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-b:20122,TotalVariants=9851866,VariantsNotRead=0,HarmonisedVariants=9851866,VariantsNotHarmonised=0,SwitchedAlleles=9851866,TotalControls=64944,StudyType=Continuous>",
    "contig": "<ID=1,length=249250621,assembly=GRCh37>",
    "contig.1": "<ID=2,length=243199373,assembly=GRCh37>",
    "contig.2": "<ID=3,length=198022430,assembly=GRCh37>",
    "contig.3": "<ID=4,length=191154276,assembly=GRCh37>",
    "contig.4": "<ID=5,length=180915260,assembly=GRCh37>",
    "contig.5": "<ID=6,length=171115067,assembly=GRCh37>",
    "contig.6": "<ID=7,length=159138663,assembly=GRCh37>",
    "contig.7": "<ID=8,length=146364022,assembly=GRCh37>",
    "contig.8": "<ID=9,length=141213431,assembly=GRCh37>",
    "contig.9": "<ID=10,length=135534747,assembly=GRCh37>",
    "contig.10": "<ID=11,length=135006516,assembly=GRCh37>",
    "contig.11": "<ID=12,length=133851895,assembly=GRCh37>",
    "contig.12": "<ID=13,length=115169878,assembly=GRCh37>",
    "contig.13": "<ID=14,length=107349540,assembly=GRCh37>",
    "contig.14": "<ID=15,length=102531392,assembly=GRCh37>",
    "contig.15": "<ID=16,length=90354753,assembly=GRCh37>",
    "contig.16": "<ID=17,length=81195210,assembly=GRCh37>",
    "contig.17": "<ID=18,length=78077248,assembly=GRCh37>",
    "contig.18": "<ID=19,length=59128983,assembly=GRCh37>",
    "contig.19": "<ID=20,length=63025520,assembly=GRCh37>",
    "contig.20": "<ID=21,length=48129895,assembly=GRCh37>",
    "contig.21": "<ID=22,length=51304566,assembly=GRCh37>",
    "contig.22": "<ID=X,length=155270560,assembly=GRCh37>",
    "contig.23": "<ID=Y,length=59373566,assembly=GRCh37>",
    "contig.24": "<ID=MT,length=16569,assembly=GRCh37>",
    "contig.25": "<ID=GL000207.1,length=4262,assembly=GRCh37>",
    "contig.26": "<ID=GL000226.1,length=15008,assembly=GRCh37>",
    "contig.27": "<ID=GL000229.1,length=19913,assembly=GRCh37>",
    "contig.28": "<ID=GL000231.1,length=27386,assembly=GRCh37>",
    "contig.29": "<ID=GL000210.1,length=27682,assembly=GRCh37>",
    "contig.30": "<ID=GL000239.1,length=33824,assembly=GRCh37>",
    "contig.31": "<ID=GL000235.1,length=34474,assembly=GRCh37>",
    "contig.32": "<ID=GL000201.1,length=36148,assembly=GRCh37>",
    "contig.33": "<ID=GL000247.1,length=36422,assembly=GRCh37>",
    "contig.34": "<ID=GL000245.1,length=36651,assembly=GRCh37>",
    "contig.35": "<ID=GL000197.1,length=37175,assembly=GRCh37>",
    "contig.36": "<ID=GL000203.1,length=37498,assembly=GRCh37>",
    "contig.37": "<ID=GL000246.1,length=38154,assembly=GRCh37>",
    "contig.38": "<ID=GL000249.1,length=38502,assembly=GRCh37>",
    "contig.39": "<ID=GL000196.1,length=38914,assembly=GRCh37>",
    "contig.40": "<ID=GL000248.1,length=39786,assembly=GRCh37>",
    "contig.41": "<ID=GL000244.1,length=39929,assembly=GRCh37>",
    "contig.42": "<ID=GL000238.1,length=39939,assembly=GRCh37>",
    "contig.43": "<ID=GL000202.1,length=40103,assembly=GRCh37>",
    "contig.44": "<ID=GL000234.1,length=40531,assembly=GRCh37>",
    "contig.45": "<ID=GL000232.1,length=40652,assembly=GRCh37>",
    "contig.46": "<ID=GL000206.1,length=41001,assembly=GRCh37>",
    "contig.47": "<ID=GL000240.1,length=41933,assembly=GRCh37>",
    "contig.48": "<ID=GL000236.1,length=41934,assembly=GRCh37>",
    "contig.49": "<ID=GL000241.1,length=42152,assembly=GRCh37>",
    "contig.50": "<ID=GL000243.1,length=43341,assembly=GRCh37>",
    "contig.51": "<ID=GL000242.1,length=43523,assembly=GRCh37>",
    "contig.52": "<ID=GL000230.1,length=43691,assembly=GRCh37>",
    "contig.53": "<ID=GL000237.1,length=45867,assembly=GRCh37>",
    "contig.54": "<ID=GL000233.1,length=45941,assembly=GRCh37>",
    "contig.55": "<ID=GL000204.1,length=81310,assembly=GRCh37>",
    "contig.56": "<ID=GL000198.1,length=90085,assembly=GRCh37>",
    "contig.57": "<ID=GL000208.1,length=92689,assembly=GRCh37>",
    "contig.58": "<ID=GL000191.1,length=106433,assembly=GRCh37>",
    "contig.59": "<ID=GL000227.1,length=128374,assembly=GRCh37>",
    "contig.60": "<ID=GL000228.1,length=129120,assembly=GRCh37>",
    "contig.61": "<ID=GL000214.1,length=137718,assembly=GRCh37>",
    "contig.62": "<ID=GL000221.1,length=155397,assembly=GRCh37>",
    "contig.63": "<ID=GL000209.1,length=159169,assembly=GRCh37>",
    "contig.64": "<ID=GL000218.1,length=161147,assembly=GRCh37>",
    "contig.65": "<ID=GL000220.1,length=161802,assembly=GRCh37>",
    "contig.66": "<ID=GL000213.1,length=164239,assembly=GRCh37>",
    "contig.67": "<ID=GL000211.1,length=166566,assembly=GRCh37>",
    "contig.68": "<ID=GL000199.1,length=169874,assembly=GRCh37>",
    "contig.69": "<ID=GL000217.1,length=172149,assembly=GRCh37>",
    "contig.70": "<ID=GL000216.1,length=172294,assembly=GRCh37>",
    "contig.71": "<ID=GL000215.1,length=172545,assembly=GRCh37>",
    "contig.72": "<ID=GL000205.1,length=174588,assembly=GRCh37>",
    "contig.73": "<ID=GL000219.1,length=179198,assembly=GRCh37>",
    "contig.74": "<ID=GL000224.1,length=179693,assembly=GRCh37>",
    "contig.75": "<ID=GL000223.1,length=180455,assembly=GRCh37>",
    "contig.76": "<ID=GL000195.1,length=182896,assembly=GRCh37>",
    "contig.77": "<ID=GL000212.1,length=186858,assembly=GRCh37>",
    "contig.78": "<ID=GL000222.1,length=186861,assembly=GRCh37>",
    "contig.79": "<ID=GL000200.1,length=187035,assembly=GRCh37>",
    "contig.80": "<ID=GL000193.1,length=189789,assembly=GRCh37>",
    "contig.81": "<ID=GL000194.1,length=191469,assembly=GRCh37>",
    "contig.82": "<ID=GL000225.1,length=211173,assembly=GRCh37>",
    "contig.83": "<ID=GL000192.1,length=547496,assembly=GRCh37>",
    "gwas_harmonisation_command": "--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/vcf_09_19b/bgzip_vcf/data.batch_102900.vcf.gz --id UKB-b:20122 --data /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/raw-output/data.batch_102900.txt.gz --cohort_controls 64944 --ref /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/human_g1k_v37.fasta --json /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/ukb_gwas.json; 1.1.1",
    "file_date": "2019-09-13T15:47:28.734336",
    "bcftools_viewVersion": "1.9-74-g6af271c+htslib-1.9-64-g226b4a8",
    "bcftools_viewCommand": "view -T ^/mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-20122/mac_discard.txt -Oz /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-20122/UKB-b-20122_raw.vcf.gz; Date=Thu Oct 17 12:38:50 2019",
    "bcftools_viewCommand.1": "view -h /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukb-b-20122/ukb-b-20122.vcf.gz; Date=Sat May  9 15:37:29 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/public/UKB-b-20122/UKB-b-20122_data.vcf.gz \
--ref-ld-chr ../reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-20122/ldsc.txt \
--w-ld-chr ../reference/eur_w_ld_chr/ 

Beginning analysis at Thu Oct 17 14:42:04 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-20122/UKB-b-20122_data.vcf.gz ...
Read summary statistics for 8624950 SNPs.
Dropped 7372 SNPs with duplicated rs numbers.
Reading reference panel LD Score from ../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 ../reference/eur_w_ld_chr/[1-22] ...
Read regression weight LD Scores for 1290028 SNPs.
After merging with reference panel LD, 1285749 SNPs remain.
After merging with regression SNP LD, 1285749 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: -0.0001 (0.006)
Lambda GC: 1.0259
Mean Chi^2: 1.0195
Intercept: 1.0196 (0.0055)
Ratio: 1.0081 (0.2799)
Analysis finished at Thu Oct 17 14:43:40 2019
Total time elapsed: 1.0m:36.66s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9462,
    "inflation_factor": 1.0475,
    "mean_EFFECT": 6.8658e-06,
    "n": "-Inf",
    "n_snps": 9851866,
    "n_clumped_hits": 0,
    "n_p_sig": 11,
    "n_mono": 0,
    "n_ns": 0,
    "n_mac": 0,
    "is_snpid_unique": true,
    "n_miss_EFFECT": 0,
    "n_miss_SE": 0,
    "n_miss_PVAL": 0,
    "n_miss_AF": 0,
    "n_miss_AF_reference": 83097,
    "n_est": "NA",
    "ratio_se_n": "NA",
    "mean_diff": "NaN",
    "ratio_diff": "NaN",
    "sd_y_est1": "NaN",
    "sd_y_est2": "NA",
    "r2_sum1": 0,
    "r2_sum2": 0,
    "r2_sum3": 0,
    "r2_sum4": 0,
    "ldsc_nsnp_merge_refpanel_ld": 1285749,
    "ldsc_nsnp_merge_regression_ld": 1285749,
    "ldsc_observed_scale_h2_beta": "NA",
    "ldsc_observed_scale_h2_se": "NA",
    "ldsc_intercept_beta": 1.0196,
    "ldsc_intercept_se": 0.0055,
    "ldsc_lambda_gc": 1.0259,
    "ldsc_mean_chisq": 1.0195,
    "ldsc_ratio": 1.0051
}

Flags

name value
af_correlation FALSE
inflation_factor FALSE
n TRUE
is_snpid_non_unique FALSE
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 logical.mean logical.count numeric.mean numeric.sd numeric.p0 numeric.p25 numeric.p50 numeric.p75 numeric.p100 numeric.hist
character ID 0 1.0000000 3 58 0 8617612 0 NA NA 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 NA NA
character ALT 0 1.0000000 1 1 0 4 0 NA NA NA NA NA NA NA NA NA NA
logical N 8624950 0.0000000 NA NA NA NA NA NaN : NA NA NA NA NA NA NA NA
numeric CHROM 0 1.0000000 NA NA NA NA NA NA NA 8.650341e+00 5.760993e+00 1.0000000 4.000000e+00 8.000000e+00 1.300000e+01 2.200000e+01 ▇▅▅▂▂
numeric POS 0 1.0000000 NA NA NA NA NA NA NA 7.877024e+07 5.637179e+07 828.0000000 3.238544e+07 6.929178e+07 1.145691e+08 2.492385e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA NA NA 6.900000e-06 3.289100e-03 -0.0295354 -1.397900e-03 -3.630000e-05 1.333100e-03 4.411500e-02 ▁▇▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA NA NA 2.691900e-03 1.837500e-03 0.0010692 1.259000e-03 1.856300e-03 3.638800e-03 1.842970e-02 ▇▂▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA NA NA 4.962331e-01 2.888761e-01 0.0000000 2.500000e-01 4.899999e-01 7.499995e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA NA NA 4.962332e-01 2.888540e-01 0.0000000 2.457949e-01 4.942903e-01 7.459030e-01 1.000000e+00 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA NA NA 2.291181e-01 2.594883e-01 0.0053900 2.519100e-02 1.138980e-01 3.626280e-01 9.946100e-01 ▇▂▁▁▁
numeric AF_reference 83097 0.9903655 NA NA NA NA NA NA NA 2.288672e-01 2.514590e-01 0.0000000 2.316290e-02 1.303910e-01 3.596250e-01 1.000000e+00 ▇▂▂▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 49298 rs200943160 T C -0.0019815 0.0019703 0.3100002 0.3145576 0.623807 0.7821490 NA
1 54676 rs2462492 C T 0.0020407 0.0019646 0.2999998 0.2989297 0.399143 NA NA
1 86028 rs114608975 T C -0.0014578 0.0031272 0.6400000 0.6411019 0.103539 0.0277556 NA
1 91536 rs6702460 G T 0.0000713 0.0019323 0.9699999 0.9705613 0.455916 0.4207270 NA
1 234313 rs8179466 C T 0.0019025 0.0038213 0.6200004 0.6185749 0.074454 NA NA
1 534192 rs6680723 C T 0.0022614 0.0022007 0.2999998 0.3041637 0.242059 NA NA
1 546697 rs12025928 A G 0.0010438 0.0027309 0.6999999 0.7023034 0.912869 NA NA
1 693731 rs12238997 A G -0.0012415 0.0018351 0.5000000 0.4987158 0.117310 0.1417730 NA
1 705882 rs72631875 G A -0.0016305 0.0026748 0.5400003 0.5421268 0.067702 0.0315495 NA
1 706368 rs55727773 A G -0.0018714 0.0013621 0.1700000 0.1694834 0.513311 0.2751600 NA
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51219006 rs28729663 G A 0.0008572 0.0016568 0.5999997 0.6048857 0.136317 0.2052720 NA
22 51219387 rs9616832 T C -0.0006963 0.0021594 0.7499995 0.7471211 0.071795 0.0654952 NA
22 51219704 rs147475742 G A 0.0007179 0.0028728 0.8000000 0.8026646 0.041186 0.0473243 NA
22 51221190 rs369304721 G A 0.0002211 0.0028931 0.9400001 0.9390902 0.048368 NA NA
22 51221731 rs115055839 T C -0.0007566 0.0021599 0.7300002 0.7261097 0.071346 0.0625000 NA
22 51222100 rs114553188 G T 0.0021234 0.0025028 0.4000000 0.3962086 0.054855 0.0880591 NA
22 51223637 rs375798137 G A 0.0022330 0.0025158 0.3700002 0.3747711 0.054474 0.0788738 NA
22 51229805 rs9616985 T C -0.0008546 0.0021666 0.6899999 0.6932391 0.071251 0.0730831 NA
22 51232488 rs376461333 A G -0.0042400 0.0049898 0.4000000 0.3954717 0.020462 NA NA
22 51237063 rs3896457 T C 0.0004174 0.0013079 0.7499995 0.7496145 0.298398 0.2050720 NA

bcf preview

1   49298   rs10399793  T   C   .   PASS    AF=0.623807 ES:SE:LP:AF:ID  -0.00198153:0.00197029:0.508638:0.623807:rs10399793
1   54676   rs2462492   C   T   .   PASS    AF=0.399143 ES:SE:LP:AF:ID  0.00204065:0.00196456:0.522879:0.399143:rs2462492
1   86028   rs114608975 T   C   .   PASS    AF=0.103539 ES:SE:LP:AF:ID  -0.00145779:0.00312724:0.19382:0.103539:rs114608975
1   91536   rs6702460   G   T   .   PASS    AF=0.455916 ES:SE:LP:AF:ID  7.13098e-05:0.00193229:0.0132283:0.455916:rs6702460
1   234313  rs8179466   C   T   .   PASS    AF=0.074454 ES:SE:LP:AF:ID  0.00190253:0.00382133:0.207608:0.074454:rs8179466
1   534192  rs6680723   C   T   .   PASS    AF=0.242059 ES:SE:LP:AF:ID  0.00226135:0.00220073:0.522879:0.242059:rs6680723
1   546697  rs12025928  A   G   .   PASS    AF=0.912869 ES:SE:LP:AF:ID  0.00104377:0.00273086:0.154902:0.912869:rs12025928
1   693731  rs12238997  A   G   .   PASS    AF=0.11731  ES:SE:LP:AF:ID  -0.00124146:0.00183509:0.30103:0.11731:rs12238997
1   705882  rs72631875  G   A   .   PASS    AF=0.067702 ES:SE:LP:AF:ID  -0.00163054:0.00267477:0.267606:0.067702:rs72631875
1   706368  rs12029736  A   G   .   PASS    AF=0.513311 ES:SE:LP:AF:ID  -0.00187137:0.00136212:0.769551:0.513311:rs12029736
1   714596  rs149887893 T   C   .   PASS    AF=0.03368  ES:SE:LP:AF:ID  -0.00194386:0.00339507:0.244125:0.03368:rs149887893
1   715265  rs12184267  C   T   .   PASS    AF=0.03746  ES:SE:LP:AF:ID  -0.000770541:0.00307916:0.09691:0.03746:rs12184267
1   715367  rs12184277  A   G   .   PASS    AF=0.037647 ES:SE:LP:AF:ID  -0.000886739:0.00306305:0.113509:0.037647:rs12184277
1   717485  rs12184279  C   A   .   PASS    AF=0.037223 ES:SE:LP:AF:ID  -0.00105163:0.00309104:0.136677:0.037223:rs12184279
1   717587  rs144155419 G   A   .   PASS    AF=0.016283 ES:SE:LP:AF:ID  -0.00583673:0.00484849:0.638272:0.016283:rs144155419
1   720381  rs116801199 G   T   .   PASS    AF=0.037863 ES:SE:LP:AF:ID  -0.000464831:0.00305258:0.0555173:0.037863:rs116801199
1   721290  rs12565286  G   C   .   PASS    AF=0.037958 ES:SE:LP:AF:ID  -0.000485735:0.0030429:0.0604807:0.037958:rs12565286
1   722670  rs116030099 T   C   .   PASS    AF=0.102738 ES:SE:LP:AF:ID  0.00166087:0.00222281:0.346787:0.102738:rs116030099
1   723891  rs2977670   G   C   .   PASS    AF=0.958087 ES:SE:LP:AF:ID  0.000268139:0.00293898:0.0315171:0.958087:rs2977670
1   724849  rs12126395  C   A   .   PASS    AF=0.031688 ES:SE:LP:AF:ID  -0.00279771:0.00538191:0.221849:0.031688:rs12126395
1   725060  rs865924913 A   T   .   PASS    AF=0.052722 ES:SE:LP:AF:ID  -0.00116026:0.00433488:0.102373:0.052722:rs865924913
1   726794  rs28454925  C   G   .   PASS    AF=0.037451 ES:SE:LP:AF:ID  -0.000513098:0.00306288:0.0604807:0.037451:rs28454925
1   729632  rs116720794 C   T   .   PASS    AF=0.03772  ES:SE:LP:AF:ID  -0.000677532:0.0030375:0.0861861:0.03772:rs116720794
1   729679  rs4951859   C   G   .   PASS    AF=0.841445 ES:SE:LP:AF:ID  0.000719244:0.00158702:0.187087:0.841445:rs4951859
1   730087  rs148120343 T   C   .   PASS    AF=0.056324 ES:SE:LP:AF:ID  0.00121633:0.00257823:0.19382:0.056324:rs148120343
1   731718  rs58276399  T   C   .   PASS    AF=0.123072 ES:SE:LP:AF:ID  -0.000826928:0.00174315:0.19382:0.123072:rs58276399
1   732989  rs369030935 C   T   .   PASS    AF=0.025132 ES:SE:LP:AF:ID  0.00318343:0.00434083:0.337242:0.025132:rs369030935
1   734349  rs141242758 T   C   .   PASS    AF=0.122324 ES:SE:LP:AF:ID  -0.000673184:0.00174371:0.154902:0.122324:rs141242758
1   736289  rs79010578  T   A   .   PASS    AF=0.134134 ES:SE:LP:AF:ID  -0.000659985:0.00171173:0.154902:0.134134:rs79010578
1   736689  rs181876450 T   C   .   PASS    AF=0.011558 ES:SE:LP:AF:ID  0.00160423:0.00610042:0.102373:0.011558:rs181876450
1   740284  rs61770167  C   T   .   PASS    AF=0.006101 ES:SE:LP:AF:ID  -0.00597617:0.00774677:0.356547:0.006101:rs61770167
1   752478  rs146277091 G   A   .   PASS    AF=0.037602 ES:SE:LP:AF:ID  -0.0012535:0.00300936:0.167491:0.037602:rs146277091
1   752566  rs3094315   G   A   .   PASS    AF=0.837032 ES:SE:LP:AF:ID  0.00121215:0.00153525:0.366532:0.837032:rs3094315
1   752721  rs3131972   A   G   .   PASS    AF=0.836736 ES:SE:LP:AF:ID  0.00106972:0.00153412:0.309804:0.836736:rs3131972
1   753405  rs3115860   C   A   .   PASS    AF=0.868568 ES:SE:LP:AF:ID  0.0012666:0.0016485:0.356547:0.868568:rs3115860
1   753541  rs2073813   G   A   .   PASS    AF=0.130999 ES:SE:LP:AF:ID  -0.00111734:0.00165274:0.30103:0.130999:rs2073813
1   754063  rs12184312  G   T   .   PASS    AF=0.038048 ES:SE:LP:AF:ID  -0.000848755:0.00296215:0.113509:0.038048:rs12184312
1   754105  rs12184325  C   T   .   PASS    AF=0.038295 ES:SE:LP:AF:ID  -0.000906264:0.00294379:0.119186:0.038295:rs12184325
1   754182  rs3131969   A   G   .   PASS    AF=0.867981 ES:SE:LP:AF:ID  0.00110103:0.00164585:0.30103:0.867981:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.868055 ES:SE:LP:AF:ID  0.00122325:0.00164653:0.337242:0.868055:rs3131968
1   754211  rs12184313  G   A   .   PASS    AF=0.038202 ES:SE:LP:AF:ID  -0.000843691:0.00295739:0.107905:0.038202:rs12184313
1   754334  rs3131967   T   C   .   PASS    AF=0.867992 ES:SE:LP:AF:ID  0.00109494:0.00164581:0.29243:0.867992:rs3131967
1   754433  rs150578204 G   A   .   PASS    AF=0.005397 ES:SE:LP:AF:ID  -0.00509302:0.00824838:0.267606:0.005397:rs150578204
1   754503  rs3115859   G   A   .   PASS    AF=0.836162 ES:SE:LP:AF:ID  0.00113871:0.00152963:0.337242:0.836162:rs3115859
1   754629  rs10454459  A   G   .   PASS    AF=0.038205 ES:SE:LP:AF:ID  -0.000822545:0.0029617:0.107905:0.038205:rs10454459
1   754964  rs3131966   C   T   .   PASS    AF=0.836796 ES:SE:LP:AF:ID  0.00125126:0.00153382:0.387216:0.836796:rs3131966
1   755240  rs181660517 T   G   .   PASS    AF=0.01303  ES:SE:LP:AF:ID  0.00477899:0.00554901:0.408935:0.01303:rs181660517
1   755435  rs184270342 T   G   .   PASS    AF=0.005662 ES:SE:LP:AF:ID  0.00640854:0.00823758:0.356547:0.005662:rs184270342
1   755775  rs3131965   A   G   .   PASS    AF=0.838112 ES:SE:LP:AF:ID  0.00106159:0.00155542:0.309804:0.838112:rs3131965
1   755890  rs3115858   A   T   .   PASS    AF=0.868233 ES:SE:LP:AF:ID  0.00128957:0.00164369:0.366532:0.868233:rs3115858