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-5112,TotalVariants=12321875,VariantsNotRead=0,HarmonisedVariants=12321875,VariantsNotHarmonised=0,SwitchedAlleles=11141410,NormalisedVariants=744,TotalControls=257643,TotalCases=38639,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/3a4fd95f-ec2d-4fc9-9942-dd278527458b/call-vcf/inputs/-261021477/upload.txt.gz --id ieu-b-5112 --json /data/cromwell-executions/qc/3a4fd95f-ec2d-4fc9-9942-dd278527458b/call-vcf/inputs/-261021477/ieu-b-5112_data.json --ref /data/cromwell-executions/qc/3a4fd95f-ec2d-4fc9-9942-dd278527458b/call-vcf/inputs/1899004205/human_g1k_v37.fasta --dbsnp /data/cromwell-executions/qc/3a4fd95f-ec2d-4fc9-9942-dd278527458b/call-vcf/inputs/-307190728/dbsnp.v153.b37.vcf.gz --out /data/igd/ieu-b-5112/ieu-b-5112.vcf.gz --alias alias.txt --cohort_cases 38639 --cohort_controls 257643; 1.3.0",
"file_date": "2023-09-18T20:42:52.534298",
"bcftools_viewVersion": "1.9+htslib-1.9",
"bcftools_viewCommand": "view -h /data/cromwell-executions/qc/3a4fd95f-ec2d-4fc9-9942-dd278527458b/call-report/inputs/-261021477/ieu-b-5112.vcf.gz; Date=Mon Sep 18 21:13:04 2023"
}
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/3a4fd95f-ec2d-4fc9-9942-dd278527458b/call-ldsc/inputs/-261021477/ieu-b-5112.vcf.gz \
--ref-ld-chr /data/ref/eur_w_ld_chr/ \
--out /data/igd/ieu-b-5112/ldsc.txt \
--w-ld-chr /data/ref/eur_w_ld_chr/
Beginning analysis at Mon Sep 18 21:00:17 2023
Reading summary statistics from /data/cromwell-executions/qc/3a4fd95f-ec2d-4fc9-9942-dd278527458b/call-ldsc/inputs/-261021477/ieu-b-5112.vcf.gz ...
Read summary statistics for 12320830 SNPs.
Dropped 206220 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: 0.0253 (0.002)
Lambda GC: 1.1361
Mean Chi^2: 1.1544
Intercept: 1.0053 (0.007)
Ratio: 0.0345 (0.0452)
Analysis finished at Mon Sep 18 21:02:18 2023
Total time elapsed: 2.0m:1.06sQC metrics
Metrics
Metrics
{
"af_correlation": 0.9501,
"inflation_factor": 1.0966,
"mean_EFFECT": 0,
"n": "-Inf",
"n_snps": 12321875,
"n_clumped_hits": 2,
"n_p_sig": 4,
"n_mono": 0,
"n_ns": 1293897,
"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": 1423040,
"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": 0.0253,
"ldsc_observed_scale_h2_se": 0.002,
"ldsc_intercept_beta": 1.0053,
"ldsc_intercept_se": 0.007,
"ldsc_lambda_gc": 1.1361,
"ldsc_mean_chisq": 1.1544,
"ldsc_ratio": 0.0343
}
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 | 675 | 0.9999452 | 3 | 58 | 0 | 12276232 | 0 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| character | REF | 0 | 1.0000000 | 1 | 88 | 0 | 17566 | 0 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| character | ALT | 0 | 1.0000000 | 1 | 662 | 0 | 71704 | 0 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| logical | N | 12321875 | 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 | 8.757492e+00 | 5.885387e+00 | 1.0000000 | 4.000000e+00 | 8.000000e+00 | 1.300000e+01 | 2.300000e+01 | ▇▅▅▂▂ |
| numeric | POS | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 7.871202e+07 | 5.622121e+07 | 302.0000000 | 3.252510e+07 | 6.928045e+07 | 1.144492e+08 | 2.492405e+08 | ▇▆▅▂▁ |
| numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 1.270000e-05 | 5.476100e-03 | -0.0796508 | -1.682600e-03 | -9.000000e-07 | 1.676600e-03 | 9.687280e-02 | ▁▁▇▁▁ |
| numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 3.897000e-03 | 3.773100e-03 | 0.0009833 | 1.359100e-03 | 2.182900e-03 | 5.039700e-03 | 6.000190e-02 | ▇▁▁▁▁ |
| numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.855873e-01 | 2.929665e-01 | 0.0000000 | 2.300001e-01 | 4.799997e-01 | 7.400005e-01 | 1.000000e+00 | ▇▇▇▆▇ |
| numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.855881e-01 | 2.929420e-01 | 0.0000000 | 2.284026e-01 | 4.807846e-01 | 7.397679e-01 | 1.000000e+00 | ▇▇▇▇▇ |
| numeric | AF | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 2.593958e-01 | 3.020920e-01 | 0.0006660 | 1.657100e-02 | 1.144810e-01 | 4.379420e-01 | 9.993480e-01 | ▇▂▁▁▁ |
| numeric | AF_reference | 1423040 | 0.8845111 | NA | NA | NA | NA | NA | NA | NA | 2.132160e-01 | 2.513550e-01 | 0.0000000 | 1.218050e-02 | 1.056310e-01 | 3.376600e-01 | 1.000000e+00 | ▇▂▁▁▁ |
Head and tail
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 10177 | rs1264289758 | AC | A | 0.0011581 | 0.0017402 | 0.5099998 | 0.5057307 | 0.599422 | NA | NA |
| 1 | 10352 | rs1557426776 | TA | T | 0.0014522 | 0.0017963 | 0.4199997 | 0.4188345 | 0.605396 | NA | NA |
| 1 | 11008 | rs575272151 | C | G | 0.0042245 | 0.0029851 | 0.1600000 | 0.1570119 | 0.086142 | 0.0880591 | NA |
| 1 | 11012 | rs544419019 | C | G | 0.0042245 | 0.0029851 | 0.1600000 | 0.1570119 | 0.086142 | 0.0880591 | NA |
| 1 | 13110 | rs540538026 | G | A | -0.0005037 | 0.0039807 | 0.9000000 | 0.8993034 | 0.058592 | 0.0267572 | NA |
| 1 | 13116 | rs62635286 | T | G | -0.0015567 | 0.0023455 | 0.5099998 | 0.5068773 | 0.189419 | 0.0970447 | NA |
| 1 | 13118 | rs200579949 | A | G | -0.0015567 | 0.0023455 | 0.5099998 | 0.5068773 | 0.189419 | 0.0970447 | NA |
| 1 | 13273 | rs531730856 | G | C | 0.0026397 | 0.0027531 | 0.3400001 | 0.3376563 | 0.134077 | 0.0950479 | NA |
| 1 | 14464 | rs546169444 | A | T | -0.0028772 | 0.0025146 | 0.2500000 | 0.2525277 | 0.156545 | 0.0958466 | NA |
| 1 | 14599 | rs531646671 | T | A | -0.0003118 | 0.0022834 | 0.8900000 | 0.8913965 | 0.191169 | 0.1475640 | NA |
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 23 | 154901936 | rs697727 | A | G | -0.0031522 | 0.0011418 | 0.0058000 | 0.0057677 | 0.750473 | 0.643179 | NA |
| 23 | 154901964 | rs697726 | G | A | -0.0023833 | 0.0012091 | 0.0490004 | 0.0486999 | 0.346086 | 0.117616 | NA |
| 23 | 154902105 | rs696316 | G | T | -0.0031422 | 0.0011418 | 0.0059000 | 0.0059220 | 0.750445 | 0.636026 | NA |
| 23 | 154902889 | rs697725 | A | T | -0.0031165 | 0.0011415 | 0.0063000 | 0.0063291 | 0.750146 | 0.584106 | NA |
| 23 | 154903118 | rs479770 | G | A | -0.0031392 | 0.0011419 | 0.0060000 | 0.0059769 | 0.750523 | 0.643444 | NA |
| 23 | 154903224 | rs480725 | A | T | -0.0031398 | 0.0011419 | 0.0060000 | 0.0059678 | 0.750526 | 0.643444 | NA |
| 23 | 154903937 | rs674707 | G | A | -0.0031438 | 0.0011420 | 0.0059000 | 0.0059047 | 0.750534 | 0.643444 | NA |
| 23 | 154909055 | rs473529 | C | G | 0.0028848 | 0.0010759 | 0.0073000 | 0.0073346 | 0.306000 | 0.463046 | NA |
| 23 | 154918266 | rs642043 | C | T | 0.0031980 | 0.0010795 | 0.0031000 | 0.0030520 | 0.303787 | 0.478675 | NA |
| 23 | 154927581 | rs644138 | G | A | 0.0032041 | 0.0010797 | 0.0030000 | 0.0030005 | 0.303671 | 0.463576 | NA |
bcf preview
1 10177 rs1264289758 AC A . PASS AF=0.599422 ES:SE:LP:AF:ID 0.00115807:0.00174015:0.29243:0.599422:rs1264289758
1 10352 rs1557426776 TA T . PASS AF=0.605396 ES:SE:LP:AF:ID 0.00145225:0.00179635:0.376751:0.605396:rs1557426776
1 11008 rs575272151 C G . PASS AF=0.086142 ES:SE:LP:AF:ID 0.00422445:0.00298507:0.79588:0.086142:rs575272151
1 11012 rs544419019 C G . PASS AF=0.086142 ES:SE:LP:AF:ID 0.00422445:0.00298507:0.79588:0.086142:rs544419019
1 13110 rs540538026 G A . PASS AF=0.058592 ES:SE:LP:AF:ID -0.000503727:0.00398073:0.0457575:0.058592:rs540538026
1 13116 rs62635286 T G . PASS AF=0.189419 ES:SE:LP:AF:ID -0.00155672:0.00234549:0.29243:0.189419:rs62635286
1 13118 rs62028691 A G . PASS AF=0.189419 ES:SE:LP:AF:ID -0.00155672:0.00234549:0.29243:0.189419:rs62028691
1 13273 rs531730856 G C . PASS AF=0.134077 ES:SE:LP:AF:ID 0.00263969:0.0027531:0.468521:0.134077:rs531730856
1 14464 rs546169444 A T . PASS AF=0.156545 ES:SE:LP:AF:ID -0.00287725:0.00251457:0.60206:0.156545:rs546169444
1 14599 rs707680 T A . PASS AF=0.191169 ES:SE:LP:AF:ID -0.000311764:0.00228336:0.05061:0.191169:rs707680
1 14604 rs1418508701 A G . PASS AF=0.191169 ES:SE:LP:AF:ID -0.000311764:0.00228336:0.05061:0.191169:rs1418508701
1 14930 rs6682385 A G . PASS AF=0.472962 ES:SE:LP:AF:ID 0.00368717:0.00176527:1.4318:0.472962:rs6682385
1 14933 rs199856693 G A . PASS AF=0.045135 ES:SE:LP:AF:ID 0.00685285:0.00434396:0.958607:0.045135:rs199856693
1 15211 rs3982632 T G . PASS AF=0.741226 ES:SE:LP:AF:ID -0.000284388:0.0020455:0.05061:0.741226:rs3982632
1 15820 rs1316988498 G T . PASS AF=0.275911 ES:SE:LP:AF:ID -0.000255207:0.00209632:0.0457575:0.275911:rs1316988498
1 15903 rs557514207 GC G . PASS AF=0.582112 ES:SE:LP:AF:ID 0.00312053:0.00172947:1.14874:0.582112:rs557514207
1 28590 rs1344649620 T TTGG . PASS AF=0.956795 ES:SE:LP:AF:ID -0.00165822:0.00495385:0.130768:0.956795:rs1344649620
1 30923 rs1165072081 G T . PASS AF=0.910081 ES:SE:LP:AF:ID 0.00042476:0.0032677:0.0457575:0.910081:rs1165072081
1 47159 rs540662756 T C . PASS AF=0.062734 ES:SE:LP:AF:ID 0.00582103:0.00373109:0.920819:0.062734:rs540662756
1 49298 rs10399793 T C . PASS AF=0.623947 ES:SE:LP:AF:ID 0.00160558:0.00207548:0.356547:0.623947:rs10399793
1 49554 rs539322794 A G . PASS AF=0.092945 ES:SE:LP:AF:ID 0.00155377:0.00318875:0.200659:0.092945:rs539322794
1 51479 rs116400033 T A . PASS AF=0.212726 ES:SE:LP:AF:ID -0.00134887:0.00222055:0.267606:0.212726:rs116400033
1 54490 rs141149254 G A . PASS AF=0.154088 ES:SE:LP:AF:ID 0.000761844:0.00249715:0.119186:0.154088:rs141149254
1 54676 rs2462492 C T . PASS AF=0.400706 ES:SE:LP:AF:ID 0.000420238:0.00206097:0.0757207:0.400706:rs2462492
1 54712 rs573184866 TTTTC T . PASS AF=0.415373 ES:SE:LP:AF:ID 0.00297175:0.00162801:1.16749:0.415373:rs573184866
1 54716 rs1166278911 C T . PASS AF=0.417404 ES:SE:LP:AF:ID -0.00233283:0.00188039:0.677781:0.417404:rs1166278911
1 55545 rs28396308 C T . PASS AF=0.253347 ES:SE:LP:AF:ID 0.0013604:0.00211425:0.283997:0.253347:rs28396308
1 58814 rs114420996 G A . PASS AF=0.089854 ES:SE:LP:AF:ID 0.00296416:0.0032247:0.443698:0.089854:rs114420996
1 59040 rs62637815 T C . PASS AF=0.08881 ES:SE:LP:AF:ID 0.000971949:0.0032318:0.119186:0.08881:rs62637815
1 60351 rs62637817 A G . PASS AF=0.080963 ES:SE:LP:AF:ID 0.00135684:0.00335499:0.161151:0.080963:rs62637817
1 62777 rs3844233 A T . PASS AF=0.438707 ES:SE:LP:AF:ID 0.000593426:0.00177923:0.130768:0.438707:rs3844233
1 63268 rs28664618 T C . PASS AF=0.382266 ES:SE:LP:AF:ID 0.000706997:0.0019169:0.148742:0.382266:rs28664618
1 63671 rs80011619 G A . PASS AF=0.159026 ES:SE:LP:AF:ID 0.000600575:0.00244056:0.091515:0.159026:rs80011619
1 63735 rs61158452 C CCTA . PASS AF=0.683734 ES:SE:LP:AF:ID -0.000962766:0.00190016:0.21467:0.683734:rs61158452
1 64931 rs62639104 G A . PASS AF=0.079629 ES:SE:LP:AF:ID 0.00140561:0.00339318:0.167491:0.079629:rs62639104
1 68082 rs367789441 T C . PASS AF=0.071018 ES:SE:LP:AF:ID 0.0028686:0.00343305:0.39794:0.071018:rs367789441
1 69428 rs140739101 T G . PASS AF=0.032945 ES:SE:LP:AF:ID -0.000800626:0.00521628:0.0555173:0.032945:rs140739101
1 69761 rs200505207 A T . PASS AF=0.074107 ES:SE:LP:AF:ID 0.00239557:0.00338124:0.318759:0.074107:rs200505207
1 69897 rs200676709 T C . PASS AF=0.751679 ES:SE:LP:AF:ID -2.93089e-05:0.00215391:0.00436481:0.751679:rs200676709
1 74790 rs13328700 C G . PASS AF=0.034296 ES:SE:LP:AF:ID -0.00263428:0.00491492:0.229148:0.034296:rs13328700
1 74792 rs1335672253 G A . PASS AF=0.034296 ES:SE:LP:AF:ID -0.00263428:0.00491492:0.229148:0.034296:rs1335672253
1 76838 rs563953605 T G . PASS AF=0.077296 ES:SE:LP:AF:ID 0.00103579:0.00344662:0.119186:0.077296:rs563953605
1 76854 rs367666799 A G . PASS AF=0.0776 ES:SE:LP:AF:ID 0.00410302:0.00333217:0.657577:0.0776:rs367666799
1 77866 rs563593912 C T . PASS AF=0.077088 ES:SE:LP:AF:ID 0.00117737:0.00344836:0.136677:0.077088:rs563593912
1 77874 rs62641297 G A . PASS AF=0.077088 ES:SE:LP:AF:ID 0.00117737:0.00344836:0.136677:0.077088:rs62641297
1 81260 rs571136476 C T . PASS AF=0.041622 ES:SE:LP:AF:ID -0.00423505:0.00479235:0.420216:0.041622:rs571136476
1 81587 rs536406113 C T . PASS AF=0.061063 ES:SE:LP:AF:ID 0.00386431:0.00366425:0.537602:0.061063:rs536406113
1 82163 rs139113303 G A . PASS AF=0.075526 ES:SE:LP:AF:ID 0.0042636:0.0033754:0.677781:0.075526:rs139113303
1 82609 rs149189449 C G . PASS AF=0.075567 ES:SE:LP:AF:ID 0.00416702:0.00337443:0.657577:0.075567:rs149189449
1 83514 rs201754587 C T . PASS AF=0.353482 ES:SE:LP:AF:ID 0.00129342:0.00193569:0.30103:0.353482:rs201754587