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-4946,TotalVariants=13567694,VariantsNotRead=0,HarmonisedVariants=13567694,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-4946/ukb-d-4946_data.json --ref /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/QC/genomes/b37/human_g1k_v37.fasta; 1.1.1",
    "file_date": "2019-11-25T16:21:09.911239",
    "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-4946/ukb-d-4946.vcf.gz -O z /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-4946/ukb-d-4946_data.vcf.gz; Date=Mon Nov 25 16:55:53 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-4946/ukb-d-4946.vcf.gz; Date=Sun May 10 05:49:25 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-4946/ukb-d-4946.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-4946/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 17:20:57 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-4946/ukb-d-4946.vcf.gz ...
Read summary statistics for 13567694 SNPs.
Dropped 12693 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, 1283503 SNPs remain.
After merging with regression SNP LD, 1283503 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: -0.0027 (0.0043)
Lambda GC: 1.0047
Mean Chi^2: 1.0035
Intercept: 1.0097 (0.0064)
Ratio: 2.7707 (1.8194)
Analysis finished at Mon Nov 25 17:23:14 2019
Total time elapsed: 2.0m:17.34s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9521,
    "inflation_factor": 1.0117,
    "mean_EFFECT": -3.6807e-06,
    "n": 116869,
    "n_snps": 13567694,
    "n_clumped_hits": 0,
    "n_p_sig": 53,
    "n_mono": 0,
    "n_ns": 1251202,
    "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": 563212,
    "n_est": 117338.7748,
    "ratio_se_n": 1.002,
    "mean_diff": -0,
    "ratio_diff": 212.9497,
    "sd_y_est1": 0.0901,
    "sd_y_est2": 0.0903,
    "r2_sum1": 0,
    "r2_sum2": 0,
    "r2_sum3": 0,
    "r2_sum4": 0,
    "ldsc_nsnp_merge_refpanel_ld": 1283503,
    "ldsc_nsnp_merge_regression_ld": 1283503,
    "ldsc_observed_scale_h2_beta": "NA",
    "ldsc_observed_scale_h2_se": "NA",
    "ldsc_intercept_beta": 1.0097,
    "ldsc_intercept_se": 0.0064,
    "ldsc_lambda_gc": 1.0047,
    "ldsc_mean_chisq": 1.0035,
    "ldsc_ratio": 2.7714
}

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 TRUE
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 13555665 0 NA NA NA NA NA NA NA NA
character REF 0 1.0000000 1 100 0 57053 0 NA NA NA NA NA NA NA NA
character ALT 0 1.0000000 1 342 0 33328 0 NA NA NA NA NA NA NA NA
numeric CHROM 0 1.0000000 NA NA NA NA NA 9.051369e+00 6.184959e+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 7.902512e+07 5.591687e+07 3.02000e+02 3.292864e+07 7.013814e+07 1.148574e+08 2.492309e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA -3.700000e-06 2.168900e-03 -3.73049e-02 -5.441000e-04 1.980000e-05 6.054000e-04 2.777270e-02 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 1.560100e-03 1.503400e-03 3.06100e-04 4.456000e-04 8.197000e-04 2.240200e-03 7.658800e-03 ▇▂▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.993216e-01 2.878092e-01 0.00000e+00 2.510169e-01 4.975033e-01 7.483504e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.993203e-01 2.878100e-01 0.00000e+00 2.510152e-01 4.975016e-01 7.483496e-01 1.000000e+00 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA 1.910597e-01 2.544605e-01 1.00000e-03 7.506700e-03 6.031390e-02 2.958250e-01 9.990000e-01 ▇▂▁▁▁
numeric AF_reference 563212 0.9584887 NA NA NA NA NA 1.965112e-01 2.471407e-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 1.168690e+05 0.000000e+00 1.16869e+05 1.168690e+05 1.168690e+05 1.168690e+05 1.168690e+05 ▁▁▇▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 692794 rs530212009 CA C 0.0000050 0.0006517 0.9939220 0.9939220 0.1115770 0.1894970 116869
1 693731 rs12238997 A G -0.0000166 0.0006163 0.9785230 0.9785231 0.1168970 0.1417730 116869
1 707522 rs371890604 G C 0.0002295 0.0006916 0.7400635 0.7400638 0.0982501 0.1293930 116869
1 717587 rs144155419 G A -0.0018246 0.0016596 0.2716008 0.2716005 0.0157095 0.0045926 116869
1 723329 rs189787166 A T -0.0015435 0.0049351 0.7544614 0.7544619 0.0016867 0.0003994 116869
1 730087 rs148120343 T C 0.0010259 0.0008594 0.2325691 0.2325675 0.0568845 0.0127796 116869
1 731718 rs142557973 T C -0.0000320 0.0005851 0.9563950 0.9563949 0.1227320 0.1543530 116869
1 732032 rs61770163 A C -0.0001109 0.0006234 0.8588450 0.8588450 0.1222520 0.1555510 116869
1 734349 rs141242758 T C 0.0000194 0.0005855 0.9735250 0.9735249 0.1219430 0.1525560 116869
1 740284 rs61770167 C T -0.0031279 0.0026160 0.2318291 0.2318264 0.0060264 0.0023962 116869
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
23 154923311 rs141127553 C T -0.0004021 0.0006824 0.5557136 0.5557118 0.0550798 0.0309934 116869
23 154923374 rs111332691 T A -0.0005319 0.0007467 0.4762906 0.4762889 0.0441092 0.0116556 116869
23 154925045 rs509981 C T -0.0002727 0.0003581 0.4464183 0.4464162 0.2437800 0.3634440 116869
23 154925895 rs538470 C T -0.0002347 0.0003662 0.5214600 0.5214594 0.2402700 0.3634440 116869
23 154927581 rs644138 G A -0.0003892 0.0003368 0.2477958 0.2477926 0.2992680 0.4635760 116869
23 154929412 rs557132 C T -0.0002780 0.0003583 0.4378224 0.4378209 0.2436020 0.3568210 116869
23 154929637 rs35185538 CT C -0.0005332 0.0003737 0.1536399 0.1536371 0.2275940 0.3011920 116869
23 154929952 rs4012982 CAA C -0.0003054 0.0003769 0.4178063 0.4178052 0.2377050 0.3165560 116869
23 154930230 rs781880 A G -0.0002957 0.0003582 0.4090025 0.4090021 0.2440820 0.3618540 116869
23 154930487 rs781879 T A 0.0008305 0.0012439 0.5043604 0.5043599 0.0190780 0.1263580 116869

bcf preview

1   692794  rs530212009 CA  C   .   PASS    AF=0.111577 ES:SE:LP:AF:SS:ID   4.96484e-06:0.000651746:0.0026477:0.111577:116869:1_692794_CA_C
1   693731  rs12238997  A   G   .   PASS    AF=0.116897 ES:SE:LP:AF:SS:ID   -1.65905e-05:0.000616276:0.00942896:0.116897:116869:rs12238997
1   707522  rs371890604 G   C   .   PASS    AF=0.0982501    ES:SE:LP:AF:SS:ID   0.000229458:0.00069162:0.130731:0.0982501:116869:rs371890604
1   717587  rs144155419 G   A   .   PASS    AF=0.0157095    ES:SE:LP:AF:SS:ID   -0.00182456:0.00165962:0.566069:0.0157095:116869:rs144155419
1   723329  rs189787166 A   T   .   PASS    AF=0.00168667   ES:SE:LP:AF:SS:ID   -0.0015435:0.00493507:0.122363:0.00168667:116869:rs189787166
1   730087  rs148120343 T   C   .   PASS    AF=0.0568845    ES:SE:LP:AF:SS:ID   0.00102594:0.000859411:0.633448:0.0568845:116869:rs148120343
1   731718  rs58276399  T   C   .   PASS    AF=0.122732 ES:SE:LP:AF:SS:ID   -3.19899e-05:0.000585059:0.0193627:0.122732:116869:rs58276399
1   732032  rs61770163  A   C   .   PASS    AF=0.122252 ES:SE:LP:AF:SS:ID   -0.000110873:0.000623426:0.0660852:0.122252:116869:rs61770163
1   734349  rs141242758 T   C   .   PASS    AF=0.121943 ES:SE:LP:AF:SS:ID   1.943e-05:0.000585457:0.0116529:0.121943:116869:rs141242758
1   740284  rs61770167  C   T   .   PASS    AF=0.00602642   ES:SE:LP:AF:SS:ID   -0.00312789:0.00261602:0.634832:0.00602642:116869:rs61770167
1   742813  rs112573343 C   T   .   PASS    AF=0.00177846   ES:SE:LP:AF:SS:ID   -0.00259452:0.00526579:0.206059:0.00177846:116869:rs112573343
1   749963  rs529266287 T   TAA .   PASS    AF=0.868711 ES:SE:LP:AF:SS:ID   -2.42693e-05:0.000577077:0.0148188:0.868711:116869:rs529266287
1   750230  rs190826124 G   C   .   PASS    AF=0.00158247   ES:SE:LP:AF:SS:ID   0.00252278:0.0051241:0.205873:0.00158247:116869:rs190826124
1   751343  rs28544273  T   A   .   PASS    AF=0.123857 ES:SE:LP:AF:SS:ID   -0.000291011:0.000571652:0.21417:0.123857:116869:rs28544273
1   751488  rs200141114 G   GA  .   PASS    AF=0.143426 ES:SE:LP:AF:SS:ID   -0.000301815:0.000566206:0.226213:0.143426:116869:rs200141114
1   751756  rs28527770  T   C   .   PASS    AF=0.123977 ES:SE:LP:AF:SS:ID   -0.000279479:0.00057082:0.204529:0.123977:116869:rs28527770
1   753405  rs3115860   C   A   .   PASS    AF=0.869921 ES:SE:LP:AF:SS:ID   4.58697e-05:0.000556033:0.029535:0.869921:116869:rs3115860
1   753425  rs3131970   T   C   .   PASS    AF=0.874599 ES:SE:LP:AF:SS:ID   0.000282649:0.000565374:0.209628:0.874599:116869:rs3131970
1   753541  rs2073813   G   A   .   PASS    AF=0.129653 ES:SE:LP:AF:SS:ID   2.91979e-07:0.000557267:0.000181573:0.129653:116869:rs2073813
1   754105  rs12184325  C   T   .   PASS    AF=0.0366136    ES:SE:LP:AF:SS:ID   0.00133343:0.00100791:0.730837:0.0366136:116869:rs12184325
1   754182  rs3131969   A   G   .   PASS    AF=0.869536 ES:SE:LP:AF:SS:ID   3.90955e-05:0.000555493:0.0250777:0.869536:116869:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.869655 ES:SE:LP:AF:SS:ID   4.46156e-05:0.000555774:0.0287163:0.869655:116869:rs3131968
1   754334  rs3131967   T   C   .   PASS    AF=0.869535 ES:SE:LP:AF:SS:ID   4.03051e-05:0.000555468:0.0258772:0.869535:116869:rs3131967
1   754433  rs150578204 G   A   .   PASS    AF=0.00511216   ES:SE:LP:AF:SS:ID   -0.0031474:0.00284115:0.571938:0.00511216:116869:rs150578204
1   754458  rs142682604 G   T   .   PASS    AF=0.00507941   ES:SE:LP:AF:SS:ID   -0.00320761:0.00284863:0.584758:0.00507941:116869:rs142682604
1   755435  rs184270342 T   G   .   PASS    AF=0.00550249   ES:SE:LP:AF:SS:ID   -0.000372917:0.00277723:0.0490591:0.00550249:116869:rs184270342
1   755890  rs3115858   A   T   .   PASS    AF=0.869651 ES:SE:LP:AF:SS:ID   5.78626e-05:0.000554539:0.0376794:0.869651:116869:rs3115858
1   756434  rs61768170  G   C   .   PASS    AF=0.126941 ES:SE:LP:AF:SS:ID   -8.56556e-05:0.00056582:0.0556782:0.126941:116869:rs61768170
1   756604  rs3131962   A   G   .   PASS    AF=0.869238 ES:SE:LP:AF:SS:ID   4.18869e-05:0.000553266:0.0270334:0.869238:116869:rs3131962
1   757640  rs3115853   G   A   .   PASS    AF=0.868444 ES:SE:LP:AF:SS:ID   7.04463e-05:0.000552608:0.0464524:0.868444:116869:rs3115853
1   757734  rs4951929   C   T   .   PASS    AF=0.869384 ES:SE:LP:AF:SS:ID   5.02967e-05:0.000553708:0.0326285:0.869384:116869:rs4951929
1   757936  rs4951862   C   A   .   PASS    AF=0.869391 ES:SE:LP:AF:SS:ID   5.09218e-05:0.000553747:0.0330463:0.869391:116869:rs4951862
1   758144  rs3131956   A   G   .   PASS    AF=0.8694   ES:SE:LP:AF:SS:ID   5.05679e-05:0.000553765:0.0328074:0.8694:116869:rs3131956
1   758626  rs3131954   C   T   .   PASS    AF=0.869823 ES:SE:LP:AF:SS:ID   7.55575e-05:0.000555172:0.0497598:0.869823:116869:rs3131954
1   759293  rs10157329  T   A   .   PASS    AF=0.0997572    ES:SE:LP:AF:SS:ID   0.000256905:0.000643988:0.161184:0.0997572:116869:rs10157329
1   759600  rs545998451 AGT A   .   PASS    AF=0.00630607   ES:SE:LP:AF:SS:ID   3.70104e-05:0.00252225:0.00511428:0.00630607:116869:1_759600_AGT_A
1   759837  rs3115851   T   A   .   PASS    AF=0.873735 ES:SE:LP:AF:SS:ID   0.000266895:0.00056356:0.196683:0.873735:116869:rs3115851
1   761732  rs2286139   C   T   .   PASS    AF=0.863118 ES:SE:LP:AF:SS:ID   -6.53158e-05:0.000552715:0.0429049:0.863118:116869:rs2286139
1   761752  rs1057213   C   T   .   PASS    AF=0.868538 ES:SE:LP:AF:SS:ID   8.24264e-05:0.000557977:0.0542553:0.868538:116869:rs1057213
1   762273  rs3115849   G   A   .   PASS    AF=0.865299 ES:SE:LP:AF:SS:ID   0.000273971:0.000557932:0.205237:0.865299:116869:rs3115849
1   762485  rs12095200  C   A   .   PASS    AF=0.0994223    ES:SE:LP:AF:SS:ID   -0.000795295:0.000668959:0.629859:0.0994223:116869:rs12095200
1   762589  rs3115848   G   C   .   PASS    AF=0.870538 ES:SE:LP:AF:SS:ID   0.000352406:0.000564329:0.273826:0.870538:116869:rs3115848
1   762592  rs3131950   C   G   .   PASS    AF=0.870538 ES:SE:LP:AF:SS:ID   0.000352401:0.000564329:0.273822:0.870538:116869:rs3131950
1   762601  rs3131949   T   C   .   PASS    AF=0.870539 ES:SE:LP:AF:SS:ID   0.000352583:0.000564358:0.273977:0.870539:116869:rs3131949
1   762632  rs3131948   T   A   .   PASS    AF=0.870932 ES:SE:LP:AF:SS:ID   0.000339978:0.000564676:0.261913:0.870932:116869:rs3131948
1   764191  rs7515915   T   G   .   PASS    AF=0.126524 ES:SE:LP:AF:SS:ID   -0.000200357:0.000565073:0.140913:0.126524:116869:rs7515915
1   766007  rs61768174  A   C   .   PASS    AF=0.106234 ES:SE:LP:AF:SS:ID   0.000368542:0.000614651:0.260604:0.106234:116869:rs61768174
1   766105  rs2519015   T   A   .   PASS    AF=0.854461 ES:SE:LP:AF:SS:ID   -6.56444e-05:0.000552675:0.0431341:0.854461:116869:rs2519015
1   767393  rs538667473 A   C   .   PASS    AF=0.00158591   ES:SE:LP:AF:SS:ID   -0.00193984:0.00497282:0.157096:0.00158591:116869:rs538667473
1   768116  rs376645387 A   AGTTTT  .   PASS    AF=0.837903 ES:SE:LP:AF:SS:ID   -0.000179681:0.000543666:0.130168:0.837903:116869:rs376645387