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:373,TotalVariants=9851866,VariantsNotRead=0,HarmonisedVariants=9851866,VariantsNotHarmonised=0,SwitchedAlleles=9851866,TotalControls=460785,TotalCases=2225,StudyType=CaseControl>",
    "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_41202_N328.vcf.gz --id UKB-b:373 --data /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/raw-output/data.batch_41202_N328.txt.gz --cohort_cases 2225 --cohort_controls 460785 --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": "2019-09-13T05:15:17.919920",
    "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-373/mac_discard.txt -Oz /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-373/UKB-b-373_raw.vcf.gz; Date=Thu Oct 17 12:41:59 2019",
    "bcftools_viewCommand.1": "view -h /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukb-b-373/ukb-b-373.vcf.gz; Date=Sun May 10 07:27:22 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-373/UKB-b-373_data.vcf.gz \
--ref-ld-chr ../reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-373/ldsc.txt \
--w-ld-chr ../reference/eur_w_ld_chr/ 

Beginning analysis at Thu Oct 17 14:43:46 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-373/UKB-b-373_data.vcf.gz ...
Read summary statistics for 3423476 SNPs.
Dropped 510 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, 838785 SNPs remain.
After merging with regression SNP LD, 838785 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.002 (0.0011)
Lambda GC: 1.0181
Mean Chi^2: 1.0144
Intercept: 0.9936 (0.0084)
Ratio < 0 (usually indicates GC correction).
Analysis finished at Thu Oct 17 14:44:36 2019
Total time elapsed: 50.52s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.8467,
    "inflation_factor": 1,
    "mean_EFFECT": -6.0889e-07,
    "n": "-Inf",
    "n_snps": 9851866,
    "n_clumped_hits": 0,
    "n_p_sig": 0,
    "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": 27472,
    "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": 838785,
    "ldsc_nsnp_merge_regression_ld": 838785,
    "ldsc_observed_scale_h2_beta": 0.002,
    "ldsc_observed_scale_h2_se": 0.0011,
    "ldsc_intercept_beta": 0.9936,
    "ldsc_intercept_se": 0.0084,
    "ldsc_lambda_gc": 1.0181,
    "ldsc_mean_chisq": 1.0144,
    "ldsc_ratio": -0.4444
}
 

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 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 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 3422969 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 3423476 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 8.662989e+00 5.774285e+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 7.855223e+07 5.672981e+07 828.0000000 3.158832e+07 6.892529e+07 1.147406e+08 2.492385e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA NA NA -6.000000e-07 1.636000e-04 -0.0009055 -1.094000e-04 -7.000000e-07 1.086000e-04 8.948000e-04 ▁▂▇▂▁
numeric SE 0 1.0000000 NA NA NA NA NA NA NA 1.611000e-04 1.600000e-05 0.0001387 1.472000e-04 1.561000e-04 1.723000e-04 3.637000e-04 ▇▁▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA NA NA 4.964877e-01 2.894996e-01 0.0000010 2.399999e-01 5.000000e-01 7.499995e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA NA NA 4.964889e-01 2.894706e-01 0.0000010 2.446117e-01 4.952135e-01 7.469525e-01 9.999996e-01 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA NA NA 4.182432e-01 1.925957e-01 0.1573040 2.492760e-01 3.807410e-01 5.655550e-01 8.426960e-01 ▇▆▅▃▂
numeric AF_reference 27472 0.9919754 NA NA NA NA NA NA NA 4.042778e-01 2.030542e-01 0.0000000 2.390180e-01 3.738020e-01 5.527160e-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 0.0005042 0.0002552 0.0479999 0.0482212 0.623765 0.782149 NA
1 54676 rs2462492 C T 0.0001961 0.0002529 0.4400003 0.4379754 0.400401 NA NA
1 91536 rs6702460 G T 0.0003517 0.0002490 0.1600000 0.1577386 0.456846 0.420727 NA
1 534192 rs6680723 C T -0.0004996 0.0002844 0.0790005 0.0789801 0.240959 NA NA
1 706368 rs55727773 A G 0.0000348 0.0001765 0.8400000 0.8436249 0.515645 0.275160 NA
1 752566 rs3094315 G A 0.0000150 0.0002000 0.9400001 0.9401574 0.838945 0.718251 NA
1 752721 rs3131972 A G -0.0000078 0.0001998 0.9699999 0.9687434 0.838573 0.653355 NA
1 754503 rs3115859 G A 0.0000019 0.0001992 0.9900000 0.9922527 0.838026 0.663938 NA
1 754964 rs3131966 C T 0.0000017 0.0001998 0.9900000 0.9931790 0.838657 0.663339 NA
1 755775 rs3131965 A G -0.0000155 0.0002025 0.9400001 0.9388140 0.839770 NA NA
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51182485 rs6009961 A G 0.0000963 0.0001667 0.5600000 0.5632732 0.715502 0.6383790 NA
22 51186143 rs2879914 T C 0.0000100 0.0001546 0.9500000 0.9484300 0.381825 0.2733630 NA
22 51186228 rs3865766 C T 0.0001603 0.0001506 0.2900000 0.2872673 0.451061 0.4532750 NA
22 51192586 rs5771006 G A 0.0001545 0.0002029 0.4500005 0.4465464 0.167627 0.0848642 NA
22 51193227 rs34608236 T G -0.0001286 0.0002075 0.5400003 0.5354829 0.168490 0.0692891 NA
22 51197266 rs61290853 A G 0.0001872 0.0001555 0.2300001 0.2287847 0.386333 0.4229230 NA
22 51198027 rs34939255 A G -0.0000648 0.0001761 0.7099994 0.7129571 0.254562 0.0984425 NA
22 51211106 rs9628250 T C -0.0001504 0.0001745 0.3900004 0.3888752 0.271547 0.1671330 NA
22 51212875 rs2238837 A C 0.0000564 0.0001659 0.7300002 0.7337415 0.331457 0.3724040 NA
22 51237063 rs3896457 T C -0.0000301 0.0001698 0.8600001 0.8591840 0.297974 0.2050720 NA

bcf preview

1   49298   rs10399793  T   C   .   PASS    AF=0.623765 ES:SE:LP:AF:ID  0.000504181:0.000255228:1.31876:0.623765:rs10399793
1   54676   rs2462492   C   T   .   PASS    AF=0.400401 ES:SE:LP:AF:ID  0.000196117:0.000252853:0.356547:0.400401:rs2462492
1   91536   rs6702460   G   T   .   PASS    AF=0.456846 ES:SE:LP:AF:ID  0.000351716:0.000248964:0.79588:0.456846:rs6702460
1   534192  rs6680723   C   T   .   PASS    AF=0.240959 ES:SE:LP:AF:ID  -0.000499557:0.000284383:1.10237:0.240959:rs6680723
1   706368  rs12029736  A   G   .   PASS    AF=0.515645 ES:SE:LP:AF:ID  3.48239e-05:0.000176539:0.0757207:0.515645:rs12029736
1   752566  rs3094315   G   A   .   PASS    AF=0.838945 ES:SE:LP:AF:ID  1.50156e-05:0.000200016:0.0268721:0.838945:rs3094315
1   752721  rs3131972   A   G   .   PASS    AF=0.838573 ES:SE:LP:AF:ID  -7.82907e-06:0.000199801:0.0132283:0.838573:rs3131972
1   754503  rs3115859   G   A   .   PASS    AF=0.838026 ES:SE:LP:AF:ID  1.93469e-06:0.000199247:0.00436481:0.838026:rs3115859
1   754964  rs3131966   C   T   .   PASS    AF=0.838657 ES:SE:LP:AF:ID  1.70813e-06:0.000199807:0.00436481:0.838657:rs3131966
1   755775  rs3131965   A   G   .   PASS    AF=0.83977  ES:SE:LP:AF:ID  -1.55447e-05:0.000202509:0.0268721:0.83977:rs3131965
1   760912  rs1048488   C   T   .   PASS    AF=0.838306 ES:SE:LP:AF:ID  3.81762e-05:0.000198869:0.0705811:0.838306:rs1048488
1   761147  rs3115850   T   C   .   PASS    AF=0.838427 ES:SE:LP:AF:ID  3.73419e-05:0.000199009:0.0705811:0.838427:rs3115850
1   763394  rs3115847   G   A   .   PASS    AF=0.706753 ES:SE:LP:AF:ID  -0.000143987:0.000206975:0.309804:0.706753:rs3115847
1   768253  rs2977608   A   C   .   PASS    AF=0.761297 ES:SE:LP:AF:ID  -9.38291e-05:0.000168928:0.236572:0.761297:rs2977608
1   776546  rs12124819  A   G   .   PASS    AF=0.265385 ES:SE:LP:AF:ID  -9.63476e-05:0.000188699:0.21467:0.265385:rs12124819
1   798400  rs10900604  A   G   .   PASS    AF=0.206591 ES:SE:LP:AF:ID  0.000173322:0.000180212:0.468521:0.206591:rs10900604
1   798959  rs11240777  G   A   .   PASS    AF=0.20642  ES:SE:LP:AF:ID  0.000176717:0.000180289:0.481486:0.20642:rs11240777
1   808631  rs11240779  G   A   .   PASS    AF=0.772619 ES:SE:LP:AF:ID  -4.3841e-05:0.000171505:0.09691:0.772619:rs11240779
1   808928  rs11240780  C   T   .   PASS    AF=0.772847 ES:SE:LP:AF:ID  -3.54113e-05:0.000171794:0.0757207:0.772847:rs11240780
1   814495  rs74461805  C   A   .   PASS    AF=0.340396 ES:SE:LP:AF:ID  -0.000230768:0.000242066:0.468521:0.340396:rs74461805
1   830181  rs28444699  A   G   .   PASS    AF=0.697255 ES:SE:LP:AF:ID  -6.33144e-05:0.000161955:0.154902:0.697255:rs28444699
1   831489  rs4970385   C   T   .   PASS    AF=0.705397 ES:SE:LP:AF:ID  -9.90541e-05:0.000159023:0.275724:0.705397:rs4970385
1   831909  rs9697642   C   T   .   PASS    AF=0.705442 ES:SE:LP:AF:ID  -0.000109397:0.000159018:0.309804:0.705442:rs9697642
1   832066  rs9697380   G   C   .   PASS    AF=0.705627 ES:SE:LP:AF:ID  -9.24146e-05:0.000159025:0.251812:0.705627:rs9697380
1   832318  rs4500250   C   A   .   PASS    AF=0.705655 ES:SE:LP:AF:ID  -8.80628e-05:0.000159042:0.236572:0.705655:rs4500250
1   832398  rs4553118   T   C   .   PASS    AF=0.730129 ES:SE:LP:AF:ID  -0.00011309:0.000163376:0.309804:0.730129:rs4553118
1   832918  rs28765502  T   C   .   PASS    AF=0.294377 ES:SE:LP:AF:ID  8.80916e-05:0.000159035:0.236572:0.294377:rs28765502
1   833223  rs13303211  C   T   .   PASS    AF=0.236703 ES:SE:LP:AF:ID  -6.78113e-05:0.000169317:0.161151:0.236703:rs13303211
1   833302  rs28752186  C   T   .   PASS    AF=0.236691 ES:SE:LP:AF:ID  -6.76049e-05:0.000169319:0.161151:0.236691:rs28752186
1   833641  rs28594623  T   C   .   PASS    AF=0.23975  ES:SE:LP:AF:ID  -5.16934e-05:0.000168776:0.119186:0.23975:rs28594623
1   833824  rs28484835  T   C   .   PASS    AF=0.236693 ES:SE:LP:AF:ID  -6.76009e-05:0.000169317:0.161151:0.236693:rs28484835
1   833927  rs28593608  T   C   .   PASS    AF=0.212421 ES:SE:LP:AF:ID  -6.18296e-05:0.000175983:0.136677:0.212421:rs28593608
1   834198  rs28385272  T   C   .   PASS    AF=0.212316 ES:SE:LP:AF:ID  -5.8454e-05:0.000176013:0.130768:0.212316:rs28385272
1   834832  rs4411087   G   C   .   PASS    AF=0.237178 ES:SE:LP:AF:ID  -6.12101e-05:0.000169188:0.142668:0.237178:rs4411087
1   834928  rs4422949   A   G   .   PASS    AF=0.212962 ES:SE:LP:AF:ID  -5.11558e-05:0.000175763:0.113509:0.212962:rs4422949
1   834999  rs28570054  G   A   .   PASS    AF=0.212924 ES:SE:LP:AF:ID  -5.62299e-05:0.000175799:0.124939:0.212924:rs28570054
1   835499  rs4422948   A   G   .   PASS    AF=0.241162 ES:SE:LP:AF:ID  -9.01646e-05:0.000168007:0.229148:0.241162:rs4422948
1   836529  rs28731045  C   G   .   PASS    AF=0.213543 ES:SE:LP:AF:ID  -3.26969e-05:0.00017554:0.0705811:0.213543:rs28731045
1   836896  rs28705752  T   C   .   PASS    AF=0.269511 ES:SE:LP:AF:ID  -8.8162e-05:0.000162113:0.229148:0.269511:rs28705752
1   836924  rs72890788  G   A   .   PASS    AF=0.213513 ES:SE:LP:AF:ID  -2.98931e-05:0.000175561:0.0655015:0.213513:rs72890788
1   838387  rs4970384   T   C   .   PASS    AF=0.214587 ES:SE:LP:AF:ID  -3.37956e-05:0.000175223:0.0705811:0.214587:rs4970384
1   838555  rs4970383   C   A   .   PASS    AF=0.246204 ES:SE:LP:AF:ID  -7.9655e-05:0.000166851:0.200659:0.246204:rs4970383
1   839103  rs28562941  A   G   .   PASS    AF=0.270019 ES:SE:LP:AF:ID  -8.1264e-05:0.000162228:0.207608:0.270019:rs28562941
1   840753  rs4970382   T   C   .   PASS    AF=0.400124 ES:SE:LP:AF:ID  0.000120887:0.000146686:0.387216:0.400124:rs4970382
1   841085  rs1574243   C   G   .   PASS    AF=0.237102 ES:SE:LP:AF:ID  -9.48661e-05:0.000170381:0.236572:0.237102:rs1574243
1   842013  rs7419119   T   G   .   PASS    AF=0.215391 ES:SE:LP:AF:ID  -5.10826e-05:0.000175341:0.113509:0.215391:rs7419119
1   842362  rs28540380  C   T   .   PASS    AF=0.235323 ES:SE:LP:AF:ID  3.42378e-07:0.000172933:-0:0.235323:rs28540380
1   843405  rs11516185  A   G   .   PASS    AF=0.362606 ES:SE:LP:AF:ID  0.000100074:0.000182089:0.236572:0.362606:rs11516185
1   844300  rs61769713  C   G   .   PASS    AF=0.818811 ES:SE:LP:AF:ID  -0.00024459:0.000187143:0.721246:0.818811:rs61769713
1   845283  rs7366404   G   T   .   PASS    AF=0.814497 ES:SE:LP:AF:ID  -0.000214671:0.000185494:0.60206:0.814497:rs7366404