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=ieu-a-7,TotalVariants=8479693,VariantsNotRead=0,HarmonisedVariants=8479693,VariantsNotHarmonised=0,SwitchedAlleles=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/ieu-a-import/processed/ieu-a-7/ieu-a-7_data.json --ref /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/QC/genomes/b37/human_g1k_v37.fasta; 1.1.1",
    "file_date": "2020-02-04T12:10:50.350448",
    "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/ieu-a-import/processed/ieu-a-7/ieu-a-7.vcf.gz -O z /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-7/ieu-a-7_data.vcf.gz; Date=Tue Feb  4 16:31:35 2020",
    "bcftools_viewVersion": "1.9-74-g6af271c+htslib-1.9-64-g226b4a8",
    "bcftools_viewCommand": "view -h /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ieu-a-7/ieu-a-7.vcf.gz; Date=Sun May 10 10:05:00 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/ieu-a-import/processed/ieu-a-7/ieu-a-7.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/ieu-a-import/processed/ieu-a-7/ldsc.txt \
--w-ld-chr /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/reference/eur_w_ld_chr/ 

Beginning analysis at Wed Feb  5 09:21:15 2020
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-7/ieu-a-7.vcf.gz ...
Read summary statistics for 8479693 SNPs.
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, 1286923 SNPs remain.
After merging with regression SNP LD, 1286923 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0659 (0.0042)
Lambda GC: 1.0465
Mean Chi^2: 1.1242
Intercept: 0.8866 (0.0072)
Ratio < 0 (usually indicates GC correction).
Analysis finished at Wed Feb  5 09:22:34 2020
Total time elapsed: 1.0m:18.76s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9621,
    "inflation_factor": 1.0011,
    "mean_EFFECT": 0.0006,
    "n": 184305,
    "n_snps": 8479693,
    "n_clumped_hits": 41,
    "n_p_sig": 2022,
    "n_mono": 0,
    "n_ns": 0,
    "n_mac": 0,
    "is_snpid_unique": true,
    "n_miss_EFFECT": 0,
    "n_miss_SE": 0,
    "n_miss_PVAL": 0,
    "n_miss_AF": 0,
    "n_miss_AF_reference": 204800,
    "n_est": 177406.6453,
    "ratio_se_n": 0.9811,
    "mean_diff": -0.0004,
    "ratio_diff": 22.3357,
    "sd_y_est1": 2.9757,
    "sd_y_est2": 2.9195,
    "r2_sum1": 0.1164,
    "r2_sum2": 0.0131,
    "r2_sum3": 0.0137,
    "r2_sum4": 0.0135,
    "ldsc_nsnp_merge_refpanel_ld": 1286923,
    "ldsc_nsnp_merge_regression_ld": 1286923,
    "ldsc_observed_scale_h2_beta": 0.0659,
    "ldsc_observed_scale_h2_se": 0.0042,
    "ldsc_intercept_beta": 0.8866,
    "ldsc_intercept_se": 0.0072,
    "ldsc_lambda_gc": 1.0465,
    "ldsc_mean_chisq": 1.1242,
    "ldsc_ratio": -0.913
}

Flags

name value
af_correlation FALSE
inflation_factor FALSE
n FALSE
is_snpid_non_unique FALSE
mean_EFFECT_nonfinite FALSE
mean_EFFECT_05 FALSE
mean_EFFECT_01 FALSE
mean_chisq FALSE
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 59 0 8479691 0 NA NA NA NA NA NA NA NA
character REF 0 1.0000000 1 1 0 4 0 NA NA NA NA NA NA NA NA
character ALT 0 1.0000000 1 1 0 4 0 NA NA NA NA NA NA NA NA
numeric CHROM 0 1.0000000 NA NA NA NA NA 8.639618e+00 5.752451e+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 7.888446e+07 5.635321e+07 8.28000e+02 3.254795e+07 6.954272e+07 1.146369e+08 2.492223e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA 5.743000e-04 2.535190e-02 -2.88636e-01 -1.061200e-02 3.160000e-04 1.133300e-02 5.503510e-01 ▁▇▁▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 2.134400e-02 1.515200e-02 9.05300e-03 1.060100e-02 1.465610e-02 2.656280e-02 1.697250e-01 ▇▁▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.987318e-01 2.905055e-01 0.00000e+00 2.474589e-01 4.997560e-01 7.502759e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.987318e-01 2.905055e-01 0.00000e+00 2.474592e-01 4.997560e-01 7.502756e-01 1.000000e+00 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA 2.440651e-01 2.513024e-01 5.77400e-03 3.966600e-02 1.424650e-01 3.867900e-01 9.931970e-01 ▇▂▂▁▁
numeric AF_reference 204800 0.9758482 NA NA NA NA NA 2.497691e-01 2.545520e-01 0.00000e+00 4.153350e-02 1.561500e-01 3.919730e-01 1.000000e+00 ▇▃▂▁▁
numeric N 0 1.0000000 NA NA NA NA NA 1.843050e+05 0.000000e+00 1.84305e+05 1.843050e+05 1.843050e+05 1.843050e+05 1.843050e+05 ▁▁▇▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 752566 rs3094315 G A -0.005243 0.0157652 0.7394605 0.7394605 0.763018 0.718251 184305
1 752721 rs3131972 A G -0.003032 0.0156381 0.8462652 0.8462656 0.740969 0.653355 184305
1 752894 rs3131971 T C 0.004640 0.0162377 0.7750666 0.7750660 0.744287 0.753195 184305
1 753474 rs2073814 C G 0.000407 0.0157456 0.9793782 0.9793782 0.716742 0.611422 184305
1 753541 rs2073813 G A 0.005802 0.0167808 0.7295297 0.7295289 0.194804 0.301917 184305
1 754182 rs3131969 A G -0.006522 0.0165571 0.6936478 0.6936478 0.760434 0.678514 184305
1 754192 rs3131968 A G -0.006791 0.0165668 0.6818675 0.6818674 0.759886 0.678514 184305
1 754334 rs3131967 T C -0.009343 0.0168482 0.5792086 0.5792094 0.747971 0.684305 184305
1 754503 rs3115859 G A -0.000146 0.0158271 0.9926398 0.9926399 0.742041 0.663938 184305
1 754964 rs3131966 C T 0.002221 0.0162312 0.8911609 0.8911610 0.727432 0.663339 184305
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51198577 rs146015776 T C -0.086545 0.0362339 0.0169169 0.0169169 0.041843 NA 184305
22 51198590 rs138731614 A G -0.078713 0.0369356 0.0330819 0.0330819 0.036627 NA 184305
22 51199281 rs4040021 T C -0.033522 0.0144953 0.0207439 0.0207440 0.390830 0.4612620 184305
22 51208568 rs148425445 G T -0.044068 0.0275991 0.1103281 0.1103284 0.059355 0.1160140 184305
22 51210268 rs2341018 T G -0.005034 0.0149657 0.7365920 0.7365925 0.441612 0.4468850 184305
22 51211031 rs9616968 A G 0.093196 0.0605079 0.1235043 0.1235046 0.050705 0.0373403 184305
22 51213613 rs34726907 C T -0.000428 0.0192738 0.9822834 0.9822834 0.133301 0.1727240 184305
22 51216731 rs5771014 T C -0.016457 0.0394971 0.6769241 0.6769246 0.252603 0.2593850 184305
22 51219006 rs28729663 G A 0.010715 0.0181365 0.5546564 0.5546561 0.172818 0.2052720 184305
23 100784211 rs188350543 C A 0.020365 0.0139109 0.1432043 0.1432049 0.746040 0.6498010 184305

bcf preview

1   752566  rs3094315   G   A   .   PASS    AF=0.763018 ES:SE:LP:AF:SS:ID   -0.005243:0.0157652:0.131085:0.763018:184305:rs3094315
1   752721  rs3131972   A   G   .   PASS    AF=0.740969 ES:SE:LP:AF:SS:ID   -0.003032:0.0156381:0.0724935:0.740969:184305:rs3131972
1   752894  rs3131971   T   C   .   PASS    AF=0.744287 ES:SE:LP:AF:SS:ID   0.00464:0.0162377:0.110661:0.744287:184305:rs3131971
1   753474  rs2073814   C   G   .   PASS    AF=0.716742 ES:SE:LP:AF:SS:ID   0.000407:0.0157456:0.00904957:0.716742:184305:rs2073814
1   753541  rs2073813   G   A   .   PASS    AF=0.194804 ES:SE:LP:AF:SS:ID   0.005802:0.0167808:0.136957:0.194804:184305:rs2073813
1   754182  rs3131969   A   G   .   PASS    AF=0.760434 ES:SE:LP:AF:SS:ID   -0.006522:0.0165571:0.158861:0.760434:184305:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.759886 ES:SE:LP:AF:SS:ID   -0.006791:0.0165668:0.1663:0.759886:184305:rs3131968
1   754334  rs3131967   T   C   .   PASS    AF=0.747971 ES:SE:LP:AF:SS:ID   -0.009343:0.0168482:0.237165:0.747971:184305:rs3131967
1   754503  rs3115859   G   A   .   PASS    AF=0.742041 ES:SE:LP:AF:SS:ID   -0.000146:0.0158271:0.00320832:0.742041:184305:rs3115859
1   754964  rs3131966   C   T   .   PASS    AF=0.727432 ES:SE:LP:AF:SS:ID   0.002221:0.0162312:0.0500439:0.727432:184305:rs3131966
1   755775  rs3131965   A   G   .   PASS    AF=0.71467  ES:SE:LP:AF:SS:ID   0.006636:0.0164734:0.162997:0.71467:184305:rs3131965
1   755890  rs3115858   A   T   .   PASS    AF=0.776798 ES:SE:LP:AF:SS:ID   -0.008914:0.0170133:0.221619:0.776798:184305:rs3115858
1   756604  rs3131962   A   G   .   PASS    AF=0.756247 ES:SE:LP:AF:SS:ID   -0.004858:0.0168188:0.111988:0.756247:184305:rs3131962
1   757640  rs3115853   G   A   .   PASS    AF=0.749175 ES:SE:LP:AF:SS:ID   -0.008785:0.0168699:0.220013:0.749175:184305:rs3115853
1   757734  rs4951929   C   T   .   PASS    AF=0.782655 ES:SE:LP:AF:SS:ID   -0.014073:0.0170176:0.389067:0.782655:184305:rs4951929
1   757936  rs4951862   C   A   .   PASS    AF=0.78203  ES:SE:LP:AF:SS:ID   -0.014716:0.0170263:0.41182:0.78203:184305:rs4951862
1   758144  rs3131956   A   G   .   PASS    AF=0.767599 ES:SE:LP:AF:SS:ID   -0.006877:0.0164376:0.170262:0.767599:184305:rs3131956
1   758626  rs3131954   C   T   .   PASS    AF=0.781067 ES:SE:LP:AF:SS:ID   -0.013634:0.0171545:0.369833:0.781067:184305:rs3131954
1   760912  rs1048488   C   T   .   PASS    AF=0.73858  ES:SE:LP:AF:SS:ID   0.005562:0.0164788:0.133286:0.73858:184305:rs1048488
1   761147  rs3115850   T   C   .   PASS    AF=0.740961 ES:SE:LP:AF:SS:ID   4.8e-05:0.0166255:0.00100159:0.740961:184305:rs3115850
1   761732  rs2286139   C   T   .   PASS    AF=0.726374 ES:SE:LP:AF:SS:ID   0.005293:0.0171078:0.12089:0.726374:184305:rs2286139
1   761752  rs1057213   C   T   .   PASS    AF=0.769413 ES:SE:LP:AF:SS:ID   -0.006653:0.0175564:0.15198:0.769413:184305:rs1057213
1   762273  rs3115849   G   A   .   PASS    AF=0.745318 ES:SE:LP:AF:SS:ID   -0.007391:0.0177444:0.169396:0.745318:184305:rs3115849
1   764191  rs7515915   T   G   .   PASS    AF=0.155298 ES:SE:LP:AF:SS:ID   -0.000659:0.018596:0.0124541:0.155298:184305:rs7515915
1   766007  rs61768174  A   C   .   PASS    AF=0.117535 ES:SE:LP:AF:SS:ID   -0.0006:0.0210901:0.00997046:0.117535:184305:rs61768174
1   768253  rs2977608   A   C   .   PASS    AF=0.648619 ES:SE:LP:AF:SS:ID   -0.010842:0.0146235:0.338713:0.648619:184305:rs2977608
1   768448  rs12562034  G   A   .   PASS    AF=0.133117 ES:SE:LP:AF:SS:ID   -0.00342:0.0172229:0.07438:0.133117:184305:rs12562034
1   769223  rs60320384  C   G   .   PASS    AF=0.147952 ES:SE:LP:AF:SS:ID   0.002734:0.0187665:0.0534641:0.147952:184305:rs60320384
1   769963  rs7518545   G   A   .   PASS    AF=0.124842 ES:SE:LP:AF:SS:ID   -0.001891:0.0184102:0.0370677:0.124842:184305:rs7518545
1   771823  rs2977605   T   C   .   PASS    AF=0.78219  ES:SE:LP:AF:SS:ID   -0.006408:0.0179203:0.142272:0.78219:184305:rs2977605
1   771967  rs59066358  G   A   .   PASS    AF=0.148426 ES:SE:LP:AF:SS:ID   0.003761:0.0184819:0.0763688:0.148426:184305:rs59066358
1   772755  rs2905039   A   C   .   PASS    AF=0.780253 ES:SE:LP:AF:SS:ID   -0.00819:0.0177487:0.19079:0.780253:184305:rs2905039
1   775181  rs61768182  A   G   .   PASS    AF=0.154809 ES:SE:LP:AF:SS:ID   0.001659:0.0177118:0.0336827:0.154809:184305:rs61768182
1   777122  rs2980319   A   T   .   PASS    AF=0.785305 ES:SE:LP:AF:SS:ID   2.8e-05:0.0173153:0.000560732:0.785305:184305:rs2980319
1   777232  rs112618790 C   T   .   PASS    AF=0.065846 ES:SE:LP:AF:SS:ID   0.035269:0.029713:0.628505:0.065846:184305:rs112618790
1   778745  rs1055606   A   G   .   PASS    AF=0.147126 ES:SE:LP:AF:SS:ID   -0.002725:0.01808:0.0554199:0.147126:184305:rs1055606
1   779322  rs4040617   A   G   .   PASS    AF=0.152134 ES:SE:LP:AF:SS:ID   -0.002915:0.017778:0.0606018:0.152134:184305:rs4040617
1   780785  rs2977612   T   A   .   PASS    AF=0.769873 ES:SE:LP:AF:SS:ID   0.001497:0.0167895:0.0320065:0.769873:184305:rs2977612
1   781845  rs61768199  A   G   .   PASS    AF=0.096234 ES:SE:LP:AF:SS:ID   -0.006469:0.0224577:0.111648:0.096234:184305:rs61768199
1   782981  rs6594026   C   T   .   PASS    AF=0.190557 ES:SE:LP:AF:SS:ID   -0.009817:0.0171273:0.246781:0.190557:184305:rs6594026
1   783318  rs6686696   A   G   .   PASS    AF=0.138281 ES:SE:LP:AF:SS:ID   -0.005518:0.018798:0.114012:0.138281:184305:rs6686696
1   785050  rs2905062   G   A   .   PASS    AF=0.763925 ES:SE:LP:AF:SS:ID   -0.000143:0.0165277:0.00300846:0.763925:184305:rs2905062
1   785989  rs2980300   T   C   .   PASS    AF=0.75437  ES:SE:LP:AF:SS:ID   0.000981:0.0163463:0.021297:0.75437:184305:rs2980300
1   786995  rs61768202  G   A   .   PASS    AF=0.151266 ES:SE:LP:AF:SS:ID   -0.002106:0.0182777:0.0417856:0.151266:184305:rs61768202
1   787121  rs12077234  T   A   .   PASS    AF=0.156307 ES:SE:LP:AF:SS:ID   -0.008706:0.0188632:0.190834:0.156307:184305:rs12077234
1   787151  rs2519065   G   A   .   PASS    AF=0.168643 ES:SE:LP:AF:SS:ID   -0.001924:0.0189121:0.0366996:0.168643:184305:rs2519065
1   787399  rs2905055   G   T   .   PASS    AF=0.747237 ES:SE:LP:AF:SS:ID   -0.000423:0.0172794:0.00856578:0.747237:184305:rs2905055
1   787606  rs3863622   G   T   .   PASS    AF=0.151655 ES:SE:LP:AF:SS:ID   -0.007309:0.0185764:0.158651:0.151655:184305:rs3863622
1   787685  rs2905054   G   T   .   PASS    AF=0.737835 ES:SE:LP:AF:SS:ID   -0.001878:0.0170068:0.0399714:0.737835:184305:rs2905054
1   787844  rs2905053   C   T   .   PASS    AF=0.764577 ES:SE:LP:AF:SS:ID   -0.000971:0.0173566:0.019821:0.764577:184305:rs2905053