:0.0272607:0.591998:0.00160564:90617:rs190826124
1   751343  rs28544273  T   A   .   PASS    AF=0.123594 ES:SE:LP:AF:SS:ID   -0.00183748:0.00306573:0.26048:0.123594:90617:rs28544273
1   751488  rs200141114 G   GA  .   PASS    AF=0.143072 ES:SE:LP:AF:SS:ID   -0.000634832:0.0030349:0.0786726:0.143072:90617:rs200141114
1   751756  rs28527770  T   C   .   PASS    AF=0.123729 ES:SE:LP:AF:SS:ID   -0.00177926:0.00306129:0.25096:0.123729:90617:rs28527770
1   753405  rs3115860   C   A   .   PASS    AF=0.870018 ES:SE:LP:AF:SS:ID   0.00192698:0.00298293:0.285436:0.870018:90617:rs3115860
1   753425  rs3131970   T   C   .   PASS    AF=0.874674 ES:SE:LP:AF:SS:ID   0.00163932:0.00303149:0.230126:0.874674:90617:rs3131970
1   753541  rs2073813   G   A   .   PASS    AF=0.129419 ES:SE:LP:AF:SS:ID   -0.0022432:0.00299216:0.343479:0.129419:90617:rs2073813
1   754105  rs12184325  C   T   .   PASS    AF=0.0358211    ES:SE:LP:AF:SS:ID   0.00535708:0.00546451:0.485559:0.0358211:90617:rs12184325
1   754182  rs3131969   A   G   .   PASS    AF=0.869667 ES:SE:LP:AF:SS:ID   0.00209486:0.00298046:0.316825:0.869667:90617:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.869744 ES:SE:LP:AF:SS:ID   0.0020545:0.00298177:0.309085:0.869744:90617:rs3131968
1   754334  rs3131967   T   C   .   PASS    AF=0.869663 ES:SE:LP:AF:SS:ID   0.00210988:0.00298034:0.319674:0.869663:90617:rs3131967
1   754433  rs150578204 G   A   .   PASS    AF=0.00530957   ES:SE:LP:AF:SS:ID   0.0103728:0.0148912:0.313299:0.00530957:90617:rs150578204
1   754458  rs142682604 G   T   .   PASS    AF=0.00527495   ES:SE:LP:AF:SS:ID   0.0101246:0.0149282:0.303089:0.00527495:90617:rs142682604
1   755435  rs184270342 T   G   .   PASS    AF=0.00566967   ES:SE:LP:AF:SS:ID   0.0162951:0.0146582:0.574655:0.00566967:90617:rs184270342
1   755890  rs3115858   A   T   .   PASS    AF=0.869648 ES:SE:LP:AF:SS:ID   0.00184397:0.00297419:0.271431:0.869648:90617:rs3115858
1   756434  rs61768170  G   C   .   PASS    AF=0.126804 ES:SE:LP:AF:SS:ID   -0.00200358:0.00303609:0.29302:0.126804:90617:rs61768170
1   756604  rs3131962   A   G   .   PASS    AF=0.86918  ES:SE:LP:AF:SS:ID   0.00163701:0.00296666:0.23576:0.86918:90617:rs3131962
1   757640  rs3115853   G   A   .   PASS    AF=0.86857  ES:SE:LP:AF:SS:ID   0.00185433:0.00296478:0.274355:0.86857:90617:rs3115853
1   757734  rs4951929   C   T   .   PASS    AF=0.869333 ES:SE:LP:AF:SS:ID   0.0018093:0.00296936:0.265751:0.869333:90617:rs4951929
1   757936  rs4951862   C   A   .   PASS    AF=0.869339 ES:SE:LP:AF:SS:ID   0.00180989:0.00296956:0.265835:0.869339:90617:rs4951862
1   758144  rs3131956   A   G   .   PASS    AF=0.869341 ES:SE:LP:AF:SS:ID   0.00181265:0.00296958:0.266325:0.869341:90617:rs3131956
1   758626  rs3131954   C   T   .   PASS    AF=0.869817 ES:SE:LP:AF:SS:ID   0.00172431:0.00297737:0.24988:0.869817:90617:rs3131954
1   759293  rs10157329  T   A   .   PASS    AF=0.0991224    ES:SE:LP:AF:SS:ID   -0.00110376:0.00346454:0.124916:0.0991224:90617:rs10157329
1   759600  rs545998451 AGT A   .   PASS    AF=0.00650958   ES:SE:LP:AF:SS:ID   0.0168648:0.0133492:0.685156:0.00650958:90617:1_759600_AGT_A
1   759837  rs3115851   T   A   .   PASS    AF=0.873813 ES:SE:LP:AF:SS:ID   0.00188189:0.00302161:0.27294:0.873813:90617:rs3115851
1   761732  rs2286139   C   T   .   PASS    AF=0.863196 ES:SE:LP:AF:SS:ID   0.00254665:0.00296401:0.40867:0.863196:90617:rs2286139
1   761752  rs1057213   C   T   .   PASS    AF=0.86861  ES:SE:LP:AF:SS:ID   0.00229427:0.00299334:0.353198:0.86861:90617:rs1057213
1   762273  rs3115849   G   A   .   PASS    AF=0.865497 ES:SE:LP:AF:SS:ID   0.00214352:0.00299383:0.324216:0.865497:90617:rs3115849
1   762485  rs12095200  C   A   .   PASS    AF=0.0994329    ES:SE:LP:AF:SS:ID   -0.00168429:0.00358316:0.194965:0.0994329:90617:rs12095200
1   762589  rs3115848   G   C   .   PASS    AF=0.870776 ES:SE:LP:AF:SS:ID   0.00221355:0.00302791:0.332781:0.870776:90617:rs3115848
1   762592  rs3131950   C   G   .   PASS    AF=0.870776 ES:SE:LP:AF:SS:ID   0.00221359:0.00302791:0.332788:0.870776:90617:rs3131950
1   762601  rs3131949   T   C   .   PASS    AF=0.870773 ES:SE:LP:AF:SS:ID   0.00221382:0.00302792:0.332829:0.870773:90617:rs3131949
1   762632  rs3131948   T   A   .   PASS    AF=0.87114  ES:SE:LP:AF:SS:ID   0.00224813:0.00302934:0.339119:0.87114:90617:rs3131948
1   764191  rs7515915   T   G   .   PASS    AF=0.1264   ES:SE:LP:AF:SS:ID   -0.00206413:0.00303265:0.304428:0.1264:90617:rs7515915
1   766007  rs61768174  A   C   .   PASS    AF=0.105965 ES:SE:LP:AF:SS:ID   -0.000961371:0.00329625:0.113199:0.105965:90617:rs61768174
1   766105  rs2519015   T   A   .   PASS    AF=0.85452  ES:SE:LP:AF:SS:ID   0.00209693:0.0029629:0.319558:0.85452:90617:rs2519015
1   767393  rs538667473 A   C   .   PASS    AF=0.0016878    ES:SE:LP:AF:SS:ID   0.0200192:0.0259518:0.356083:0.0016878:90617:rs538667473
1   768116  rs376645387 A   AGTTTT  .   PASS    AF=0.839298 ES:SE:LP:AF:SS:ID   0.00124457:0.00292699:0.17348:0.839298:90617:rs376645387