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=PROT-b-36,TotalVariants=5136688,VariantsNotRead=0,HarmonisedVariants=5135036,VariantsNotHarmonised=1652,SwitchedAlleles=3978052,TotalControls=3394.0,StudyType=Continuous>",
    "contig": "<ID=1,length=249250621,assembly=HG19/GRCh37>",
    "contig.1": "<ID=2,length=243199373,assembly=HG19/GRCh37>",
    "contig.2": "<ID=3,length=198022430,assembly=HG19/GRCh37>",
    "contig.3": "<ID=4,length=191154276,assembly=HG19/GRCh37>",
    "contig.4": "<ID=5,length=180915260,assembly=HG19/GRCh37>",
    "contig.5": "<ID=6,length=171115067,assembly=HG19/GRCh37>",
    "contig.6": "<ID=7,length=159138663,assembly=HG19/GRCh37>",
    "contig.7": "<ID=8,length=146364022,assembly=HG19/GRCh37>",
    "contig.8": "<ID=9,length=141213431,assembly=HG19/GRCh37>",
    "contig.9": "<ID=10,length=135534747,assembly=HG19/GRCh37>",
    "contig.10": "<ID=11,length=135006516,assembly=HG19/GRCh37>",
    "contig.11": "<ID=12,length=133851895,assembly=HG19/GRCh37>",
    "contig.12": "<ID=13,length=115169878,assembly=HG19/GRCh37>",
    "contig.13": "<ID=14,length=107349540,assembly=HG19/GRCh37>",
    "contig.14": "<ID=15,length=102531392,assembly=HG19/GRCh37>",
    "contig.15": "<ID=16,length=90354753,assembly=HG19/GRCh37>",
    "contig.16": "<ID=17,length=81195210,assembly=HG19/GRCh37>",
    "contig.17": "<ID=18,length=78077248,assembly=HG19/GRCh37>",
    "contig.18": "<ID=19,length=59128983,assembly=HG19/GRCh37>",
    "contig.19": "<ID=20,length=63025520,assembly=HG19/GRCh37>",
    "contig.20": "<ID=21,length=48129895,assembly=HG19/GRCh37>",
    "contig.21": "<ID=22,length=51304566,assembly=HG19/GRCh37>",
    "contig.22": "<ID=X,length=155270560,assembly=HG19/GRCh37>",
    "contig.23": "<ID=Y,length=59373566,assembly=HG19/GRCh37>",
    "contig.24": "<ID=MT,length=16569,assembly=HG19/GRCh37>",
    "contig.25": "<ID=GL000207.1,length=4262,assembly=HG19/GRCh37>",
    "contig.26": "<ID=GL000226.1,length=15008,assembly=HG19/GRCh37>",
    "contig.27": "<ID=GL000229.1,length=19913,assembly=HG19/GRCh37>",
    "contig.28": "<ID=GL000231.1,length=27386,assembly=HG19/GRCh37>",
    "contig.29": "<ID=GL000210.1,length=27682,assembly=HG19/GRCh37>",
    "contig.30": "<ID=GL000239.1,length=33824,assembly=HG19/GRCh37>",
    "contig.31": "<ID=GL000235.1,length=34474,assembly=HG19/GRCh37>",
    "contig.32": "<ID=GL000201.1,length=36148,assembly=HG19/GRCh37>",
    "contig.33": "<ID=GL000247.1,length=36422,assembly=HG19/GRCh37>",
    "contig.34": "<ID=GL000245.1,length=36651,assembly=HG19/GRCh37>",
    "contig.35": "<ID=GL000197.1,length=37175,assembly=HG19/GRCh37>",
    "contig.36": "<ID=GL000203.1,length=37498,assembly=HG19/GRCh37>",
    "contig.37": "<ID=GL000246.1,length=38154,assembly=HG19/GRCh37>",
    "contig.38": "<ID=GL000249.1,length=38502,assembly=HG19/GRCh37>",
    "contig.39": "<ID=GL000196.1,length=38914,assembly=HG19/GRCh37>",
    "contig.40": "<ID=GL000248.1,length=39786,assembly=HG19/GRCh37>",
    "contig.41": "<ID=GL000244.1,length=39929,assembly=HG19/GRCh37>",
    "contig.42": "<ID=GL000238.1,length=39939,assembly=HG19/GRCh37>",
    "contig.43": "<ID=GL000202.1,length=40103,assembly=HG19/GRCh37>",
    "contig.44": "<ID=GL000234.1,length=40531,assembly=HG19/GRCh37>",
    "contig.45": "<ID=GL000232.1,length=40652,assembly=HG19/GRCh37>",
    "contig.46": "<ID=GL000206.1,length=41001,assembly=HG19/GRCh37>",
    "contig.47": "<ID=GL000240.1,length=41933,assembly=HG19/GRCh37>",
    "contig.48": "<ID=GL000236.1,length=41934,assembly=HG19/GRCh37>",
    "contig.49": "<ID=GL000241.1,length=42152,assembly=HG19/GRCh37>",
    "contig.50": "<ID=GL000243.1,length=43341,assembly=HG19/GRCh37>",
    "contig.51": "<ID=GL000242.1,length=43523,assembly=HG19/GRCh37>",
    "contig.52": "<ID=GL000230.1,length=43691,assembly=HG19/GRCh37>",
    "contig.53": "<ID=GL000237.1,length=45867,assembly=HG19/GRCh37>",
    "contig.54": "<ID=GL000233.1,length=45941,assembly=HG19/GRCh37>",
    "contig.55": "<ID=GL000204.1,length=81310,assembly=HG19/GRCh37>",
    "contig.56": "<ID=GL000198.1,length=90085,assembly=HG19/GRCh37>",
    "contig.57": "<ID=GL000208.1,length=92689,assembly=HG19/GRCh37>",
    "contig.58": "<ID=GL000191.1,length=106433,assembly=HG19/GRCh37>",
    "contig.59": "<ID=GL000227.1,length=128374,assembly=HG19/GRCh37>",
    "contig.60": "<ID=GL000228.1,length=129120,assembly=HG19/GRCh37>",
    "contig.61": "<ID=GL000214.1,length=137718,assembly=HG19/GRCh37>",
    "contig.62": "<ID=GL000221.1,length=155397,assembly=HG19/GRCh37>",
    "contig.63": "<ID=GL000209.1,length=159169,assembly=HG19/GRCh37>",
    "contig.64": "<ID=GL000218.1,length=161147,assembly=HG19/GRCh37>",
    "contig.65": "<ID=GL000220.1,length=161802,assembly=HG19/GRCh37>",
    "contig.66": "<ID=GL000213.1,length=164239,assembly=HG19/GRCh37>",
    "contig.67": "<ID=GL000211.1,length=166566,assembly=HG19/GRCh37>",
    "contig.68": "<ID=GL000199.1,length=169874,assembly=HG19/GRCh37>",
    "contig.69": "<ID=GL000217.1,length=172149,assembly=HG19/GRCh37>",
    "contig.70": "<ID=GL000216.1,length=172294,assembly=HG19/GRCh37>",
    "contig.71": "<ID=GL000215.1,length=172545,assembly=HG19/GRCh37>",
    "contig.72": "<ID=GL000205.1,length=174588,assembly=HG19/GRCh37>",
    "contig.73": "<ID=GL000219.1,length=179198,assembly=HG19/GRCh37>",
    "contig.74": "<ID=GL000224.1,length=179693,assembly=HG19/GRCh37>",
    "contig.75": "<ID=GL000223.1,length=180455,assembly=HG19/GRCh37>",
    "contig.76": "<ID=GL000195.1,length=182896,assembly=HG19/GRCh37>",
    "contig.77": "<ID=GL000212.1,length=186858,assembly=HG19/GRCh37>",
    "contig.78": "<ID=GL000222.1,length=186861,assembly=HG19/GRCh37>",
    "contig.79": "<ID=GL000200.1,length=187035,assembly=HG19/GRCh37>",
    "contig.80": "<ID=GL000193.1,length=189789,assembly=HG19/GRCh37>",
    "contig.81": "<ID=GL000194.1,length=191469,assembly=HG19/GRCh37>",
    "contig.82": "<ID=GL000225.1,length=211173,assembly=HG19/GRCh37>",
    "contig.83": "<ID=GL000192.1,length=547496,assembly=HG19/GRCh37>",
    "gwas_harmonisation_command": "--json /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/folkersen/processed/PROT-b-36/PROT-b-36_data.json --ref /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/QC/genomes/b37/human_g1k_v37.fasta; 1.1.1",
    "file_date": "2019-10-28T01:49:08.161160",
    "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/folkersen/processed/PROT-b-36/PROT-b-36.vcf.gz -O z /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/folkersen/processed/PROT-b-36/PROT-b-36_data.vcf.gz; Date=Mon Oct 28 02:22:57 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/prot-b-36/prot-b-36.vcf.gz; Date=Sat May  9 18:05:57 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/folkersen-pqtl-gwas-import/processed/PROT-b-36/PROT-b-36.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/folkersen-pqtl-gwas-import/processed/PROT-b-36/ldsc.txt \
--w-ld-chr /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/reference/eur_w_ld_chr/ 

Beginning analysis at Mon Oct 28 22:10:24 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/folkersen-pqtl-gwas-import/processed/PROT-b-36/PROT-b-36.vcf.gz ...
Read summary statistics for 5135036 SNPs.
Dropped 1 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, 759193 SNPs remain.
After merging with regression SNP LD, 759193 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.2218 (0.164)
Lambda GC: 1.0148
Mean Chi^2: 1.0101
Intercept: 0.993 (0.0097)
Ratio < 0 (usually indicates GC correction).
Analysis finished at Mon Oct 28 22:11:13 2019
Total time elapsed: 48.91s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9563,
    "inflation_factor": 0.9995,
    "mean_EFFECT": -0.001,
    "n": "-Inf",
    "n_snps": 5135036,
    "n_clumped_hits": 1,
    "n_p_sig": 3,
    "n_mono": 545,
    "n_ns": 317497,
    "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": 377170,
    "n_est": "NA",
    "ratio_se_n": "NA",
    "mean_diff": "NaN",
    "ratio_diff": "NaN",
    "sd_y_est1": "NaN",
    "sd_y_est2": "NA",
    "r2_sum1": 0,
    "r2_sum2": 0,
    "r2_sum3": 0,
    "r2_sum4": 0,
    "ldsc_nsnp_merge_refpanel_ld": 759193,
    "ldsc_nsnp_merge_regression_ld": 759193,
    "ldsc_observed_scale_h2_beta": 0.2218,
    "ldsc_observed_scale_h2_se": 0.164,
    "ldsc_intercept_beta": 0.993,
    "ldsc_intercept_se": 0.0097,
    "ldsc_lambda_gc": 1.0148,
    "ldsc_mean_chisq": 1.0101,
    "ldsc_ratio": -0.6931
}

Flags

name value
af_correlation FALSE
inflation_factor FALSE
n TRUE
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 logical.mean logical.count numeric.mean numeric.sd numeric.p0 numeric.p25 numeric.p50 numeric.p75 numeric.p100 numeric.hist
character ID 0 1.0000000 3 58 0 5135032 0 NA NA NA NA NA NA NA NA NA NA
character REF 0 1.0000000 1 3 0 80 0 NA NA NA NA NA NA NA NA NA NA
character ALT 0 1.0000000 1 3 0 80 0 NA NA NA NA NA NA NA NA NA NA
logical N 5135036 0.0000000 NA NA NA NA NA NaN : NA NA NA NA NA NA NA NA
numeric CHROM 0 1.0000000 NA NA NA NA NA NA NA 8.356760e+00 5.629048e+00 1.0000 3.000000e+00 7.000000e+00 1.200000e+01 2.200000e+01 ▇▅▃▂▂
numeric POS 0 1.0000000 NA NA NA NA NA NA NA 7.977423e+07 5.495317e+07 29422.0000 3.532730e+07 7.050636e+07 1.143548e+08 2.492183e+08 ▇▇▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA NA NA -9.995000e-04 2.688251e-01 -9.1971 -3.710000e-02 1.000000e-04 3.700000e-02 8.489500e+00 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA NA NA 1.345846e-01 2.434840e-01 0.0233 3.380000e-02 4.730000e-02 1.088000e-01 3.401800e+00 ▇▁▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA NA NA 5.000761e-01 2.889181e-01 0.0000 2.484998e-01 5.001002e-01 7.506993e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA NA NA 4.999132e-01 2.890193e-01 0.0000 2.482467e-01 4.999676e-01 7.505936e-01 1.000000e+00 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA NA NA 2.781589e-01 2.817943e-01 0.0000 3.560000e-02 1.762000e-01 4.617000e-01 1.000000e+00 ▇▃▂▂▁
numeric AF_reference 377170 0.9265497 NA NA NA NA NA NA NA 2.522964e-01 2.538675e-01 0.0000 3.654150e-02 1.659350e-01 4.039540e-01 1.000000e+00 ▇▃▂▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 780785 rs2977612 T A -0.0260 0.0464 0.5746997 0.5752443 0.8252 0.669329 NA
1 782981 rs6594026 C T 0.0257 0.0457 0.5748003 0.5738686 0.1534 0.297923 NA
1 783318 rs6686696 A G 0.0402 0.0717 0.5746997 0.5750229 0.0799 0.183107 NA
1 785050 rs2905062 G A -0.0191 0.0340 0.5746997 0.5742763 0.8365 0.626997 NA
1 785989 rs2980300 T C -0.0211 0.0377 0.5746997 0.5756966 0.8083 0.626997 NA
1 787121 rs12077234 T A 0.0334 0.0596 0.5746997 0.5752048 0.1319 NA NA
1 787399 rs2905055 G T -0.0259 0.0461 0.5746997 0.5742372 0.8001 0.646366 NA
1 787685 rs2905054 G T -0.0248 0.0441 0.5743002 0.5738719 0.7668 0.622204 NA
1 787844 rs2905053 C T -0.0269 0.0479 0.5746997 0.5743977 0.8114 0.651757 NA
1 790758 1_790758_GTA_G G GTA -0.0286 0.0509 0.5746997 0.5741937 0.7799 NA NA
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51163039 rs715584 G T 0.0307 0.0301 0.3078003 0.3077600 0.4131 0.4736420 NA
22 51163138 rs715586 C T 0.0618 0.0361 0.0867401 0.0869130 0.1273 0.0902556 NA
22 51163910 rs192700691 C T 0.0788 0.1072 0.4627005 0.4622940 0.0304 0.0295527 NA
22 51164109 rs5770995 G C 0.0223 0.0283 0.4293001 0.4307050 0.4411 0.5109820 NA
22 51164115 rs5770996 C T 0.0221 0.0284 0.4371002 0.4364694 0.4446 0.5147760 NA
22 51164287 rs6009957 T C -0.0117 0.0273 0.6683993 0.6682351 0.3052 0.4155350 NA
22 51165664 rs8137951 G A -0.0110 0.0266 0.6782003 0.6792155 0.2954 0.4063500 NA
22 51171693 rs756638 G A -0.0061 0.0386 0.8748001 0.8744323 0.3046 0.3049120 NA
22 51175626 rs3810648 A G -0.0220 0.0603 0.7157000 0.7152290 0.0735 0.1084270 NA
22 51178090 rs2285395 G A -0.0058 0.0572 0.9194999 0.9192340 0.0481 0.0666933 NA

bcf preview

1   780785  rs2977612   T   A   .   PASS    AF=0.8252   ES:SE:LP:AF:ID  -0.026:0.0464:0.240559:0.8252:rs2977612
1   782981  rs6594026   C   T   .   PASS    AF=0.1534   ES:SE:LP:AF:ID  0.0257:0.0457:0.240483:0.1534:rs6594026
1   783318  rs6686696   A   G   .   PASS    AF=0.0799   ES:SE:LP:AF:ID  0.0402:0.0717:0.240559:0.0799:rs6686696
1   785050  rs2905062   G   A   .   PASS    AF=0.8365   ES:SE:LP:AF:ID  -0.0191:0.034:0.240559:0.8365:rs2905062
1   785989  rs2980300   T   C   .   PASS    AF=0.8083   ES:SE:LP:AF:ID  -0.0211:0.0377:0.240559:0.8083:rs2980300
1   787121  rs12077234  T   A   .   PASS    AF=0.1319   ES:SE:LP:AF:ID  0.0334:0.0596:0.240559:0.1319:rs12077234
1   787399  rs2905055   G   T   .   PASS    AF=0.8001   ES:SE:LP:AF:ID  -0.0259:0.0461:0.240559:0.8001:rs2905055
1   787685  rs2905054   G   T   .   PASS    AF=0.7668   ES:SE:LP:AF:ID  -0.0248:0.0441:0.240861:0.7668:rs2905054
1   787844  rs2905053   C   T   .   PASS    AF=0.8114   ES:SE:LP:AF:ID  -0.0269:0.0479:0.240559:0.8114:rs2905053
1   790758  1_790758_GTA_G  G   GTA .   PASS    AF=0.7799   ES:SE:LP:AF:ID  -0.0286:0.0509:0.240559:0.7799:1_790758_GTA_G
1   1108637 rs4970421   G   A   .   PASS    AF=0.0713   ES:SE:LP:AF:ID  0.0564:0.0757:0.34094:0.0713:rs4970421
1   1112982 rs6671609   C   T   .   PASS    AF=0.1436   ES:SE:LP:AF:ID  -0.0376:0.06:0.275151:0.1436:rs6671609
1   1115994 rs13376597  G   A   .   PASS    AF=0.1429   ES:SE:LP:AF:ID  -0.0383:0.058:0.2926:0.1429:rs13376597
1   1116231 rs13374146  T   C   .   PASS    AF=0.0678   ES:SE:LP:AF:ID  0.0388:0.0612:0.279179:0.0678:rs13374146
1   1117398 rs12097586  A   G   .   PASS    AF=0.4246   ES:SE:LP:AF:ID  -0.0458:0.0437:0.53062:0.4246:rs12097586
1   1117486 rs13376670  A   G   .   PASS    AF=0.1481   ES:SE:LP:AF:ID  -0.0353:0.057:0.270673:0.1481:rs13376670
1   1118275 rs61733845  C   T   .   PASS    AF=0.05 ES:SE:LP:AF:ID  0.0441:0.0575:0.353204:0.05:rs61733845
1   1118578 rs111290899 G   A   .   PASS    AF=0.0504   ES:SE:LP:AF:ID  0.0446:0.0588:0.348819:0.0504:rs111290899
1   1119657 rs4560982   G   C   .   PASS    AF=0.4012   ES:SE:LP:AF:ID  -0.0497:0.0392:0.689944:0.4012:rs4560982
1   1119858 rs1320565   C   T   .   PASS    AF=0.1126   ES:SE:LP:AF:ID  0.0476:0.0603:0.366936:0.1126:rs1320565
1   1120431 rs1320571   G   A   .   PASS    AF=0.0525   ES:SE:LP:AF:ID  0.0158:0.0551:0.111259:0.0525:rs1320571
1   1121014 rs3813204   G   A   .   PASS    AF=0.1364   ES:SE:LP:AF:ID  -0.0946:0.057:1.01305:0.1364:rs3813204
1   1121341 rs4297230   C   T   .   PASS    AF=0.1422   ES:SE:LP:AF:ID  -0.0826:0.0556:0.861697:0.1422:rs4297230
1   1121358 rs80057011  A   C   .   PASS    AF=0.0928   ES:SE:LP:AF:ID  -0.1532:0.0655:1.71197:0.0928:rs80057011
1   1121480 rs12063663  T   C   .   PASS    AF=0.0923   ES:SE:LP:AF:ID  -0.1587:0.0653:1.81959:0.0923:rs12063663
1   1121625 rs4081334   C   G   .   PASS    AF=0.1418   ES:SE:LP:AF:ID  -0.078:0.0551:0.803547:0.1418:rs4081334
1   1121657 rs11260548  T   C   .   PASS    AF=0.2302   ES:SE:LP:AF:ID  -0.0881:0.0371:1.75845:0.2302:rs11260548
1   1121715 rs4081333   C   T   .   PASS    AF=0.0882   ES:SE:LP:AF:ID  -0.1602:0.0642:1.89757:0.0882:rs4081333
1   1121794 rs11260549  G   A   .   PASS    AF=0.1326   ES:SE:LP:AF:ID  -0.0842:0.0549:0.902396:0.1326:rs11260549
1   1121835 rs57346441  C   CTG .   PASS    AF=0.2304   ES:SE:LP:AF:ID  -0.0845:0.0363:1.70268:0.2304:1_1121835_C_CTG
1   1122024 rs4314833   T   C   .   PASS    AF=0.1279   ES:SE:LP:AF:ID  -0.0936:0.056:1.02383:0.1279:rs4314833
1   1122196 rs4634847   A   G   .   PASS    AF=0.1342   ES:SE:LP:AF:ID  -0.0825:0.0547:0.882397:0.1342:rs4634847
1   1122283 rs12064046  T   G   .   PASS    AF=0.0862   ES:SE:LP:AF:ID  -0.1583:0.0637:1.88372:0.0862:rs12064046
1   1122319 rs7415847   C   T   .   PASS    AF=0.1199   ES:SE:LP:AF:ID  -0.1011:0.0598:1.04191:0.1199:rs7415847
1   1122468 rs7545694   T   C   .   PASS    AF=0.2031   ES:SE:LP:AF:ID  -0.0997:0.0399:1.9024:0.2031:rs7545694
1   1122516 rs11260551  G   A   .   PASS    AF=0.1274   ES:SE:LP:AF:ID  -0.0944:0.0558:1.04211:0.1274:rs11260551
1   1122539 rs12063897  A   G   .   PASS    AF=0.0866   ES:SE:LP:AF:ID  -0.1571:0.0629:1.90032:0.0866:rs12063897
1   1122915 rs28595293  A   G   .   PASS    AF=0.2718   ES:SE:LP:AF:ID  -0.059:0.0319:1.1901:0.2718:rs28595293
1   1122916 rs28460227  A   G   .   PASS    AF=0.0856   ES:SE:LP:AF:ID  -0.157:0.063:1.89211:0.0856:rs28460227
1   1122937 rs28648687  G   A   .   PASS    AF=0.0856   ES:SE:LP:AF:ID  -0.1569:0.063:1.89076:0.0856:rs28648687
1   1123106 rs12401472  G   A   .   PASS    AF=0.128    ES:SE:LP:AF:ID  -0.0936:0.0554:1.04148:0.128:rs12401472
1   1123434 rs12066716  T   A   .   PASS    AF=0.1323   ES:SE:LP:AF:ID  -0.0888:0.0536:1.00908:0.1323:rs12066716
1   1124257 rs10907172  A   G   .   PASS    AF=0.1273   ES:SE:LP:AF:ID  -0.0933:0.0551:1.04287:0.1273:rs10907172
1   1124399 rs10907173  C   G   .   PASS    AF=0.1324   ES:SE:LP:AF:ID  -0.0844:0.0539:0.929593:0.1324:rs10907173
1   1124663 rs6684820   G   A   .   PASS    AF=0.2737   ES:SE:LP:AF:ID  -0.0578:0.0312:1.19192:0.2737:rs6684820
1   1124819 rs6694487   C   T   .   PASS    AF=0.0867   ES:SE:LP:AF:ID  -0.1547:0.0624:1.88008:0.0867:rs6694487
1   1124891 rs61768485  G   A   .   PASS    AF=0.1266   ES:SE:LP:AF:ID  -0.0931:0.0549:1.04537:0.1266:rs61768485
1   1125110 rs12124436  T   C   .   PASS    AF=0.1248   ES:SE:LP:AF:ID  -0.094:0.0547:1.06732:0.1248:rs12124436
1   1125220 rs12065129  C   T   .   PASS    AF=0.0864   ES:SE:LP:AF:ID  -0.1534:0.0618:1.8814:0.0864:rs12065129
1   1125348 rs12029885  T   C   .   PASS    AF=0.1261   ES:SE:LP:AF:ID  -0.084:0.0551:0.893809:0.1261:rs12029885