Summary

Summary {data-width=650}

Manhattan plot

manhattan_plot

QQ plot

qq_plot

AF plot

af_plot

P-Z plot

pz_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-b-5102,TotalVariants=7659767,VariantsNotRead=0,HarmonisedVariants=7659767,VariantsNotHarmonised=0,SwitchedAlleles=7659767,NormalisedVariants=0,TotalControls=75889,TotalCases=52017,StudyType=CaseControl>",
    "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>",
    "Gwas2VCF_command": "--data /data/cromwell-executions/qc/7ac5cdec-8ad2-4e55-b74a-623512103a9d/call-vcf/inputs/-261021508/upload.txt.gz --id ieu-b-5102 --json /data/cromwell-executions/qc/7ac5cdec-8ad2-4e55-b74a-623512103a9d/call-vcf/inputs/-261021508/ieu-b-5102_data.json --ref /data/cromwell-executions/qc/7ac5cdec-8ad2-4e55-b74a-623512103a9d/call-vcf/inputs/1899004205/human_g1k_v37.fasta --dbsnp /data/cromwell-executions/qc/7ac5cdec-8ad2-4e55-b74a-623512103a9d/call-vcf/inputs/-307190728/dbsnp.v153.b37.vcf.gz --out /data/igd/ieu-b-5102/ieu-b-5102.vcf.gz --alias alias.txt --cohort_cases 52017 --cohort_controls 75889; 1.3.0",
    "file_date": "2023-02-03T13:18:20.131911",
    "bcftools_viewVersion": "1.9+htslib-1.9",
    "bcftools_viewCommand": "view -h /data/cromwell-executions/qc/7ac5cdec-8ad2-4e55-b74a-623512103a9d/call-report/inputs/-261021508/ieu-b-5102.vcf.gz; Date=Fri Feb  3 13:41:28 2023"
}

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 /data/cromwell-executions/qc/7ac5cdec-8ad2-4e55-b74a-623512103a9d/call-ldsc/inputs/-261021508/ieu-b-5102.vcf.gz \
--ref-ld-chr /data/ref/eur_w_ld_chr/ \
--out /data/igd/ieu-b-5102/ldsc.txt \
--w-ld-chr /data/ref/eur_w_ld_chr/ 

Beginning analysis at Fri Feb  3 13:32:07 2023
Reading summary statistics from /data/cromwell-executions/qc/7ac5cdec-8ad2-4e55-b74a-623512103a9d/call-ldsc/inputs/-261021508/ieu-b-5102.vcf.gz ...
Read summary statistics for 7659654 SNPs.
Dropped 26958 SNPs with duplicated rs numbers.
Reading reference panel LD Score from /data/ref/eur_w_ld_chr/[1-22] ... (ldscore_fromlist)
Read reference panel LD Scores for 1290028 SNPs.
Removing partitioned LD Scores with zero variance.
Reading regression weight LD Score from /data/ref/eur_w_ld_chr/[1-22] ... (ldscore_fromlist)
Read regression weight LD Scores for 1290028 SNPs.
After merging with reference panel LD, 1213856 SNPs remain.
After merging with regression SNP LD, 1213856 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.3578 (0.0117)
Lambda GC: 1.7367
Mean Chi^2: 2.0097
Intercept: 1.0778 (0.0108)
Ratio: 0.0771 (0.0107)
Analysis finished at Fri Feb  3 13:33:54 2023
Total time elapsed: 1.0m:47.2s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9444,
    "inflation_factor": 1.6147,
    "mean_EFFECT": 0.0021,
    "n": 130644,
    "n_snps": 7659767,
    "n_clumped_hits": 158,
    "n_p_sig": 20457,
    "n_mono": 0,
    "n_ns": 0,
    "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": 75969,
    "n_est": 129136.5882,
    "ratio_se_n": 0.9942,
    "mean_diff": -0.0012,
    "ratio_diff": 25.9719,
    "sd_y_est1": 2.2348,
    "sd_y_est2": 2.2218,
    "r2_sum1": 0.2672,
    "r2_sum2": 0.0535,
    "r2_sum3": 0.0541,
    "r2_sum4": 0.0538,
    "ldsc_nsnp_merge_refpanel_ld": 1213856,
    "ldsc_nsnp_merge_regression_ld": 1213856,
    "ldsc_observed_scale_h2_beta": 0.3578,
    "ldsc_observed_scale_h2_se": 0.0117,
    "ldsc_intercept_beta": 1.0778,
    "ldsc_intercept_se": 0.0108,
    "ldsc_lambda_gc": 1.7367,
    "ldsc_mean_chisq": 2.0097,
    "ldsc_ratio": 0.0771
}

Flags

name value
af_correlation FALSE
inflation_factor TRUE
n FALSE
is_snpid_non_unique TRUE
mean_EFFECT_nonfinite FALSE
mean_EFFECT_05 FALSE
mean_EFFECT_01 FALSE
mean_chisq TRUE
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 79 0.9999897 3 58 0 7654735 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 8.659724e+00 5.763148e+00 1.0000 4.000000e+00 8.000000e+00 1.300000e+01 2.200000e+01 ▇▅▅▂▂
numeric POS 0 1.0000000 NA NA NA NA NA 7.868527e+07 5.645465e+07 828.0000 3.219049e+07 6.913809e+07 1.145949e+08 2.492225e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA 2.082000e-03 2.505950e-02 -0.7751 -1.099930e-02 1.300900e-03 1.409890e-02 3.086060e-01 ▁▁▁▇▁
numeric SE 0 1.0000000 NA NA NA NA NA 1.790980e-02 1.122700e-02 0.0085 9.600000e-03 1.300000e-02 2.270000e-02 1.516000e-01 ▇▁▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.230276e-01 3.068999e-01 0.0000 1.388999e-01 3.914002e-01 6.874007e-01 1.000000e+00 ▇▅▅▅▅
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.230225e-01 3.069064e-01 0.0000 1.388863e-01 3.913864e-01 6.873473e-01 1.000000e+00 ▇▅▅▅▅
numeric AF 0 1.0000000 NA NA NA NA NA 2.555133e-01 2.604380e-01 0.0100 4.300000e-02 1.510000e-01 4.030000e-01 9.891000e-01 ▇▂▂▁▁
numeric AF_reference 75969 0.9900821 NA NA NA NA NA 2.549318e-01 2.526404e-01 0.0000 4.772360e-02 1.653350e-01 3.985620e-01 1.000000e+00 ▇▃▂▁▁
numeric N 0 1.0000000 NA NA NA NA NA 1.280093e+05 8.873299e+03 65499.0000 1.306440e+05 1.306440e+05 1.306440e+05 1.306440e+05 ▁▁▁▁▇

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 693731 rs12238997 A G -0.0011993 0.0172 0.9428001 0.9444121 0.128 0.1417730 126849
1 705882 rs72631875 G A 0.0004001 0.0532 0.9933000 0.9939997 0.064 0.0315495 81262
1 706368 rs55727773 A G -0.0086029 0.0163 0.5981994 0.5976488 0.487 0.2751600 126849
1 714596 rs149887893 T C 0.0589966 0.0417 0.1572002 0.1571311 0.033 NA 93692
1 715265 rs12184267 C T 0.0571949 0.0390 0.1428999 0.1425023 0.034 0.0275559 93692
1 715367 rs12184277 A G 0.0540972 0.0388 0.1631999 0.1632398 0.035 0.0281550 93692
1 717485 rs12184279 C A 0.0530000 0.0392 0.1764002 0.1763623 0.034 NA 93692
1 717587 rs144155419 G A 0.0361973 0.0563 0.5205998 0.5202656 0.016 0.0045927 122898
1 720381 rs116801199 G T 0.0577033 0.0385 0.1331999 0.1339289 0.035 0.0359425 93692
1 721290 rs12565286 G C 0.0591027 0.0382 0.1214999 0.1218172 0.035 0.0371406 93692
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51219387 rs9616832 T C 0.0419998 0.0207 0.0421803 0.0424608 0.070 0.0654952 130644
22 51219704 rs147475742 G A 0.0515986 0.0275 0.0611294 0.0606124 0.042 0.0473243 130644
22 51220517 rs9616980 C G 0.1126980 0.0754 0.1348000 0.1350010 0.012 0.0027955 70830
22 51221190 rs369304721 G A 0.0579046 0.0277 0.0368901 0.0365802 0.049 NA 130644
22 51221731 rs115055839 T C 0.0419998 0.0209 0.0438198 0.0444778 0.070 0.0625000 130644
22 51222100 rs114553188 G T -0.0120965 0.0223 0.5892004 0.5875127 0.055 0.0880591 130644
22 51223637 rs375798137 G A -0.0112960 0.0225 0.6172001 0.6156363 0.054 0.0788738 130644
22 51229805 rs9616985 T C 0.0406033 0.0211 0.0545997 0.0543136 0.070 0.0730831 130644
22 51232488 rs376461333 A G -0.0162965 0.0468 0.7276005 0.7276781 0.021 NA 130504
22 51237063 rs3896457 T C 0.0026034 0.0124 0.8360000 0.8337061 0.303 0.2050720 130263

bcf preview

1   693731  rs12238997  A   G   .   PASS    AF=0.128    ES:SE:LP:AF:SS:SI:NC:ID -0.00119928:0.0172:0.0255804:0.128:126849:0.557:51788:rs12238997
1   705882  rs72631875  G   A   .   PASS    AF=0.064    ES:SE:LP:AF:SS:SI:NC:ID 0.00040008:0.0532:0.00291956:0.064:81262:0.172:32586:rs72631875
1   706368  rs963699400 A   G   .   PASS    AF=0.487    ES:SE:LP:AF:SS:SI:NC:ID -0.00860289:0.0163:0.223154:0.487:126849:0.286:51788:rs963699400
1   714596  rs149887893 T   C   .   PASS    AF=0.033    ES:SE:LP:AF:SS:SI:NC:ID 0.0589966:0.0417:0.803547:0.033:93692:0.413:40598:rs149887893
1   715265  rs12184267  C   T   .   PASS    AF=0.034    ES:SE:LP:AF:SS:SI:NC:ID 0.0571949:0.039:0.844968:0.034:93692:0.45:40598:rs12184267
1   715367  rs12184277  A   G   .   PASS    AF=0.035    ES:SE:LP:AF:SS:SI:NC:ID 0.0540972:0.0388:0.78728:0.035:93692:0.453:40598:rs12184277
1   717485  rs12184279  C   A   .   PASS    AF=0.034    ES:SE:LP:AF:SS:SI:NC:ID 0.053:0.0392:0.753501:0.034:93692:0.451:40598:rs12184279
1   717587  rs144155419 G   A   .   PASS    AF=0.016    ES:SE:LP:AF:SS:SI:NC:ID 0.0361973:0.0563:0.283496:0.016:122898:0.332:49709:rs144155419
1   720381  rs116801199 G   T   .   PASS    AF=0.035    ES:SE:LP:AF:SS:SI:NC:ID 0.0577033:0.0385:0.875496:0.035:93692:0.453:40598:rs116801199
1   721290  rs12565286  G   C   .   PASS    AF=0.035    ES:SE:LP:AF:SS:SI:NC:ID 0.0591027:0.0382:0.915424:0.035:93692:0.458:40598:rs12565286
1   722670  rs116030099 T   C   .   PASS    AF=0.101    ES:SE:LP:AF:SS:SI:NC:ID 0.0657019:0.0328:1.34123:0.101:88498:0.275:35713:rs116030099
1   723891  rs2977670   G   C   .   PASS    AF=0.9507   ES:SE:LP:AF:SS:SI:NC:ID -0.0399993:0.0341:0.617803:0.9507:105429:0.381:43539:rs2977670
1   726794  rs28454925  C   G   .   PASS    AF=0.034    ES:SE:LP:AF:SS:SI:NC:ID 0.0513986:0.0385:0.741363:0.034:93692:0.463:40598:rs28454925
1   729632  rs116720794 C   T   .   PASS    AF=0.034    ES:SE:LP:AF:SS:SI:NC:ID 0.0505988:0.0385:0.723079:0.034:93692:0.462:40598:rs116720794
1   729679  rs4951859   C   G   .   PASS    AF=0.823    ES:SE:LP:AF:SS:SI:NC:ID -0.00519647:0.0138:0.152612:0.823:126849:0.659:51788:rs4951859
1   730087  rs148120343 T   C   .   PASS    AF=0.057    ES:SE:LP:AF:SS:SI:NC:ID -0.0222995:0.0269:0.391474:0.057:126849:0.48:51788:rs148120343
1   731453  rs186002080 G   A   .   PASS    AF=0.014    ES:SE:LP:AF:SS:SI:NC:ID 0.0527997:0.1146:0.190306:0.014:70622:0.187:28767:rs186002080
1   731718  rs58276399  T   C   .   PASS    AF=0.137    ES:SE:LP:AF:SS:SI:NC:ID 0.000700245:0.0153:0.0166444:0.137:126849:0.66:51788:rs58276399
1   732989  rs369030935 C   T   .   PASS    AF=0.021    ES:SE:LP:AF:SS:SI:NC:ID -0.0226026:0.0728:0.121363:0.021:90044:0.244:35818:rs369030935
1   734349  rs141242758 T   C   .   PASS    AF=0.136    ES:SE:LP:AF:SS:SI:NC:ID 0.00120072:0.0152:0.0271032:0.136:127964:0.664:51974:rs141242758
1   736289  rs1254887344    T   A   .   PASS    AF=0.142    ES:SE:LP:AF:SS:SI:NC:ID 0.00640044:0.0153:0.171082:0.142:126849:0.636:51788:rs1254887344
1   752478  rs146277091 G   A   .   PASS    AF=0.034    ES:SE:LP:AF:SS:SI:NC:ID 0.0471964:0.0381:0.66736:0.034:93692:0.482:40598:rs146277091
1   752566  rs3094315   G   A   .   PASS    AF=0.824    ES:SE:LP:AF:SS:SI:NC:ID -0.00370313:0.0127:0.112214:0.824:126849:0.78:51788:rs3094315
1   752721  rs3131972   A   G   .   PASS    AF=0.821    ES:SE:LP:AF:SS:SI:NC:ID -0.0034042:0.0126:0.103584:0.821:126849:0.774:51788:rs3131972
1   753405  rs3115860   C   A   .   PASS    AF=0.852    ES:SE:LP:AF:SS:SI:NC:ID 0.00120072:0.0137:0.0303977:0.852:126849:0.773:51788:rs3115860
1   753541  rs1388595942    G   A   .   PASS    AF=0.151    ES:SE:LP:AF:SS:SI:NC:ID -0:0.0137:0.000738929:0.151:126849:0.757:51788:rs1388595942
1   754063  rs12184312  G   T   .   PASS    AF=0.034    ES:SE:LP:AF:SS:SI:NC:ID 0.0564011:0.039:0.827981:0.034:93692:0.458:40598:rs12184312
1   754105  rs12184325  C   T   .   PASS    AF=0.034    ES:SE:LP:AF:SS:SI:NC:ID 0.0628972:0.039:0.971836:0.034:93692:0.458:40598:rs12184325
1   754182  rs3131969   A   G   .   PASS    AF=0.847    ES:SE:LP:AF:SS:SI:NC:ID 0.0010005:0.0136:0.0263181:0.847:126849:0.763:51788:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.847    ES:SE:LP:AF:SS:SI:NC:ID 0.00110061:0.0136:0.0296066:0.847:126849:0.763:51788:rs3131968
1   754211  rs12184313  G   A   .   PASS    AF=0.034    ES:SE:LP:AF:SS:SI:NC:ID 0.0596969:0.0388:0.907982:0.034:93692:0.459:40598:rs12184313
1   754334  rs3131967   T   C   .   PASS    AF=0.848    ES:SE:LP:AF:SS:SI:NC:ID 0.00130085:0.0136:0.0356932:0.848:126849:0.764:51788:rs3131967
1   754503  rs3115859   G   A   .   PASS    AF=0.821    ES:SE:LP:AF:SS:SI:NC:ID -0.0030952:0.0127:0.0931265:0.821:126849:0.764:51788:rs3115859
1   754629  rs10454459  A   G   .   PASS    AF=0.034    ES:SE:LP:AF:SS:SI:NC:ID 0.060196:0.0387:0.920096:0.034:93692:0.46:40598:rs10454459
1   754964  rs3131966   C   T   .   PASS    AF=0.821    ES:SE:LP:AF:SS:SI:NC:ID -0.0036035:0.0127:0.109747:0.821:126849:0.762:51788:rs3131966
1   755775  rs3131965   A   G   .   PASS    AF=0.825    ES:SE:LP:AF:SS:SI:NC:ID -0.00479847:0.0129:0.148253:0.825:126849:0.754:51788:rs3131965
1   755890  rs1280367067    A   T   .   PASS    AF=0.851    ES:SE:LP:AF:SS:SI:NC:ID 0.00110061:0.0137:0.0282141:0.851:127964:0.765:51974:rs1280367067
1   756604  rs3131962   A   G   .   PASS    AF=0.851    ES:SE:LP:AF:SS:SI:NC:ID 0.00140098:0.0137:0.0381045:0.851:127964:0.766:51974:rs3131962
1   757640  rs3115853   G   A   .   PASS    AF=0.845    ES:SE:LP:AF:SS:SI:NC:ID 0.00130085:0.0135:0.033389:0.845:126849:0.763:51788:rs3115853
1   757734  rs1557551770    C   T   .   PASS    AF=0.851    ES:SE:LP:AF:SS:SI:NC:ID 0.00140098:0.0137:0.0382942:0.851:127964:0.766:51974:rs1557551770
1   757936  rs1360886751    C   A   .   PASS    AF=0.851    ES:SE:LP:AF:SS:SI:NC:ID 0.00150113:0.0137:0.0385314:0.851:127964:0.767:51974:rs1360886751
1   758144  rs3131956   A   G   .   PASS    AF=0.851    ES:SE:LP:AF:SS:SI:NC:ID 0.00150113:0.0137:0.0408632:0.851:127964:0.767:51974:rs3131956
1   758626  rs3131954   C   T   .   PASS    AF=0.852    ES:SE:LP:AF:SS:SI:NC:ID 0.00190181:0.0137:0.0506588:0.852:127964:0.764:51974:rs3131954
1   759036  rs114525117 G   A   .   PASS    AF=0.035    ES:SE:LP:AF:SS:SI:NC:ID 0.0476998:0.039:0.655804:0.035:99653:0.423:41559:rs114525117
1   760912  rs1048488   C   T   .   PASS    AF=0.825    ES:SE:LP:AF:SS:SI:NC:ID -0.00350385:0.0129:0.105296:0.825:126849:0.763:51788:rs1048488
1   760998  rs148828841 C   A   .   PASS    AF=0.034    ES:SE:LP:AF:SS:SI:NC:ID 0.0488962:0.0392:0.672437:0.034:99653:0.42:41559:rs148828841
1   761147  rs3115850   T   C   .   PASS    AF=0.825    ES:SE:LP:AF:SS:SI:NC:ID -0.0034042:0.0129:0.10111:0.825:126849:0.762:51788:rs3115850
1   761606  rs377377186 G   A   .   PASS    AF=0.033    ES:SE:LP:AF:SS:SI:NC:ID 0.0482978:0.0403:0.638272:0.033:99653:0.411:41559:rs377377186
1   761732  rs2286139   C   T   .   PASS    AF=0.842    ES:SE:LP:AF:SS:SI:NC:ID -0.000499875:0.0135:0.0121104:0.842:126849:0.762:51788:rs2286139
1   761881  rs374493323 A   C   .   PASS    AF=0.031    ES:SE:LP:AF:SS:SI:NC:ID 0.0551005:0.0422:0.716021:0.031:93692:0.428:40598:rs374493323