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-22607_1,TotalVariants=13566906,VariantsNotRead=0,HarmonisedVariants=13566906,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-22607_1/ukb-d-22607_1_data.json --ref /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/QC/genomes/b37/human_g1k_v37.fasta; 1.1.1",
    "file_date": "2019-11-25T15:13:25.613601",
    "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-22607_1/ukb-d-22607_1.vcf.gz -O z /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-22607_1/ukb-d-22607_1_data.vcf.gz; Date=Mon Nov 25 15:48:03 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-22607_1/ukb-d-22607_1.vcf.gz; Date=Sun May 10 23:24:50 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-22607_1/ukb-d-22607_1.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-22607_1/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 16:36:59 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-22607_1/ukb-d-22607_1.vcf.gz ...
Read summary statistics for 13566906 SNPs.
Dropped 12682 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: 0.0466 (0.0059)
Lambda GC: 1.0844
Mean Chi^2: 1.0865
Intercept: 1.0043 (0.0068)
Ratio: 0.0499 (0.0791)
Analysis finished at Mon Nov 25 16:39:17 2019
Total time elapsed: 2.0m:17.93s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9521,
    "inflation_factor": 1.0521,
    "mean_EFFECT": 0.0001,
    "n": 90145,
    "n_snps": 13566906,
    "n_clumped_hits": 1,
    "n_p_sig": 36,
    "n_mono": 0,
    "n_ns": 1251222,
    "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": 563168,
    "n_est": 90469.0032,
    "ratio_se_n": 1.0018,
    "mean_diff": 0.0001,
    "ratio_diff": 82.2084,
    "sd_y_est1": 0.4996,
    "sd_y_est2": 0.5005,
    "r2_sum1": 0.0001,
    "r2_sum2": 0.0004,
    "r2_sum3": 0.0004,
    "r2_sum4": 0.0004,
    "ldsc_nsnp_merge_refpanel_ld": 1283504,
    "ldsc_nsnp_merge_regression_ld": 1283504,
    "ldsc_observed_scale_h2_beta": 0.0466,
    "ldsc_observed_scale_h2_se": 0.0059,
    "ldsc_intercept_beta": 1.0043,
    "ldsc_intercept_se": 0.0068,
    "ldsc_lambda_gc": 1.0844,
    "ldsc_mean_chisq": 1.0865,
    "ldsc_ratio": 0.0497
}

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 13554888 0 NA NA NA NA NA NA NA NA
character REF 0 1.0000000 1 100 0 57046 0 NA NA NA NA NA NA NA NA
character ALT 0 1.0000000 1 342 0 33331 0 NA NA NA NA NA NA NA NA
numeric CHROM 0 1.0000000 NA NA NA NA NA 9.051311e+00 6.184953e+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 7.902483e+07 5.591673e+07 3.02000e+02 3.292761e+07 7.013477e+07 1.148626e+08 2.492309e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA 6.620000e-05 1.373090e-02 -1.62547e-01 -3.690200e-03 2.670000e-05 3.777000e-03 1.627730e-01 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 9.847300e-03 9.489900e-03 1.94110e-03 2.813400e-03 5.175100e-03 1.413970e-02 4.773580e-02 ▇▂▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.918584e-01 2.909521e-01 0.00000e+00 2.374029e-01 4.890475e-01 7.440412e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.918566e-01 2.909531e-01 0.00000e+00 2.373996e-01 4.890460e-01 7.440412e-01 1.000000e+00 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA 1.910656e-01 2.544726e-01 1.00000e-03 7.499100e-03 6.029750e-02 2.957600e-01 9.990000e-01 ▇▂▁▁▁
numeric AF_reference 563168 0.9584896 NA NA NA NA NA 1.965220e-01 2.471439e-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 9.014500e+04 0.000000e+00 9.01450e+04 9.014500e+04 9.014500e+04 9.014500e+04 9.014500e+04 ▁▁▇▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 692794 rs530212009 CA C 0.0026658 0.0041108 0.5166709 0.5166691 0.1113110 0.1894970 90145
1 693731 rs12238997 A G 0.0035140 0.0038928 0.3666942 0.3666900 0.1162900 0.1417730 90145
1 707522 rs371890604 G C 0.0009390 0.0043748 0.8300440 0.8300429 0.0977515 0.1293930 90145
1 717587 rs144155419 G A -0.0077200 0.0104408 0.4596603 0.4596582 0.0157464 0.0045926 90145
1 723329 rs189787166 A T 0.0216604 0.0306324 0.4795015 0.4794997 0.0017529 0.0003994 90145
1 730087 rs148120343 T C 0.0026534 0.0053990 0.6231075 0.6231067 0.0568458 0.0127796 90145
1 731718 rs142557973 T C 0.0011840 0.0036943 0.7485848 0.7485839 0.1221550 0.1543530 90145
1 732032 rs61770163 A C 0.0016729 0.0039395 0.6710904 0.6710892 0.1218610 0.1555510 90145
1 734349 rs141242758 T C 0.0012153 0.0036972 0.7423693 0.7423674 0.1213840 0.1525560 90145
1 740284 rs61770167 C T -0.0034243 0.0169369 0.8397749 0.8397752 0.0057634 0.0023962 90145
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
23 154923311 rs141127553 C T 0.0023582 0.0043188 0.5850446 0.5850430 0.0553120 0.0309934 90145
23 154923374 rs111332691 T A 0.0045979 0.0047003 0.3279676 0.3279654 0.0448888 0.0116556 90145
23 154925045 rs509981 C T -0.0017436 0.0022649 0.4413986 0.4413958 0.2445900 0.3634440 90145
23 154925895 rs538470 C T -0.0015016 0.0023155 0.5166733 0.5166705 0.2410980 0.3634440 90145
23 154927581 rs644138 G A -0.0009795 0.0021305 0.6456795 0.6456798 0.3003080 0.4635760 90145
23 154929412 rs557132 C T -0.0018191 0.0022656 0.4220141 0.4220117 0.2444460 0.3568210 90145
23 154929637 rs35185538 CT C -0.0019511 0.0023658 0.4095520 0.4095511 0.2288140 0.3011920 90145
23 154929952 rs4012982 CAA C -0.0022591 0.0023846 0.3434488 0.3434460 0.2383540 0.3165560 90145
23 154930230 rs781880 A G -0.0018389 0.0022648 0.4168348 0.4168327 0.2449110 0.3618540 90145
23 154930487 rs781879 T A -0.0070286 0.0076820 0.3602260 0.3602232 0.0196680 0.1263580 90145

bcf preview

1   692794  rs530212009 CA  C   .   PASS    AF=0.111311 ES:SE:LP:AF:SS:ID   0.00266578:0.00411076:0.286786:0.111311:90145:1_692794_CA_C
1   693731  rs12238997  A   G   .   PASS    AF=0.11629  ES:SE:LP:AF:SS:ID   0.00351395:0.00389275:0.435696:0.11629:90145:rs12238997
1   707522  rs371890604 G   C   .   PASS    AF=0.0977515    ES:SE:LP:AF:SS:ID   0.000939038:0.00437481:0.0808989:0.0977515:90145:rs371890604
1   717587  rs144155419 G   A   .   PASS    AF=0.0157464    ES:SE:LP:AF:SS:ID   -0.00772003:0.0104408:0.337563:0.0157464:90145:rs144155419
1   723329  rs189787166 A   T   .   PASS    AF=0.00175286   ES:SE:LP:AF:SS:ID   0.0216604:0.0306324:0.31921:0.00175286:90145:rs189787166
1   730087  rs148120343 T   C   .   PASS    AF=0.0568458    ES:SE:LP:AF:SS:ID   0.00265336:0.00539902:0.205437:0.0568458:90145:rs148120343
1   731718  rs58276399  T   C   .   PASS    AF=0.122155 ES:SE:LP:AF:SS:ID   0.00118404:0.00369427:0.125759:0.122155:90145:rs58276399
1   732032  rs61770163  A   C   .   PASS    AF=0.121861 ES:SE:LP:AF:SS:ID   0.00167294:0.00393954:0.173219:0.121861:90145:rs61770163
1   734349  rs141242758 T   C   .   PASS    AF=0.121384 ES:SE:LP:AF:SS:ID   0.00121533:0.00369716:0.12938:0.121384:90145:rs141242758
1   740284  rs61770167  C   T   .   PASS    AF=0.00576344   ES:SE:LP:AF:SS:ID   -0.00342432:0.0169369:0.0758371:0.00576344:90145:rs61770167
1   742813  rs112573343 C   T   .   PASS    AF=0.00181816   ES:SE:LP:AF:SS:ID   -0.0337165:0.0324798:0.523985:0.00181816:90145:rs112573343
1   749963  rs529266287 T   TAA .   PASS    AF=0.869117 ES:SE:LP:AF:SS:ID   -0.00152738:0.0036372:0.170994:0.869117:90145:rs529266287
1   750230  rs190826124 G   C   .   PASS    AF=0.00159834   ES:SE:LP:AF:SS:ID   0.0267542:0.0321471:0.39225:0.00159834:90145:rs190826124
1   751343  rs28544273  T   A   .   PASS    AF=0.123502 ES:SE:LP:AF:SS:ID   0.00131863:0.00360586:0.145939:0.123502:90145:rs28544273
1   751488  rs200141114 G   GA  .   PASS    AF=0.143012 ES:SE:LP:AF:SS:ID   0.0033802:0.00356954:0.463867:0.143012:90145:rs200141114
1   751756  rs28527770  T   C   .   PASS    AF=0.123637 ES:SE:LP:AF:SS:ID   0.00115397:0.00360064:0.125751:0.123637:90145:rs28527770
1   753405  rs3115860   C   A   .   PASS    AF=0.870111 ES:SE:LP:AF:SS:ID   -0.00055318:0.0035084:0.0581334:0.870111:90145:rs3115860
1   753425  rs3131970   T   C   .   PASS    AF=0.874755 ES:SE:LP:AF:SS:ID   -0.000419569:0.00356542:0.0427165:0.874755:90145:rs3131970
1   753541  rs2073813   G   A   .   PASS    AF=0.129319 ES:SE:LP:AF:SS:ID   0.00101045:0.00351936:0.111244:0.129319:90145:rs2073813
1   754105  rs12184325  C   T   .   PASS    AF=0.0358644    ES:SE:LP:AF:SS:ID   0.0137067:0.00642231:1.48378:0.0358644:90145:rs12184325
1   754182  rs3131969   A   G   .   PASS    AF=0.869758 ES:SE:LP:AF:SS:ID   -0.00058691:0.00350547:0.0619639:0.869758:90145:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.869836 ES:SE:LP:AF:SS:ID   -0.000479192:0.00350702:0.0499678:0.869836:90145:rs3131968
1   754334  rs3131967   T   C   .   PASS    AF=0.869754 ES:SE:LP:AF:SS:ID   -0.000577793:0.00350532:0.0609422:0.869754:90145:rs3131967
1   754433  rs150578204 G   A   .   PASS    AF=0.00532358   ES:SE:LP:AF:SS:ID   0.0323348:0.0174825:1.19124:0.00532358:90145:rs150578204
1   754458  rs142682604 G   T   .   PASS    AF=0.00528889   ES:SE:LP:AF:SS:ID   0.0324885:0.0175259:1.19532:0.00528889:90145:rs142682604
1   755435  rs184270342 T   G   .   PASS    AF=0.00566273   ES:SE:LP:AF:SS:ID   -0.0171758:0.0172464:0.495802:0.00566273:90145:rs184270342
1   755890  rs3115858   A   T   .   PASS    AF=0.869737 ES:SE:LP:AF:SS:ID   -0.000812371:0.00349811:0.0881188:0.869737:90145:rs3115858
1   756434  rs61768170  G   C   .   PASS    AF=0.126726 ES:SE:LP:AF:SS:ID   0.00136654:0.00357075:0.1537:0.126726:90145:rs61768170
1   756604  rs3131962   A   G   .   PASS    AF=0.869261 ES:SE:LP:AF:SS:ID   -0.00123959:0.00348899:0.141237:0.869261:90145:rs3131962
1   757640  rs3115853   G   A   .   PASS    AF=0.86865  ES:SE:LP:AF:SS:ID   -0.000667148:0.00348675:0.0714705:0.86865:90145:rs3115853
1   757734  rs4951929   C   T   .   PASS    AF=0.869414 ES:SE:LP:AF:SS:ID   -0.000899525:0.00349218:0.0986888:0.869414:90145:rs4951929
1   757936  rs4951862   C   A   .   PASS    AF=0.869419 ES:SE:LP:AF:SS:ID   -0.000893619:0.00349242:0.0979704:0.869419:90145:rs4951862
1   758144  rs3131956   A   G   .   PASS    AF=0.869421 ES:SE:LP:AF:SS:ID   -0.00089542:0.00349244:0.0981865:0.869421:90145:rs3131956
1   758626  rs3131954   C   T   .   PASS    AF=0.869904 ES:SE:LP:AF:SS:ID   -0.000601731:0.00350182:0.063703:0.869904:90145:rs3131954
1   759293  rs10157329  T   A   .   PASS    AF=0.0990489    ES:SE:LP:AF:SS:ID   -5.29959e-05:0.00407458:0.00453022:0.0990489:90145:rs10157329
1   759600  rs545998451 AGT A   .   PASS    AF=0.00650816   ES:SE:LP:AF:SS:ID   -0.0249916:0.0157013:0.952885:0.00650816:90145:1_759600_AGT_A
1   759837  rs3115851   T   A   .   PASS    AF=0.873894 ES:SE:LP:AF:SS:ID   -0.000484473:0.00355375:0.049848:0.873894:90145:rs3115851
1   761732  rs2286139   C   T   .   PASS    AF=0.863267 ES:SE:LP:AF:SS:ID   -0.0011191:0.00348585:0.125994:0.863267:90145:rs2286139
1   761752  rs1057213   C   T   .   PASS    AF=0.868697 ES:SE:LP:AF:SS:ID   -0.00106472:0.00352042:0.117865:0.868697:90145:rs1057213
1   762273  rs3115849   G   A   .   PASS    AF=0.865579 ES:SE:LP:AF:SS:ID   -0.000612563:0.00352102:0.0645497:0.865579:90145:rs3115849
1   762485  rs12095200  C   A   .   PASS    AF=0.0993705    ES:SE:LP:AF:SS:ID   0.000392339:0.00421421:0.0334711:0.0993705:90145:rs12095200
1   762589  rs3115848   G   C   .   PASS    AF=0.870867 ES:SE:LP:AF:SS:ID   -0.000706679:0.00356126:0.0743244:0.870867:90145:rs3115848
1   762592  rs3131950   C   G   .   PASS    AF=0.870867 ES:SE:LP:AF:SS:ID   -0.000707251:0.00356126:0.0743894:0.870867:90145:rs3131950
1   762601  rs3131949   T   C   .   PASS    AF=0.870864 ES:SE:LP:AF:SS:ID   -0.00070659:0.00356127:0.0743141:0.870864:90145:rs3131949
1   762632  rs3131948   T   A   .   PASS    AF=0.87123  ES:SE:LP:AF:SS:ID   -0.00101039:0.00356297:0.109728:0.87123:90145:rs3131948
1   764191  rs7515915   T   G   .   PASS    AF=0.126315 ES:SE:LP:AF:SS:ID   0.000980789:0.00356682:0.106052:0.126315:90145:rs7515915
1   766007  rs61768174  A   C   .   PASS    AF=0.105889 ES:SE:LP:AF:SS:ID   0.00107627:0.0038768:0.107179:0.105889:90145:rs61768174
1   766105  rs2519015   T   A   .   PASS    AF=0.854607 ES:SE:LP:AF:SS:ID   -0.000757987:0.00348462:0.0820741:0.854607:90145:rs2519015
1   767393  rs538667473 A   C   .   PASS    AF=0.00166577   ES:SE:LP:AF:SS:ID   0.016151:0.0307262:0.222474:0.00166577:90145:rs538667473
1   768116  rs376645387 A   AGTTTT  .   PASS    AF=0.839373 ES:SE:LP:AF:SS:ID   -0.00307101:0.00344265:0.429026:0.839373:90145:rs376645387