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-22617_2319,TotalVariants=10103437,VariantsNotRead=0,HarmonisedVariants=10103437,VariantsNotHarmonised=0,SwitchedAlleles=211,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-22617_2319/ukb-d-22617_2319_data.json --ref /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/QC/genomes/b37/human_g1k_v37.fasta; 1.1.1",
    "file_date": "2019-11-25T13:27:12.845180",
    "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-22617_2319/ukb-d-22617_2319.vcf.gz -O z /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-22617_2319/ukb-d-22617_2319_data.vcf.gz; Date=Mon Nov 25 14:16:21 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-22617_2319/ukb-d-22617_2319.vcf.gz; Date=Sun May 10 09:37:08 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-22617_2319/ukb-d-22617_2319.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-22617_2319/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 14:59:15 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-22617_2319/ukb-d-22617_2319.vcf.gz ...
Read summary statistics for 10103437 SNPs.
Dropped 7842 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, 1278820 SNPs remain.
After merging with regression SNP LD, 1278820 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0033 (0.0047)
Lambda GC: 1.0058
Mean Chi^2: 1.0057
Intercept: 0.9999 (0.0059)
Ratio < 0 (usually indicates GC correction).
Analysis finished at Mon Nov 25 15:00:56 2019
Total time elapsed: 1.0m:40.79s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9421,
    "inflation_factor": 0.9945,
    "mean_EFFECT": -3.9325e-06,
    "n": 91149,
    "n_snps": 10103437,
    "n_clumped_hits": 0,
    "n_p_sig": 1,
    "n_mono": 0,
    "n_ns": 1089212,
    "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": 199312,
    "n_est": 91200.0897,
    "ratio_se_n": 1.0003,
    "mean_diff": -0,
    "ratio_diff": 10.0915,
    "sd_y_est1": 0.1327,
    "sd_y_est2": 0.1328,
    "r2_sum1": 0,
    "r2_sum2": 0,
    "r2_sum3": 0,
    "r2_sum4": 0,
    "ldsc_nsnp_merge_refpanel_ld": 1278820,
    "ldsc_nsnp_merge_regression_ld": 1278820,
    "ldsc_observed_scale_h2_beta": 0.0033,
    "ldsc_observed_scale_h2_se": 0.0047,
    "ldsc_intercept_beta": 0.9999,
    "ldsc_intercept_se": 0.0059,
    "ldsc_lambda_gc": 1.0058,
    "ldsc_mean_chisq": 1.0057,
    "ldsc_ratio": -0.0175
}

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 10096149 0 NA NA NA NA NA NA NA NA
character REF 0 1.0000000 1 100 0 48511 0 NA NA NA NA NA NA NA NA
character ALT 0 1.0000000 1 342 0 30269 0 NA NA NA NA NA NA NA NA
numeric CHROM 0 1.0000000 NA NA NA NA NA 9.080254e+00 6.177679e+00 1.0000e+00 4.000000e+00 8.000000e+00 1.300000e+01 2.300000e+01 ▇▅▅▂▂
numeric POS 0 1.0000000 NA NA NA NA NA 7.876422e+07 5.607621e+07 3.0200e+02 3.249899e+07 6.967647e+07 1.147336e+08 2.492297e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA -3.900000e-06 1.536200e-03 -1.4345e-02 -6.990000e-04 -1.030000e-05 6.813000e-04 1.777050e-02 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 1.306400e-03 8.098000e-04 5.1370e-04 6.862000e-04 9.403000e-04 1.695500e-03 4.682800e-03 ▇▂▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 5.008961e-01 2.884138e-01 0.0000e+00 2.517028e-01 5.011918e-01 7.504936e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 5.008943e-01 2.884148e-01 0.0000e+00 2.517000e-01 5.011907e-01 7.504919e-01 1.000000e+00 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA 2.522148e-01 2.629520e-01 7.6828e-03 3.673710e-02 1.459310e-01 4.027000e-01 9.923160e-01 ▇▂▂▁▁
numeric AF_reference 199312 0.9802729 NA NA NA NA NA 2.519129e-01 2.538006e-01 0.0000e+00 4.053510e-02 1.619410e-01 3.989620e-01 1.000000e+00 ▇▃▂▁▁
numeric N 0 1.0000000 NA NA NA NA NA 9.114900e+04 0.000000e+00 9.1149e+04 9.114900e+04 9.114900e+04 9.114900e+04 9.114900e+04 ▁▁▇▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 692794 rs530212009 CA C 0.0007043 0.0010867 0.5169220 0.5169201 0.1114870 0.1894970 91149
1 693731 rs12238997 A G 0.0005908 0.0010292 0.5659304 0.5659290 0.1164590 0.1417730 91149
1 707522 rs371890604 G C 0.0004182 0.0011566 0.7176406 0.7176405 0.0978765 0.1293930 91149
1 717587 rs144155419 G A -0.0005597 0.0027571 0.8391430 0.8391422 0.0157837 0.0045926 91149
1 730087 rs148120343 T C 0.0005597 0.0014266 0.6948195 0.6948171 0.0569973 0.0127796 91149
1 731718 rs142557973 T C 0.0005819 0.0009767 0.5513025 0.5513017 0.1223590 0.1543530 91149
1 732032 rs61770163 A C 0.0002685 0.0010414 0.7965151 0.7965147 0.1220470 0.1555510 91149
1 734349 rs141242758 T C 0.0005975 0.0009774 0.5410233 0.5410209 0.1215880 0.1525560 91149
1 749963 rs529266287 T TAA -0.0004171 0.0009615 0.6644098 0.6644097 0.8689170 0.7641770 91149
1 751343 rs28544273 T A 0.0002726 0.0009532 0.7748703 0.7748697 0.1236990 0.2426120 91149
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
23 154923311 rs141127553 C T -0.0014849 0.0011433 0.1940318 0.1940261 0.0552869 0.0309934 91149
23 154923374 rs111332691 T A -0.0007519 0.0012442 0.5456184 0.5456176 0.0448387 0.0116556 91149
23 154925045 rs509981 C T 0.0002274 0.0005996 0.7045114 0.7045116 0.2444670 0.3634440 91149
23 154925895 rs538470 C T 0.0001442 0.0006130 0.8139931 0.8139921 0.2409490 0.3634440 91149
23 154927581 rs644138 G A -0.0001267 0.0005640 0.8222830 0.8222825 0.3001640 0.4635760 91149
23 154929412 rs557132 C T 0.0002144 0.0005998 0.7206925 0.7206911 0.2443160 0.3568210 91149
23 154929637 rs35185538 CT C 0.0002021 0.0006263 0.7469198 0.7469187 0.2286640 0.3011920 91149
23 154929952 rs4012982 CAA C 0.0002233 0.0006313 0.7234991 0.7234986 0.2382530 0.3165560 91149
23 154930230 rs781880 A G 0.0002120 0.0005996 0.7237074 0.7237069 0.2447660 0.3618540 91149
23 154930487 rs781879 T A -0.0014587 0.0020335 0.4731720 0.4731711 0.0196632 0.1263580 91149

bcf preview

1   692794  rs530212009 CA  C   .   PASS    AF=0.111487 ES:SE:LP:AF:SS:ID   0.000704297:0.00108671:0.286575:0.111487:91149:1_692794_CA_C
1   693731  rs12238997  A   G   .   PASS    AF=0.116459 ES:SE:LP:AF:SS:ID   0.000590837:0.00102923:0.247237:0.116459:91149:rs12238997
1   707522  rs371890604 G   C   .   PASS    AF=0.0978765    ES:SE:LP:AF:SS:ID   0.00041825:0.00115662:0.144093:0.0978765:91149:rs371890604
1   717587  rs144155419 G   A   .   PASS    AF=0.0157837    ES:SE:LP:AF:SS:ID   -0.000559672:0.00275713:0.076164:0.0157837:91149:rs144155419
1   730087  rs148120343 T   C   .   PASS    AF=0.0569973    ES:SE:LP:AF:SS:ID   0.000559685:0.00142658:0.158128:0.0569973:91149:rs148120343
1   731718  rs58276399  T   C   .   PASS    AF=0.122359 ES:SE:LP:AF:SS:ID   0.000581914:0.000976676:0.25861:0.122359:91149:rs58276399
1   732032  rs61770163  A   C   .   PASS    AF=0.122047 ES:SE:LP:AF:SS:ID   0.000268528:0.00104137:0.098806:0.122047:91149:rs61770163
1   734349  rs141242758 T   C   .   PASS    AF=0.121588 ES:SE:LP:AF:SS:ID   0.000597465:0.000977416:0.266784:0.121588:91149:rs141242758
1   749963  rs529266287 T   TAA .   PASS    AF=0.868917 ES:SE:LP:AF:SS:ID   -0.00041711:0.000961453:0.177564:0.868917:91149:rs529266287
1   751343  rs28544273  T   A   .   PASS    AF=0.123699 ES:SE:LP:AF:SS:ID   0.000272628:0.000953208:0.110771:0.123699:91149:rs28544273
1   751488  rs200141114 G   GA  .   PASS    AF=0.143202 ES:SE:LP:AF:SS:ID   0.000671277:0.000943682:0.321594:0.143202:91149:rs200141114
1   751756  rs28527770  T   C   .   PASS    AF=0.123834 ES:SE:LP:AF:SS:ID   0.000276299:0.000951829:0.112607:0.123834:91149:rs28527770
1   753405  rs3115860   C   A   .   PASS    AF=0.869892 ES:SE:LP:AF:SS:ID   -0.000474554:0.000927465:0.215465:0.869892:91149:rs3115860
1   753425  rs3131970   T   C   .   PASS    AF=0.874553 ES:SE:LP:AF:SS:ID   -0.000463265:0.000942506:0.205473:0.874553:91149:rs3131970
1   753541  rs2073813   G   A   .   PASS    AF=0.129529 ES:SE:LP:AF:SS:ID   0.000379302:0.000930376:0.165258:0.129529:91149:rs2073813
1   754105  rs12184325  C   T   .   PASS    AF=0.0358205    ES:SE:LP:AF:SS:ID   -0.00140051:0.00169969:0.387266:0.0358205:91149:rs12184325
1   754182  rs3131969   A   G   .   PASS    AF=0.869539 ES:SE:LP:AF:SS:ID   -0.00044958:0.00092669:0.202335:0.869539:91149:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.869616 ES:SE:LP:AF:SS:ID   -0.000458916:0.000927094:0.20719:0.869616:91149:rs3131968
1   754334  rs3131967   T   C   .   PASS    AF=0.869535 ES:SE:LP:AF:SS:ID   -0.000451955:0.000926651:0.203604:0.869535:91149:rs3131967
1   755890  rs3115858   A   T   .   PASS    AF=0.86952  ES:SE:LP:AF:SS:ID   -0.000575688:0.000924742:0.272794:0.86952:91149:rs3115858
1   756434  rs61768170  G   C   .   PASS    AF=0.126911 ES:SE:LP:AF:SS:ID   0.000542644:0.000943999:0.247641:0.126911:91149:rs61768170
1   756604  rs3131962   A   G   .   PASS    AF=0.86905  ES:SE:LP:AF:SS:ID   -0.000575679:0.000922347:0.273653:0.86905:91149:rs3131962
1   757640  rs3115853   G   A   .   PASS    AF=0.868436 ES:SE:LP:AF:SS:ID   -0.00051702:0.000921763:0.240434:0.868436:91149:rs3115853
1   757734  rs4951929   C   T   .   PASS    AF=0.869199 ES:SE:LP:AF:SS:ID   -0.000556414:0.000923183:0.262249:0.869199:91149:rs4951929
1   757936  rs4951862   C   A   .   PASS    AF=0.869205 ES:SE:LP:AF:SS:ID   -0.000557017:0.000923244:0.262574:0.869205:91149:rs4951862
1   758144  rs3131956   A   G   .   PASS    AF=0.869207 ES:SE:LP:AF:SS:ID   -0.000556933:0.000923252:0.262523:0.869207:91149:rs3131956
1   758626  rs3131954   C   T   .   PASS    AF=0.869687 ES:SE:LP:AF:SS:ID   -0.000581223:0.000925722:0.275644:0.869687:91149:rs3131954
1   759293  rs10157329  T   A   .   PASS    AF=0.0991787    ES:SE:LP:AF:SS:ID   0.000685783:0.00107731:0.280331:0.0991787:91149:rs10157329
1   759837  rs3115851   T   A   .   PASS    AF=0.873682 ES:SE:LP:AF:SS:ID   -0.000586323:0.000939432:0.273642:0.873682:91149:rs3115851
1   761732  rs2286139   C   T   .   PASS    AF=0.863058 ES:SE:LP:AF:SS:ID   -0.000456577:0.000921508:0.207418:0.863058:91149:rs2286139
1   761752  rs1057213   C   T   .   PASS    AF=0.868472 ES:SE:LP:AF:SS:ID   -0.000622923:0.00093065:0.298191:0.868472:91149:rs1057213
1   762273  rs3115849   G   A   .   PASS    AF=0.865369 ES:SE:LP:AF:SS:ID   -0.000586056:0.000930825:0.276584:0.865369:91149:rs3115849
1   762485  rs12095200  C   A   .   PASS    AF=0.0995228    ES:SE:LP:AF:SS:ID   0.000584252:0.00111402:0.221874:0.0995228:91149:rs12095200
1   762589  rs3115848   G   C   .   PASS    AF=0.870657 ES:SE:LP:AF:SS:ID   -0.000528655:0.000941429:0.240765:0.870657:91149:rs3115848
1   762592  rs3131950   C   G   .   PASS    AF=0.870657 ES:SE:LP:AF:SS:ID   -0.000528646:0.000941429:0.24076:0.870657:91149:rs3131950
1   762601  rs3131949   T   C   .   PASS    AF=0.870654 ES:SE:LP:AF:SS:ID   -0.000528774:0.000941432:0.240829:0.870654:91149:rs3131949
1   762632  rs3131948   T   A   .   PASS    AF=0.871019 ES:SE:LP:AF:SS:ID   -0.000570792:0.000941869:0.264001:0.871019:91149:rs3131948
1   764191  rs7515915   T   G   .   PASS    AF=0.126515 ES:SE:LP:AF:SS:ID   0.000465903:0.000942917:0.206747:0.126515:91149:rs7515915
1   766007  rs61768174  A   C   .   PASS    AF=0.106037 ES:SE:LP:AF:SS:ID   0.000544011:0.00102496:0.225058:0.106037:91149:rs61768174
1   766105  rs2519015   T   A   .   PASS    AF=0.85438  ES:SE:LP:AF:SS:ID   -0.000924555:0.000921152:0.500961:0.85438:91149:rs2519015
1   768116  rs376645387 A   AGTTTT  .   PASS    AF=0.839153 ES:SE:LP:AF:SS:ID   -0.000920292:0.000910138:0.505923:0.839153:91149:rs376645387
1   768253  rs2977608   A   C   .   PASS    AF=0.763195 ES:SE:LP:AF:SS:ID   -0.00105438:0.000731795:0.824955:0.763195:91149:rs2977608
1   768448  rs12562034  G   A   .   PASS    AF=0.105092 ES:SE:LP:AF:SS:ID   0.00125514:0.00100842:0.671084:0.105092:91149:rs12562034
1   768819  rs12562811  C   T   .   PASS    AF=0.00772317   ES:SE:LP:AF:SS:ID   0.0012535:0.00373658:0.132372:0.00772317:91149:rs12562811
1   769138  rs59306077  CAT C   .   PASS    AF=0.129904 ES:SE:LP:AF:SS:ID   0.000475986:0.000929747:0.215607:0.129904:91149:rs762168062
1   769223  rs60320384  C   G   .   PASS    AF=0.129636 ES:SE:LP:AF:SS:ID   0.000545729:0.000928524:0.254372:0.129636:91149:rs60320384
1   769963  rs7518545   G   A   .   PASS    AF=0.104365 ES:SE:LP:AF:SS:ID   0.00133223:0.00101625:0.721505:0.104365:91149:rs7518545
1   770181  rs146076599 A   G   .   PASS    AF=0.00906976   ES:SE:LP:AF:SS:ID   -0.00729565:0.00357287:1.38554:0.00906976:91149:rs146076599
1   770377  rs112563271 A   T   .   PASS    AF=0.00773917   ES:SE:LP:AF:SS:ID   0.000935114:0.00375218:0.0951806:0.00773917:91149:rs112563271
1   770886  rs371458725 G   A   .   PASS    AF=0.103379 ES:SE:LP:AF:SS:ID   0.00131695:0.00102504:0.701424:0.103379:91149:rs371458725