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-5012,TotalVariants=13560285,VariantsNotRead=0,HarmonisedVariants=13560285,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-5012/ukb-d-5012_data.json --ref /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/QC/genomes/b37/human_g1k_v37.fasta; 1.1.1",
    "file_date": "2019-11-25T16:21:57.217354",
    "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-5012/ukb-d-5012.vcf.gz -O z /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-5012/ukb-d-5012_data.vcf.gz; Date=Mon Nov 25 16:54:24 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-5012/ukb-d-5012.vcf.gz; Date=Sun May 10 23:22:51 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-5012/ukb-d-5012.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-5012/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 17:20:28 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-5012/ukb-d-5012.vcf.gz ...
Read summary statistics for 13560285 SNPs.
Dropped 12681 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, 1283500 SNPs remain.
After merging with regression SNP LD, 1283500 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.1036 (0.0082)
Lambda GC: 1.1379
Mean Chi^2: 1.1575
Intercept: 1.0044 (0.007)
Ratio: 0.0279 (0.0448)
Analysis finished at Mon Nov 25 17:22:43 2019
Total time elapsed: 2.0m:14.52s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9521,
    "inflation_factor": 1.0818,
    "mean_EFFECT": -0,
    "n": 75692,
    "n_snps": 13560285,
    "n_clumped_hits": 4,
    "n_p_sig": 79,
    "n_mono": 0,
    "n_ns": 1251011,
    "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": 561141,
    "n_est": 76013.8246,
    "ratio_se_n": 1.0021,
    "mean_diff": -0.0001,
    "ratio_diff": 41.3318,
    "sd_y_est1": 0.4739,
    "sd_y_est2": 0.4749,
    "r2_sum1": 0.0004,
    "r2_sum2": 0.0018,
    "r2_sum3": 0.0018,
    "r2_sum4": 0.0018,
    "ldsc_nsnp_merge_refpanel_ld": 1283500,
    "ldsc_nsnp_merge_regression_ld": 1283500,
    "ldsc_observed_scale_h2_beta": 0.1036,
    "ldsc_observed_scale_h2_se": 0.0082,
    "ldsc_intercept_beta": 1.0044,
    "ldsc_intercept_se": 0.007,
    "ldsc_lambda_gc": 1.1379,
    "ldsc_mean_chisq": 1.1575,
    "ldsc_ratio": 0.0279
}

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 13548267 0 NA NA NA NA NA NA NA NA
character REF 0 1.0000000 1 100 0 57042 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 9.051635e+00 6.184905e+00 1.000000 4.000000e+00 8.000000e+00 1.300000e+01 2.300000e+01 ▇▅▅▂▂
numeric POS 0 1.0000000 NA NA NA NA NA 7.902396e+07 5.591667e+07 302.000000 3.292773e+07 7.013545e+07 1.148551e+08 2.492309e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA -4.770000e-05 1.425130e-02 -0.174012 -3.951500e-03 -9.300000e-06 3.914000e-03 1.609700e-01 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 1.018100e-02 9.807600e-03 0.002002 2.911700e-03 5.351600e-03 1.461530e-02 4.973850e-02 ▇▂▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.871489e-01 2.926428e-01 0.000000 2.302778e-01 4.829676e-01 7.408256e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.871468e-01 2.926441e-01 0.000000 2.302739e-01 4.829652e-01 7.408249e-01 9.999999e-01 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA 1.911583e-01 2.544857e-01 0.001000 7.530600e-03 6.041590e-02 2.959770e-01 9.990000e-01 ▇▂▁▁▁
numeric AF_reference 561141 0.9586188 NA NA NA NA NA 1.965855e-01 2.471594e-01 0.000000 5.790700e-03 8.466450e-02 3.085060e-01 1.000000e+00 ▇▂▁▁▁
numeric N 0 1.0000000 NA NA NA NA NA 7.569200e+04 0.000000e+00 75692.000000 7.569200e+04 7.569200e+04 7.569200e+04 7.569200e+04 ▁▁▇▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 692794 rs530212009 CA C -0.0022908 0.0042518 0.5900407 0.5900394 0.1123220 0.1894970 75692
1 693731 rs12238997 A G -0.0022860 0.0040217 0.5697574 0.5697561 0.1176250 0.1417730 75692
1 707522 rs371890604 G C -0.0024068 0.0045155 0.5940254 0.5940233 0.0986233 0.1293930 75692
1 717587 rs144155419 G A 0.0044302 0.0108823 0.6839337 0.6839315 0.0156471 0.0045926 75692
1 723329 rs189787166 A T 0.0111077 0.0318330 0.7271366 0.7271369 0.0017292 0.0003994 75692
1 730087 rs148120343 T C -0.0037710 0.0055981 0.5005552 0.5005535 0.0573192 0.0127796 75692
1 731718 rs142557973 T C -0.0028162 0.0038205 0.4610436 0.4610417 0.1234080 0.1543530 75692
1 732032 rs61770163 A C -0.0026629 0.0040696 0.5128921 0.5128895 0.1227430 0.1555510 75692
1 734349 rs141242758 T C -0.0029600 0.0038233 0.4388064 0.4388029 0.1225940 0.1525560 75692
1 740284 rs61770167 C T -0.0117095 0.0171197 0.4939921 0.4939890 0.0060204 0.0023962 75692
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
23 154923311 rs141127553 C T 0.0028547 0.0044673 0.5228137 0.5228121 0.0550520 0.0309934 75692
23 154923374 rs111332691 T A -0.0060358 0.0048684 0.2150552 0.2150517 0.0445027 0.0116556 75692
23 154925045 rs509981 C T -0.0004440 0.0023415 0.8496119 0.8496119 0.2435720 0.3634440 75692
23 154925895 rs538470 C T -0.0006132 0.0023934 0.7977900 0.7977891 0.2400870 0.3634440 75692
23 154927581 rs644138 G A 0.0003198 0.0022032 0.8845930 0.8845926 0.2990340 0.4635760 75692
23 154929412 rs557132 C T -0.0005002 0.0023425 0.8309250 0.8309249 0.2433900 0.3568210 75692
23 154929637 rs35185538 CT C -0.0002479 0.0024427 0.9191500 0.9191500 0.2277940 0.3011920 75692
23 154929952 rs4012982 CAA C -0.0001849 0.0024638 0.9401830 0.9401824 0.2376030 0.3165560 75692
23 154930230 rs781880 A G -0.0005363 0.0023421 0.8188970 0.8188964 0.2438310 0.3618540 75692
23 154930487 rs781879 T A 0.0149259 0.0081058 0.0655692 0.0655665 0.0190614 0.1263580 75692

bcf preview

1   692794  rs530212009 CA  C   .   PASS    AF=0.112322 ES:SE:LP:AF:SS:ID   -0.00229078:0.0042518:0.229118:0.112322:75692:1_692794_CA_C
1   693731  rs12238997  A   G   .   PASS    AF=0.117625 ES:SE:LP:AF:SS:ID   -0.002286:0.00402174:0.24431:0.117625:75692:rs12238997
1   707522  rs371890604 G   C   .   PASS    AF=0.0986233    ES:SE:LP:AF:SS:ID   -0.00240685:0.00451554:0.226195:0.0986233:75692:rs371890604
1   717587  rs144155419 G   A   .   PASS    AF=0.0156471    ES:SE:LP:AF:SS:ID   0.00443023:0.0108823:0.164986:0.0156471:75692:rs144155419
1   723329  rs189787166 A   T   .   PASS    AF=0.00172917   ES:SE:LP:AF:SS:ID   0.0111077:0.031833:0.138384:0.00172917:75692:rs189787166
1   730087  rs148120343 T   C   .   PASS    AF=0.0573192    ES:SE:LP:AF:SS:ID   -0.00377098:0.00559809:0.300548:0.0573192:75692:rs148120343
1   731718  rs58276399  T   C   .   PASS    AF=0.123408 ES:SE:LP:AF:SS:ID   -0.00281623:0.00382052:0.336258:0.123408:75692:rs58276399
1   732032  rs61770163  A   C   .   PASS    AF=0.122743 ES:SE:LP:AF:SS:ID   -0.00266289:0.00406955:0.289974:0.122743:75692:rs61770163
1   734349  rs141242758 T   C   .   PASS    AF=0.122594 ES:SE:LP:AF:SS:ID   -0.00296003:0.00382326:0.357727:0.122594:75692:rs141242758
1   740284  rs61770167  C   T   .   PASS    AF=0.0060204    ES:SE:LP:AF:SS:ID   -0.0117095:0.0171197:0.30628:0.0060204:75692:rs61770167
1   742813  rs112573343 C   T   .   PASS    AF=0.00178375   ES:SE:LP:AF:SS:ID   0.0221226:0.0345825:0.282025:0.00178375:75692:rs112573343
1   749963  rs529266287 T   TAA .   PASS    AF=0.868143 ES:SE:LP:AF:SS:ID   0.00355743:0.00377183:0.461423:0.868143:75692:rs529266287
1   750230  rs190826124 G   C   .   PASS    AF=0.00161654   ES:SE:LP:AF:SS:ID   -0.0353787:0.0330865:0.545236:0.00161654:75692:rs190826124
1   751343  rs28544273  T   A   .   PASS    AF=0.12446  ES:SE:LP:AF:SS:ID   -0.00386841:0.00373463:0.522462:0.12446:75692:rs28544273
1   751488  rs200141114 G   GA  .   PASS    AF=0.144111 ES:SE:LP:AF:SS:ID   -0.00394747:0.00369948:0.543696:0.144111:75692:rs200141114
1   751756  rs28527770  T   C   .   PASS    AF=0.124607 ES:SE:LP:AF:SS:ID   -0.0039011:0.00372871:0.529504:0.124607:75692:rs28527770
1   753405  rs3115860   C   A   .   PASS    AF=0.869209 ES:SE:LP:AF:SS:ID   0.00369148:0.00363255:0.509303:0.869209:75692:rs3115860
1   753425  rs3131970   T   C   .   PASS    AF=0.873939 ES:SE:LP:AF:SS:ID   0.0041707:0.00369266:0.587188:0.873939:75692:rs3131970
1   753541  rs2073813   G   A   .   PASS    AF=0.130444 ES:SE:LP:AF:SS:ID   -0.00336286:0.00363997:0.44909:0.130444:75692:rs2073813
1   754105  rs12184325  C   T   .   PASS    AF=0.0368599    ES:SE:LP:AF:SS:ID   -0.0102758:0.00656701:0.929441:0.0368599:75692:rs12184325
1   754182  rs3131969   A   G   .   PASS    AF=0.868773 ES:SE:LP:AF:SS:ID   0.00353683:0.00362847:0.481893:0.868773:75692:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.868908 ES:SE:LP:AF:SS:ID   0.00343028:0.00363058:0.462497:0.868908:75692:rs3131968
1   754334  rs3131967   T   C   .   PASS    AF=0.868773 ES:SE:LP:AF:SS:ID   0.00358265:0.0036283:0.490205:0.868773:75692:rs3131967
1   754433  rs150578204 G   A   .   PASS    AF=0.00512101   ES:SE:LP:AF:SS:ID   -0.0249113:0.0185363:0.7472:0.00512101:75692:rs150578204
1   754458  rs142682604 G   T   .   PASS    AF=0.0050863    ES:SE:LP:AF:SS:ID   -0.0255588:0.0185899:0.771666:0.0050863:75692:rs142682604
1   755435  rs184270342 T   G   .   PASS    AF=0.0053082    ES:SE:LP:AF:SS:ID   0.00393689:0.0185823:0.0797645:0.0053082:75692:rs184270342
1   755890  rs3115858   A   T   .   PASS    AF=0.868919 ES:SE:LP:AF:SS:ID   0.00354001:0.00362302:0.483426:0.868919:75692:rs3115858
1   756434  rs61768170  G   C   .   PASS    AF=0.127628 ES:SE:LP:AF:SS:ID   -0.00348389:0.00369734:0.460851:0.127628:75692:rs61768170
1   756604  rs3131962   A   G   .   PASS    AF=0.86848  ES:SE:LP:AF:SS:ID   0.00317447:0.00361435:0.42046:0.86848:75692:rs3131962
1   757640  rs3115853   G   A   .   PASS    AF=0.867615 ES:SE:LP:AF:SS:ID   0.00313734:0.00360891:0.414914:0.867615:75692:rs3115853
1   757734  rs4951929   C   T   .   PASS    AF=0.868642 ES:SE:LP:AF:SS:ID   0.00338282:0.00361747:0.456278:0.868642:75692:rs4951929
1   757936  rs4951862   C   A   .   PASS    AF=0.868649 ES:SE:LP:AF:SS:ID   0.00339008:0.00361772:0.457519:0.868649:75692:rs4951862
1   758144  rs3131956   A   G   .   PASS    AF=0.868657 ES:SE:LP:AF:SS:ID   0.00337875:0.00361784:0.455495:0.868657:75692:rs3131956
1   758626  rs3131954   C   T   .   PASS    AF=0.869075 ES:SE:LP:AF:SS:ID   0.00359805:0.003627:0.493234:0.869075:75692:rs3131954
1   759293  rs10157329  T   A   .   PASS    AF=0.100202 ES:SE:LP:AF:SS:ID   -0.00252737:0.00420691:0.261221:0.100202:75692:rs10157329
1   759600  rs545998451 AGT A   .   PASS    AF=0.0060957    ES:SE:LP:AF:SS:ID   -0.000785704:0.0168672:0.0164427:0.0060957:75692:1_759600_AGT_A
1   759837  rs3115851   T   A   .   PASS    AF=0.873067 ES:SE:LP:AF:SS:ID   0.00348242:0.00368159:0.463188:0.873067:75692:rs3115851
1   761732  rs2286139   C   T   .   PASS    AF=0.862343 ES:SE:LP:AF:SS:ID   0.00432962:0.00361079:0.637327:0.862343:75692:rs2286139
1   761752  rs1057213   C   T   .   PASS    AF=0.867857 ES:SE:LP:AF:SS:ID   0.00320818:0.00364554:0.421536:0.867857:75692:rs1057213
1   762273  rs3115849   G   A   .   PASS    AF=0.864642 ES:SE:LP:AF:SS:ID   0.00410084:0.0036449:0.584102:0.864642:75692:rs3115849
1   762485  rs12095200  C   A   .   PASS    AF=0.0997611    ES:SE:LP:AF:SS:ID   -0.00548046:0.00437043:0.678089:0.0997611:75692:rs12095200
1   762589  rs3115848   G   C   .   PASS    AF=0.869955 ES:SE:LP:AF:SS:ID   0.00431001:0.00368685:0.615471:0.869955:75692:rs3115848
1   762592  rs3131950   C   G   .   PASS    AF=0.869954 ES:SE:LP:AF:SS:ID   0.00430972:0.00368685:0.615414:0.869954:75692:rs3131950
1   762601  rs3131949   T   C   .   PASS    AF=0.869958 ES:SE:LP:AF:SS:ID   0.0043272:0.00368713:0.618775:0.869958:75692:rs3131949
1   762632  rs3131948   T   A   .   PASS    AF=0.870303 ES:SE:LP:AF:SS:ID   0.00466047:0.00368908:0.685122:0.870303:75692:rs3131948
1   764191  rs7515915   T   G   .   PASS    AF=0.127192 ES:SE:LP:AF:SS:ID   -0.00358811:0.00369235:0.47995:0.127192:75692:rs7515915
1   766007  rs61768174  A   C   .   PASS    AF=0.106883 ES:SE:LP:AF:SS:ID   -0.0029375:0.00400862:0.333778:0.106883:75692:rs61768174
1   766105  rs2519015   T   A   .   PASS    AF=0.853559 ES:SE:LP:AF:SS:ID   0.0026537:0.00360928:0.335176:0.853559:75692:rs2519015
1   767393  rs538667473 A   C   .   PASS    AF=0.00161685   ES:SE:LP:AF:SS:ID   0.000649009:0.0321843:0.00704418:0.00161685:75692:rs538667473
1   768116  rs376645387 A   AGTTTT  .   PASS    AF=0.837428 ES:SE:LP:AF:SS:ID   -0.00139953:0.00354993:0.159014:0.837428:75692:rs376645387