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-22506_111,TotalVariants=10552526,VariantsNotRead=0,HarmonisedVariants=10552526,VariantsNotHarmonised=0,SwitchedAlleles=214,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-22506_111/ukb-d-22506_111_data.json --ref /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/QC/genomes/b37/human_g1k_v37.fasta; 1.1.1",
    "file_date": "2019-11-25T13:07:16.547661",
    "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-22506_111/ukb-d-22506_111.vcf.gz -O z /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-22506_111/ukb-d-22506_111_data.vcf.gz; Date=Mon Nov 25 13:51:49 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-22506_111/ukb-d-22506_111.vcf.gz; Date=Sat May  9 18:58:53 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-22506_111/ukb-d-22506_111.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-22506_111/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 14:46:54 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-22506_111/ukb-d-22506_111.vcf.gz ...
Read summary statistics for 10552526 SNPs.
Dropped 8460 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, 1280896 SNPs remain.
After merging with regression SNP LD, 1280896 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0096 (0.0049)
Lambda GC: 1.0265
Mean Chi^2: 1.0222
Intercept: 1.005 (0.0063)
Ratio: 0.2261 (0.2827)
Analysis finished at Mon Nov 25 14:48:38 2019
Total time elapsed: 1.0m:43.79s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9442,
    "inflation_factor": 1.0249,
    "mean_EFFECT": -1.4593e-06,
    "n": 91353,
    "n_snps": 10552526,
    "n_clumped_hits": 0,
    "n_p_sig": 1,
    "n_mono": 0,
    "n_ns": 1114751,
    "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": 207694,
    "n_est": 91447.9379,
    "ratio_se_n": 1.0005,
    "mean_diff": -7.2747e-06,
    "ratio_diff": 7.8632,
    "sd_y_est1": 0.151,
    "sd_y_est2": 0.1511,
    "r2_sum1": 0,
    "r2_sum2": 0,
    "r2_sum3": 0,
    "r2_sum4": 0,
    "ldsc_nsnp_merge_refpanel_ld": 1280896,
    "ldsc_nsnp_merge_regression_ld": 1280896,
    "ldsc_observed_scale_h2_beta": 0.0096,
    "ldsc_observed_scale_h2_se": 0.0049,
    "ldsc_intercept_beta": 1.005,
    "ldsc_intercept_se": 0.0063,
    "ldsc_lambda_gc": 1.0265,
    "ldsc_mean_chisq": 1.0222,
    "ldsc_ratio": 0.2252
}

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 10544634 0 NA NA NA NA NA NA NA NA
character REF 0 1.0000000 1 100 0 49864 0 NA NA NA NA NA NA NA NA
character ALT 0 1.0000000 1 342 0 30826 0 NA NA NA NA NA NA NA NA
numeric CHROM 0 1.0000000 NA NA NA NA NA 9.075281e+00 6.178367e+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 7.879828e+07 5.605385e+07 3.02000e+02 3.256183e+07 6.974314e+07 1.147425e+08 2.492309e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA -1.500000e-06 1.951800e-03 -1.77392e-02 -8.427000e-04 -1.340000e-05 8.212000e-04 2.323120e-02 ▁▂▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 1.611400e-03 1.084200e-03 5.83700e-04 7.870000e-04 1.112400e-03 2.121900e-03 6.075800e-03 ▇▂▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.965967e-01 2.893713e-01 0.00000e+00 2.452088e-01 4.947160e-01 7.473086e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.965950e-01 2.893724e-01 0.00000e+00 2.452057e-01 4.947146e-01 7.473082e-01 1.000000e+00 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA 2.423110e-01 2.625580e-01 5.88510e-03 2.999580e-02 1.316830e-01 3.878720e-01 9.941150e-01 ▇▂▂▁▁
numeric AF_reference 207694 0.9803181 NA NA NA NA NA 2.422361e-01 2.535114e-01 0.00000e+00 3.095050e-02 1.485620e-01 3.849840e-01 1.000000e+00 ▇▂▂▁▁
numeric N 0 1.0000000 NA NA NA NA NA 9.135300e+04 0.000000e+00 9.13530e+04 9.135300e+04 9.135300e+04 9.135300e+04 9.135300e+04 ▁▁▇▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 692794 rs530212009 CA C -0.0015794 0.0012352 0.2010282 0.2010243 0.1114110 0.1894970 91353
1 693731 rs12238997 A G -0.0014751 0.0011699 0.2073782 0.2073733 0.1163870 0.1417730 91353
1 707522 rs371890604 G C -0.0024264 0.0013152 0.0650459 0.0650429 0.0978018 0.1293930 91353
1 717587 rs144155419 G A -0.0002713 0.0031379 0.9311130 0.9311129 0.0157459 0.0045926 91353
1 730087 rs148120343 T C -0.0009376 0.0016222 0.5632757 0.5632744 0.0569530 0.0127796 91353
1 731718 rs142557973 T C -0.0014220 0.0011103 0.2002940 0.2002908 0.1222870 0.1543530 91353
1 732032 rs61770163 A C -0.0019382 0.0011840 0.1016410 0.1016365 0.1219550 0.1555510 91353
1 734349 rs141242758 T C -0.0014344 0.0011112 0.1967361 0.1967332 0.1215170 0.1525560 91353
1 749963 rs529266287 T TAA 0.0011604 0.0010930 0.2883872 0.2883841 0.8690100 0.7641770 91353
1 751343 rs28544273 T A -0.0010720 0.0010836 0.3225537 0.3225502 0.1236040 0.2426120 91353
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
23 154923311 rs141127553 C T -0.0011468 0.0012987 0.3772020 0.3771992 0.0553192 0.0309934 91353
23 154923374 rs111332691 T A 0.0008943 0.0014132 0.5268488 0.5268482 0.0448863 0.0116556 91353
23 154925045 rs509981 C T -0.0003923 0.0006814 0.5648446 0.5648430 0.2442380 0.3634440 91353
23 154925895 rs538470 C T -0.0003778 0.0006967 0.5876043 0.5876028 0.2407140 0.3634440 91353
23 154927581 rs644138 G A -0.0006202 0.0006409 0.3332261 0.3332238 0.2999670 0.4635760 91353
23 154929412 rs557132 C T -0.0003921 0.0006816 0.5651816 0.5651809 0.2440870 0.3568210 91353
23 154929637 rs35185538 CT C -0.0005655 0.0007118 0.4268861 0.4268840 0.2285200 0.3011920 91353
23 154929952 rs4012982 CAA C -0.0003886 0.0007174 0.5880524 0.5880514 0.2380650 0.3165560 91353
23 154930230 rs781880 A G -0.0003977 0.0006814 0.5594664 0.5594658 0.2445480 0.3618540 91353
23 154930487 rs781879 T A 0.0025360 0.0023110 0.2725003 0.2724976 0.0196444 0.1263580 91353

bcf preview

1   692794  rs530212009 CA  C   .   PASS    AF=0.111411 ES:SE:LP:AF:SS:ID   -0.0015794:0.00123522:0.696743:0.111411:91353:1_692794_CA_C
1   693731  rs12238997  A   G   .   PASS    AF=0.116387 ES:SE:LP:AF:SS:ID   -0.00147506:0.00116992:0.683237:0.116387:91353:rs12238997
1   707522  rs371890604 G   C   .   PASS    AF=0.0978018    ES:SE:LP:AF:SS:ID   -0.00242644:0.00131517:1.18678:0.0978018:91353:rs371890604
1   717587  rs144155419 G   A   .   PASS    AF=0.0157459    ES:SE:LP:AF:SS:ID   -0.000271255:0.0031379:0.0309976:0.0157459:91353:rs144155419
1   730087  rs148120343 T   C   .   PASS    AF=0.056953 ES:SE:LP:AF:SS:ID   -0.00093763:0.00162224:0.249279:0.056953:91353:rs148120343
1   731718  rs58276399  T   C   .   PASS    AF=0.122287 ES:SE:LP:AF:SS:ID   -0.001422:0.00111031:0.698332:0.122287:91353:rs58276399
1   732032  rs61770163  A   C   .   PASS    AF=0.121955 ES:SE:LP:AF:SS:ID   -0.00193819:0.00118401:0.992931:0.121955:91353:rs61770163
1   734349  rs141242758 T   C   .   PASS    AF=0.121517 ES:SE:LP:AF:SS:ID   -0.0014344:0.00111115:0.706116:0.121517:91353:rs141242758
1   749963  rs529266287 T   TAA .   PASS    AF=0.86901  ES:SE:LP:AF:SS:ID   0.00116043:0.00109302:0.540024:0.86901:91353:rs529266287
1   751343  rs28544273  T   A   .   PASS    AF=0.123604 ES:SE:LP:AF:SS:ID   -0.00107198:0.00108365:0.491398:0.123604:91353:rs28544273
1   751488  rs200141114 G   GA  .   PASS    AF=0.143109 ES:SE:LP:AF:SS:ID   -0.000907357:0.00107269:0.400525:0.143109:91353:rs200141114
1   751756  rs28527770  T   C   .   PASS    AF=0.12374  ES:SE:LP:AF:SS:ID   -0.00111067:0.00108208:0.516135:0.12374:91353:rs28527770
1   753405  rs3115860   C   A   .   PASS    AF=0.869977 ES:SE:LP:AF:SS:ID   0.0010895:0.00105435:0.520785:0.869977:91353:rs3115860
1   753425  rs3131970   T   C   .   PASS    AF=0.874656 ES:SE:LP:AF:SS:ID   0.00114104:0.00107153:0.54221:0.874656:91353:rs3131970
1   753541  rs2073813   G   A   .   PASS    AF=0.129446 ES:SE:LP:AF:SS:ID   -0.00105453:0.0010576:0.496589:0.129446:91353:rs2073813
1   754105  rs12184325  C   T   .   PASS    AF=0.0358609    ES:SE:LP:AF:SS:ID   0.00235726:0.00193056:0.653491:0.0358609:91353:rs12184325
1   754182  rs3131969   A   G   .   PASS    AF=0.869624 ES:SE:LP:AF:SS:ID   0.00109567:0.00105342:0.52536:0.869624:91353:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.869701 ES:SE:LP:AF:SS:ID   0.00108684:0.00105388:0.5194:0.869701:91353:rs3131968
1   754334  rs3131967   T   C   .   PASS    AF=0.86962  ES:SE:LP:AF:SS:ID   0.00109709:0.00105337:0.526298:0.86962:91353:rs3131967
1   755890  rs3115858   A   T   .   PASS    AF=0.8696   ES:SE:LP:AF:SS:ID   0.00100401:0.00105124:0.469104:0.8696:91353:rs3115858
1   756434  rs61768170  G   C   .   PASS    AF=0.126828 ES:SE:LP:AF:SS:ID   -0.00129117:0.00107319:0.640288:0.126828:91353:rs61768170
1   756604  rs3131962   A   G   .   PASS    AF=0.869129 ES:SE:LP:AF:SS:ID   0.00107599:0.00104851:0.515991:0.869129:91353:rs3131962
1   757640  rs3115853   G   A   .   PASS    AF=0.868516 ES:SE:LP:AF:SS:ID   0.00108351:0.0010478:0.521292:0.868516:91353:rs3115853
1   757734  rs4951929   C   T   .   PASS    AF=0.869278 ES:SE:LP:AF:SS:ID   0.00104471:0.00104946:0.495513:0.869278:91353:rs4951929
1   757936  rs4951862   C   A   .   PASS    AF=0.869283 ES:SE:LP:AF:SS:ID   0.0010465:0.00104953:0.496602:0.869283:91353:rs4951862
1   758144  rs3131956   A   G   .   PASS    AF=0.869286 ES:SE:LP:AF:SS:ID   0.00104703:0.00104954:0.49693:0.869286:91353:rs3131956
1   758626  rs3131954   C   T   .   PASS    AF=0.869767 ES:SE:LP:AF:SS:ID   0.00100917:0.00105236:0.471622:0.869767:91353:rs3131954
1   759293  rs10157329  T   A   .   PASS    AF=0.0991021    ES:SE:LP:AF:SS:ID   -0.00213135:0.00122502:1.08678:0.0991021:91353:rs10157329
1   759600  rs545998451 AGT A   .   PASS    AF=0.00647948   ES:SE:LP:AF:SS:ID   -0.00174129:0.00473131:0.147004:0.00647948:91353:1_759600_AGT_A
1   759837  rs3115851   T   A   .   PASS    AF=0.873778 ES:SE:LP:AF:SS:ID   0.00117108:0.00106799:0.564078:0.873778:91353:rs3115851
1   761732  rs2286139   C   T   .   PASS    AF=0.86314  ES:SE:LP:AF:SS:ID   0.000895687:0.00104752:0.406136:0.86314:91353:rs2286139
1   761752  rs1057213   C   T   .   PASS    AF=0.868548 ES:SE:LP:AF:SS:ID   0.000993644:0.00105797:0.458884:0.868548:91353:rs1057213
1   762273  rs3115849   G   A   .   PASS    AF=0.865453 ES:SE:LP:AF:SS:ID   0.000895316:0.00105816:0.400667:0.865453:91353:rs3115849
1   762485  rs12095200  C   A   .   PASS    AF=0.0994287    ES:SE:LP:AF:SS:ID   -0.00103479:0.00126673:0.38301:0.0994287:91353:rs12095200
1   762589  rs3115848   G   C   .   PASS    AF=0.870755 ES:SE:LP:AF:SS:ID   0.00108142:0.00107025:0.505438:0.870755:91353:rs3115848
1   762592  rs3131950   C   G   .   PASS    AF=0.870755 ES:SE:LP:AF:SS:ID   0.00108162:0.00107025:0.505564:0.870755:91353:rs3131950
1   762601  rs3131949   T   C   .   PASS    AF=0.870752 ES:SE:LP:AF:SS:ID   0.00108166:0.00107026:0.505587:0.870752:91353:rs3131949
1   762632  rs3131948   T   A   .   PASS    AF=0.871109 ES:SE:LP:AF:SS:ID   0.00108635:0.00107074:0.50821:0.871109:91353:rs3131948
1   764191  rs7515915   T   G   .   PASS    AF=0.126424 ES:SE:LP:AF:SS:ID   -0.0011389:0.00107194:0.540567:0.126424:91353:rs7515915
1   766007  rs61768174  A   C   .   PASS    AF=0.105999 ES:SE:LP:AF:SS:ID   -0.00166243:0.00116513:0.81351:0.105999:91353:rs61768174
1   766105  rs2519015   T   A   .   PASS    AF=0.854464 ES:SE:LP:AF:SS:ID   0.000910722:0.00104717:0.415139:0.854464:91353:rs2519015
1   768116  rs376645387 A   AGTTTT  .   PASS    AF=0.83913  ES:SE:LP:AF:SS:ID   -0.000832296:0.00103428:0.37573:0.83913:91353:rs376645387
1   768253  rs2977608   A   C   .   PASS    AF=0.763198 ES:SE:LP:AF:SS:ID   -0.000257154:0.000831412:0.12085:0.763198:91353:rs2977608
1   768448  rs12562034  G   A   .   PASS    AF=0.105174 ES:SE:LP:AF:SS:ID   0.00175063:0.00114559:0.897985:0.105174:91353:rs12562034
1   768819  rs12562811  C   T   .   PASS    AF=0.00772034   ES:SE:LP:AF:SS:ID   -0.00877696:0.00424769:1.41112:0.00772034:91353:rs12562811
1   769138  rs59306077  CAT C   .   PASS    AF=0.129817 ES:SE:LP:AF:SS:ID   -0.001118:0.00105697:0.537336:0.129817:91353:rs762168062
1   769223  rs60320384  C   G   .   PASS    AF=0.129553 ES:SE:LP:AF:SS:ID   -0.00105308:0.00105554:0.49697:0.129553:91353:rs60320384
1   769963  rs7518545   G   A   .   PASS    AF=0.104452 ES:SE:LP:AF:SS:ID   0.00182709:0.00115445:0.944977:0.104452:91353:rs7518545
1   770181  rs146076599 A   G   .   PASS    AF=0.00907063   ES:SE:LP:AF:SS:ID   -0.000561487:0.00405935:0.0506159:0.00907063:91353:rs146076599
1   770377  rs112563271 A   T   .   PASS    AF=0.00773618   ES:SE:LP:AF:SS:ID   -0.00864804:0.00426561:1.37033:0.00773618:91353:rs112563271