Summary
Summary {data-width=650}
Manhattan plot
manhattan_plot
QQ plot
qq_plot
AF plot
af_plot
P-Z plot
pz_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=ieu-b-5088,TotalVariants=12243540,VariantsNotRead=0,HarmonisedVariants=12243540,VariantsNotHarmonised=0,SwitchedAlleles=102,NormalisedVariants=737,TotalControls=451301,TotalCases=11568,StudyType=CaseControl>",
"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>",
"Gwas2VCF_command": "--data /data/cromwell-executions/qc/a04df373-03e0-4e48-a2ac-5d8be2b12c83/call-vcf/inputs/-261022215/upload.txt.gz --id ieu-b-5088 --json /data/cromwell-executions/qc/a04df373-03e0-4e48-a2ac-5d8be2b12c83/call-vcf/inputs/-261022215/ieu-b-5088_data.json --ref /data/cromwell-executions/qc/a04df373-03e0-4e48-a2ac-5d8be2b12c83/call-vcf/inputs/1899004205/human_g1k_v37.fasta --dbsnp /data/cromwell-executions/qc/a04df373-03e0-4e48-a2ac-5d8be2b12c83/call-vcf/inputs/-307190728/dbsnp.v153.b37.vcf.gz --out /data/igd/ieu-b-5088/ieu-b-5088.vcf.gz --alias alias.txt --cohort_cases 11568 --cohort_controls 451301; 1.3.0",
"file_date": "2022-10-27T21:32:14.011330",
"bcftools_viewVersion": "1.9+htslib-1.9",
"bcftools_viewCommand": "view -h /data/cromwell-executions/qc/a04df373-03e0-4e48-a2ac-5d8be2b12c83/call-report/inputs/-261022215/ieu-b-5088.vcf.gz; Date=Thu Oct 27 21:58:51 2022"
}
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 /data/cromwell-executions/qc/a04df373-03e0-4e48-a2ac-5d8be2b12c83/call-ldsc/inputs/-261022215/ieu-b-5088.vcf.gz \
--ref-ld-chr /data/ref/eur_w_ld_chr/ \
--out /data/igd/ieu-b-5088/ldsc.txt \
--w-ld-chr /data/ref/eur_w_ld_chr/
Beginning analysis at Thu Oct 27 21:47:02 2022
Reading summary statistics from /data/cromwell-executions/qc/a04df373-03e0-4e48-a2ac-5d8be2b12c83/call-ldsc/inputs/-261022215/ieu-b-5088.vcf.gz ...
Read summary statistics for 12242540 SNPs.
Dropped 231422 SNPs with duplicated rs numbers.
Reading reference panel LD Score from /data/ref/eur_w_ld_chr/[1-22] ... (ldscore_fromlist)
Read reference panel LD Scores for 1290028 SNPs.
Removing partitioned LD Scores with zero variance.
Reading regression weight LD Score from /data/ref/eur_w_ld_chr/[1-22] ... (ldscore_fromlist)
Read regression weight LD Scores for 1290028 SNPs.
After merging with reference panel LD, 1220578 SNPs remain.
After merging with regression SNP LD, 1220578 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0033 (0.0009)
Lambda GC: 1.0328
Mean Chi^2: 1.0321
Intercept: 1.002 (0.006)
Ratio: 0.0627 (0.1857)
Analysis finished at Thu Oct 27 21:48:55 2022
Total time elapsed: 1.0m:53.2sQC metrics
Metrics
Metrics
{
"af_correlation": 0.95,
"inflation_factor": 1.0279,
"mean_EFFECT": -0.0002,
"n": "-Inf",
"n_snps": 12243540,
"n_clumped_hits": 0,
"n_p_sig": 0,
"n_mono": 0,
"n_ns": 1279900,
"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": 404183,
"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": 1220578,
"ldsc_nsnp_merge_regression_ld": 1220578,
"ldsc_observed_scale_h2_beta": 0.0033,
"ldsc_observed_scale_h2_se": 0.0009,
"ldsc_intercept_beta": 1.002,
"ldsc_intercept_se": 0.006,
"ldsc_lambda_gc": 1.0328,
"ldsc_mean_chisq": 1.0321,
"ldsc_ratio": 0.0623
}
Flags
| name | value |
|---|---|
| af_correlation | FALSE |
| inflation_factor | FALSE |
| n | TRUE |
| 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 betweenAFandAF_reference.inflation_factor(lambda): Genomic inflation factor.mean_EFFECT: Mean ofEFFECTsize.n: Maximum value of reported sample size across all SNPs, \(n\).n_clumped_hits: Number of clumped hits.n_snps: Number of SNPsn_p_sig: Number of SNPs with pvalue below5e-8.n_mono: Number of monomorphic (MAF == 1orMAF == 0) SNPs.n_ns: Number of SNPs with nonsense values:- alleles other than
A, C, G or T. - P-values
< 0or> 1. - negative or infinite standard errors (
<= 0or= Infinity). - infinite beta estimates or allele frequencies
< 0or> 1.
- alleles other than
n_mac: Number of cases whereMAC(\(2 \times N \times MAF\)) is less than6.is_snpid_unique:trueif the combination ofIDREFALTis unique and therefore no duplication in snpid.n_miss_<*>: Number ofNAobservations 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 expectratio_se_nto 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 ofdiffand the mean ofdiff2(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<*>:r2statistics under various assumptions1: \(r^2 = \sum_j{\frac{2 \times \beta_j^2 \times {MAF}_j \times (1 - {MAF}_j)}{\texttt{var1}}}\), \(\texttt{var1} = 1\).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: NOTis_snpid_unique.mean_EFFECT_nonfinite:mean(EFFECT)isNA,NaN, orInf.mean_EFFECT_05:abs(mean(EFFECT))> 0.5.mean_EFFECT_01:abs(mean(EFFECT))> 0.1.mean_chisq:ldsc_mean_chisq> 1.3 orldsc_mean_chisq< 0.7.n_p_sig:n_p_sig> 1000.miss_<*>:n_miss_<*>/n_snps> 0.01.ldsc_ratio:ldsc_ratio> 0.5ldsc_intercept_beta:ldsc_intercept_beta> 1.5n_clumped_hits:n_clumped_hits> 1000r2_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 | 566 | 0.9999538 | 3 | 58 | 0 | 12193990 | 0 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| character | REF | 0 | 1.0000000 | 1 | 101 | 0 | 56052 | 0 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| character | ALT | 0 | 1.0000000 | 1 | 662 | 0 | 34526 | 0 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| logical | N | 12243540 | 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 | 8.635974e+00 | 5.758637e+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 | 7.869393e+07 | 5.629933e+07 | 302.0000000 | 3.250309e+07 | 6.911922e+07 | 1.143452e+08 | 2.492405e+08 | ▇▆▅▂▁ |
| numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | -1.990000e-04 | 8.696170e-02 | -25.9891000 | -1.888870e-02 | -1.342000e-04 | 1.841410e-02 | 3.410840e+01 | ▁▁▇▁▁ |
| numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.675600e-02 | 8.239420e-02 | 0.0129077 | 1.566670e-02 | 2.532910e-02 | 5.848480e-02 | 2.117240e+01 | ▇▁▁▁▁ |
| numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.958393e-01 | 2.897946e-01 | 0.0000003 | 2.439681e-01 | 4.940729e-01 | 7.470437e-01 | 9.999999e-01 | ▇▇▇▇▇ |
| numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.958393e-01 | 2.897946e-01 | 0.0000003 | 2.439681e-01 | 4.940722e-01 | 7.470431e-01 | 9.999999e-01 | ▇▇▇▇▇ |
| numeric | AF | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 2.127948e-01 | 2.602010e-01 | 0.0000054 | 1.457920e-02 | 8.849450e-02 | 3.382510e-01 | 9.999950e-01 | ▇▂▁▁▁ |
| numeric | AF_reference | 404183 | 0.9669881 | NA | NA | NA | NA | NA | NA | NA | 2.160784e-01 | 2.512172e-01 | 0.0000000 | 1.357830e-02 | 1.106230e-01 | 3.426520e-01 | 1.000000e+00 | ▇▂▁▁▁ |
Head and tail
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 10177 | rs367896724 | A | AC | 0.0239320 | 0.0199771 | 0.2309277 | 0.2309280 | 0.3989090 | 0.4253190 | NA |
| 1 | 10352 | rs555500075 | T | TA | 0.0241459 | 0.0205657 | 0.2403604 | 0.2403606 | 0.3932350 | 0.4375000 | NA |
| 1 | 11008 | rs575272151 | C | G | -0.0218043 | 0.0340917 | 0.5224479 | 0.5224470 | 0.0862238 | 0.0880591 | NA |
| 1 | 11012 | rs544419019 | C | G | -0.0218043 | 0.0340917 | 0.5224479 | 0.5224470 | 0.0862238 | 0.0880591 | NA |
| 1 | 13110 | rs540538026 | G | A | -0.0098554 | 0.0454133 | 0.8281965 | 0.8281963 | 0.0586862 | 0.0267572 | NA |
| 1 | 13116 | rs62635286 | T | G | -0.0050375 | 0.0268945 | 0.8514219 | 0.8514216 | 0.1891810 | 0.0970447 | NA |
| 1 | 13118 | rs200579949 | A | G | -0.0050375 | 0.0268945 | 0.8514219 | 0.8514216 | 0.1891810 | 0.0970447 | NA |
| 1 | 13273 | rs531730856 | G | C | 0.0420562 | 0.0314627 | 0.1813210 | 0.1813205 | 0.1341340 | 0.0950479 | NA |
| 1 | 14464 | rs546169444 | A | T | -0.0428916 | 0.0286725 | 0.1346766 | 0.1346760 | 0.1568960 | 0.0958466 | NA |
| 1 | 14599 | rs531646671 | T | A | 0.0357521 | 0.0260905 | 0.1705886 | 0.1705898 | 0.1915560 | 0.1475640 | NA |
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 22 | 51233182 | rs4040317 | G | A | 0.0278066 | 0.0163275 | 0.0885584 | 0.0885581 | 0.3200850 | 0.2633790 | NA |
| 22 | 51233300 | rs9616839 | C | T | 0.0239053 | 0.0162955 | 0.1423797 | 0.1423794 | 0.3343160 | 0.3146960 | NA |
| 22 | 51233312 | rs62240043 | A | G | 0.0194809 | 0.0171633 | 0.2563610 | 0.2563618 | 0.2729920 | 0.2134580 | NA |
| 22 | 51233347 | rs62240044 | T | C | 0.0194809 | 0.0171633 | 0.2563610 | 0.2563618 | 0.2729920 | 0.2134580 | NA |
| 22 | 51234799 | rs191117135 | G | A | -0.0840618 | 0.0608731 | 0.1672985 | 0.1672989 | 0.0156525 | 0.0059904 | NA |
| 22 | 51235959 | rs200189535 | T | C | 0.0342492 | 0.0199917 | 0.0866802 | 0.0866811 | 0.1953560 | 0.1996810 | NA |
| 22 | 51235979 | rs62240045 | G | A | -0.0354109 | 0.0222085 | 0.1108294 | 0.1108297 | 0.2637950 | 0.2400160 | NA |
| 22 | 51236013 | rs200507571 | A | AT | -0.0079175 | 0.0171947 | 0.6451831 | 0.6451836 | 0.2513350 | 0.1487620 | NA |
| 22 | 51237063 | rs3896457 | T | C | 0.0136831 | 0.0157926 | 0.3862558 | 0.3862573 | 0.2979790 | 0.2050720 | NA |
| 22 | 51237712 | rs370652263 | G | A | -0.0507820 | 0.0315958 | 0.1080021 | 0.1080020 | 0.0553517 | 0.0690895 | NA |
bcf preview
1 10177 rs1264289758 A AC . PASS AF=0.398909 ES:SE:LP:AF:ID 0.023932:0.0199771:0.636524:0.398909:rs1264289758
1 10352 rs1557426776 T TA . PASS AF=0.393235 ES:SE:LP:AF:ID 0.0241459:0.0205657:0.619137:0.393235:rs1557426776
1 11008 rs575272151 C G . PASS AF=0.0862238 ES:SE:LP:AF:ID -0.0218043:0.0340917:0.281957:0.0862238:rs575272151
1 11012 rs544419019 C G . PASS AF=0.0862238 ES:SE:LP:AF:ID -0.0218043:0.0340917:0.281957:0.0862238:rs544419019
1 13110 rs540538026 G A . PASS AF=0.0586862 ES:SE:LP:AF:ID -0.00985539:0.0454133:0.0818666:0.0586862:rs540538026
1 13116 rs62635286 T G . PASS AF=0.189181 ES:SE:LP:AF:ID -0.00503747:0.0268945:0.0698552:0.189181:rs62635286
1 13118 rs62028691 A G . PASS AF=0.189181 ES:SE:LP:AF:ID -0.00503747:0.0268945:0.0698552:0.189181:rs62028691
1 13273 rs531730856 G C . PASS AF=0.134134 ES:SE:LP:AF:ID 0.0420562:0.0314627:0.741552:0.134134:rs531730856
1 14464 rs546169444 A T . PASS AF=0.156896 ES:SE:LP:AF:ID -0.0428916:0.0286725:0.870708:0.156896:rs546169444
1 14599 rs707680 T A . PASS AF=0.191556 ES:SE:LP:AF:ID 0.0357521:0.0260905:0.76805:0.191556:rs707680
1 14604 rs1418508701 A G . PASS AF=0.191556 ES:SE:LP:AF:ID 0.0357521:0.0260905:0.76805:0.191556:rs1418508701
1 14930 rs6682385 A G . PASS AF=0.47382 ES:SE:LP:AF:ID 0.00531532:0.0202382:0.10082:0.47382:rs6682385
1 14933 rs199856693 G A . PASS AF=0.0450772 ES:SE:LP:AF:ID -0.037712:0.0497654:0.348166:0.0450772:rs199856693
1 15211 rs3982632 T G . PASS AF=0.741354 ES:SE:LP:AF:ID -0.0181075:0.023399:0.357522:0.741354:rs3982632
1 15820 rs1316988498 G T . PASS AF=0.275123 ES:SE:LP:AF:ID -0.00267011:0.0240267:0.0402374:0.275123:rs1316988498
1 15903 rs557514207 G GC . PASS AF=0.418839 ES:SE:LP:AF:ID -0.0036548:0.0198079:0.0687395:0.418839:rs557514207
1 28590 rs1344649620 T TTGG . PASS AF=0.95657 ES:SE:LP:AF:ID 0.0426652:0.0562507:0.348565:0.95657:rs1344649620
1 30923 rs1165072081 G T . PASS AF=0.910222 ES:SE:LP:AF:ID -0.007182:0.0373812:0.0717877:0.910222:rs1165072081
1 47159 rs540662756 T C . PASS AF=0.0627122 ES:SE:LP:AF:ID -0.021891:0.0427005:0.215964:0.0627122:rs540662756
1 49298 rs10399793 T C . PASS AF=0.623769 ES:SE:LP:AF:ID 0.0133215:0.0237362:0.240604:0.623769:rs10399793
1 49554 rs539322794 A G . PASS AF=0.0929559 ES:SE:LP:AF:ID -0.0267843:0.0365164:0.334174:0.0929559:rs539322794
1 51479 rs116400033 T A . PASS AF=0.213261 ES:SE:LP:AF:ID -0.0109207:0.0254269:0.175506:0.213261:rs116400033
1 54490 rs141149254 G A . PASS AF=0.15439 ES:SE:LP:AF:ID 0.00380134:0.0285535:0.0486188:0.15439:rs141149254
1 54676 rs2462492 C T . PASS AF=0.400396 ES:SE:LP:AF:ID -0.000886954:0.0235038:0.0132741:0.400396:rs2462492
1 54712 rs573184866 T TTTTC . PASS AF=0.585266 ES:SE:LP:AF:ID 0.00879583:0.0186184:0.196118:0.585266:rs573184866
1 54716 rs1166278911 C T . PASS AF=0.417369 ES:SE:LP:AF:ID 0.014407:0.0214778:0.298987:0.417369:rs1166278911
1 55545 rs28396308 C T . PASS AF=0.253778 ES:SE:LP:AF:ID -0.0359831:0.0241683:0.864787:0.253778:rs28396308
1 58814 rs114420996 G A . PASS AF=0.0899991 ES:SE:LP:AF:ID -0.0421569:0.036821:0.598177:0.0899991:rs114420996
1 59040 rs62637815 T C . PASS AF=0.0887901 ES:SE:LP:AF:ID -0.0455775:0.0369295:0.663266:0.0887901:rs62637815
1 60351 rs62637817 A G . PASS AF=0.0809852 ES:SE:LP:AF:ID -0.0351892:0.038317:0.445602:0.0809852:rs62637817
1 62777 rs3844233 A T . PASS AF=0.438264 ES:SE:LP:AF:ID -0.0144478:0.0204143:0.319562:0.438264:rs3844233
1 63268 rs28664618 T C . PASS AF=0.382183 ES:SE:LP:AF:ID -0.0202877:0.0219613:0.449044:0.382183:rs28664618
1 63671 rs80011619 G A . PASS AF=0.158758 ES:SE:LP:AF:ID -0.0688015:0.027928:1.86145:0.158758:rs80011619
1 63735 rs61158452 CCTA C . PASS AF=0.315972 ES:SE:LP:AF:ID 0.0164919:0.0217781:0.347861:0.315972:rs61158452
1 64931 rs62639104 G A . PASS AF=0.0795808 ES:SE:LP:AF:ID -0.0360687:0.0388032:0.4527:0.0795808:rs62639104
1 68082 rs367789441 T C . PASS AF=0.0707815 ES:SE:LP:AF:ID -0.00770986:0.0392961:0.0734239:0.0707815:rs367789441
1 69428 rs140739101 T G . PASS AF=0.0329171 ES:SE:LP:AF:ID -0.0556473:0.0594707:0.456649:0.0329171:rs140739101
1 69761 rs200505207 A T . PASS AF=0.0738755 ES:SE:LP:AF:ID 0.00182371:0.0386804:0.0166466:0.0738755:rs200505207
1 69897 rs200676709 T C . PASS AF=0.75122 ES:SE:LP:AF:ID 0.0256645:0.0246645:0.525656:0.75122:rs200676709
1 74790 rs13328700 C G . PASS AF=0.0340935 ES:SE:LP:AF:ID -0.0941684:0.0565569:1.01814:0.0340935:rs13328700
1 74792 rs1335672253 G A . PASS AF=0.0340935 ES:SE:LP:AF:ID -0.0941684:0.0565569:1.01814:0.0340935:rs1335672253
1 76838 rs563953605 T G . PASS AF=0.0771376 ES:SE:LP:AF:ID -0.0429128:0.0394606:0.557799:0.0771376:rs563953605
1 76854 rs367666799 A G . PASS AF=0.0775039 ES:SE:LP:AF:ID -0.0277825:0.0381794:0.330863:0.0775039:rs367666799
1 77866 rs563593912 C T . PASS AF=0.0769428 ES:SE:LP:AF:ID -0.044448:0.0394703:0.58483:0.0769428:rs563593912
1 77874 rs62641297 G A . PASS AF=0.0769428 ES:SE:LP:AF:ID -0.044448:0.0394703:0.58483:0.0769428:rs62641297
1 81260 rs571136476 C T . PASS AF=0.0414644 ES:SE:LP:AF:ID 0.107121:0.0550906:1.28533:0.0414644:rs571136476
1 81587 rs536406113 C T . PASS AF=0.0609442 ES:SE:LP:AF:ID -0.016392:0.0418708:0.157743:0.0609442:rs536406113
1 82163 rs139113303 G A . PASS AF=0.0754483 ES:SE:LP:AF:ID -0.0293118:0.038687:0.348091:0.0754483:rs139113303
1 82609 rs149189449 C G . PASS AF=0.0754758 ES:SE:LP:AF:ID -0.030205:0.0386808:0.361638:0.0754758:rs149189449
1 83514 rs201754587 C T . PASS AF=0.352797 ES:SE:LP:AF:ID 0.0205878:0.0221157:0.453584:0.352797:rs201754587