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-4828,TotalVariants=7974415,VariantsNotRead=0,HarmonisedVariants=7974403,VariantsNotHarmonised=12,SwitchedAlleles=3531581,NormalisedVariants=0,StudyType=Continuous>",
"contig": "<ID=1,length=249250621,assembly=HG19/GRCh37>",
"contig.1": "<ID=2,length=243199373,assembly=HG19/GRCh37>",
"contig.2": "<ID=3,length=198022430,assembly=HG19/GRCh37>",
"contig.3": "<ID=4,length=191154276,assembly=HG19/GRCh37>",
"contig.4": "<ID=5,length=180915260,assembly=HG19/GRCh37>",
"contig.5": "<ID=6,length=171115067,assembly=HG19/GRCh37>",
"contig.6": "<ID=7,length=159138663,assembly=HG19/GRCh37>",
"contig.7": "<ID=8,length=146364022,assembly=HG19/GRCh37>",
"contig.8": "<ID=9,length=141213431,assembly=HG19/GRCh37>",
"contig.9": "<ID=10,length=135534747,assembly=HG19/GRCh37>",
"contig.10": "<ID=11,length=135006516,assembly=HG19/GRCh37>",
"contig.11": "<ID=12,length=133851895,assembly=HG19/GRCh37>",
"contig.12": "<ID=13,length=115169878,assembly=HG19/GRCh37>",
"contig.13": "<ID=14,length=107349540,assembly=HG19/GRCh37>",
"contig.14": "<ID=15,length=102531392,assembly=HG19/GRCh37>",
"contig.15": "<ID=16,length=90354753,assembly=HG19/GRCh37>",
"contig.16": "<ID=17,length=81195210,assembly=HG19/GRCh37>",
"contig.17": "<ID=18,length=78077248,assembly=HG19/GRCh37>",
"contig.18": "<ID=19,length=59128983,assembly=HG19/GRCh37>",
"contig.19": "<ID=20,length=63025520,assembly=HG19/GRCh37>",
"contig.20": "<ID=21,length=48129895,assembly=HG19/GRCh37>",
"contig.21": "<ID=22,length=51304566,assembly=HG19/GRCh37>",
"contig.22": "<ID=X,length=155270560,assembly=HG19/GRCh37>",
"contig.23": "<ID=Y,length=59373566,assembly=HG19/GRCh37>",
"contig.24": "<ID=MT,length=16569,assembly=HG19/GRCh37>",
"contig.25": "<ID=GL000207.1,length=4262,assembly=HG19/GRCh37>",
"contig.26": "<ID=GL000226.1,length=15008,assembly=HG19/GRCh37>",
"contig.27": "<ID=GL000229.1,length=19913,assembly=HG19/GRCh37>",
"contig.28": "<ID=GL000231.1,length=27386,assembly=HG19/GRCh37>",
"contig.29": "<ID=GL000210.1,length=27682,assembly=HG19/GRCh37>",
"contig.30": "<ID=GL000239.1,length=33824,assembly=HG19/GRCh37>",
"contig.31": "<ID=GL000235.1,length=34474,assembly=HG19/GRCh37>",
"contig.32": "<ID=GL000201.1,length=36148,assembly=HG19/GRCh37>",
"contig.33": "<ID=GL000247.1,length=36422,assembly=HG19/GRCh37>",
"contig.34": "<ID=GL000245.1,length=36651,assembly=HG19/GRCh37>",
"contig.35": "<ID=GL000197.1,length=37175,assembly=HG19/GRCh37>",
"contig.36": "<ID=GL000203.1,length=37498,assembly=HG19/GRCh37>",
"contig.37": "<ID=GL000246.1,length=38154,assembly=HG19/GRCh37>",
"contig.38": "<ID=GL000249.1,length=38502,assembly=HG19/GRCh37>",
"contig.39": "<ID=GL000196.1,length=38914,assembly=HG19/GRCh37>",
"contig.40": "<ID=GL000248.1,length=39786,assembly=HG19/GRCh37>",
"contig.41": "<ID=GL000244.1,length=39929,assembly=HG19/GRCh37>",
"contig.42": "<ID=GL000238.1,length=39939,assembly=HG19/GRCh37>",
"contig.43": "<ID=GL000202.1,length=40103,assembly=HG19/GRCh37>",
"contig.44": "<ID=GL000234.1,length=40531,assembly=HG19/GRCh37>",
"contig.45": "<ID=GL000232.1,length=40652,assembly=HG19/GRCh37>",
"contig.46": "<ID=GL000206.1,length=41001,assembly=HG19/GRCh37>",
"contig.47": "<ID=GL000240.1,length=41933,assembly=HG19/GRCh37>",
"contig.48": "<ID=GL000236.1,length=41934,assembly=HG19/GRCh37>",
"contig.49": "<ID=GL000241.1,length=42152,assembly=HG19/GRCh37>",
"contig.50": "<ID=GL000243.1,length=43341,assembly=HG19/GRCh37>",
"contig.51": "<ID=GL000242.1,length=43523,assembly=HG19/GRCh37>",
"contig.52": "<ID=GL000230.1,length=43691,assembly=HG19/GRCh37>",
"contig.53": "<ID=GL000237.1,length=45867,assembly=HG19/GRCh37>",
"contig.54": "<ID=GL000233.1,length=45941,assembly=HG19/GRCh37>",
"contig.55": "<ID=GL000204.1,length=81310,assembly=HG19/GRCh37>",
"contig.56": "<ID=GL000198.1,length=90085,assembly=HG19/GRCh37>",
"contig.57": "<ID=GL000208.1,length=92689,assembly=HG19/GRCh37>",
"contig.58": "<ID=GL000191.1,length=106433,assembly=HG19/GRCh37>",
"contig.59": "<ID=GL000227.1,length=128374,assembly=HG19/GRCh37>",
"contig.60": "<ID=GL000228.1,length=129120,assembly=HG19/GRCh37>",
"contig.61": "<ID=GL000214.1,length=137718,assembly=HG19/GRCh37>",
"contig.62": "<ID=GL000221.1,length=155397,assembly=HG19/GRCh37>",
"contig.63": "<ID=GL000209.1,length=159169,assembly=HG19/GRCh37>",
"contig.64": "<ID=GL000218.1,length=161147,assembly=HG19/GRCh37>",
"contig.65": "<ID=GL000220.1,length=161802,assembly=HG19/GRCh37>",
"contig.66": "<ID=GL000213.1,length=164239,assembly=HG19/GRCh37>",
"contig.67": "<ID=GL000211.1,length=166566,assembly=HG19/GRCh37>",
"contig.68": "<ID=GL000199.1,length=169874,assembly=HG19/GRCh37>",
"contig.69": "<ID=GL000217.1,length=172149,assembly=HG19/GRCh37>",
"contig.70": "<ID=GL000216.1,length=172294,assembly=HG19/GRCh37>",
"contig.71": "<ID=GL000215.1,length=172545,assembly=HG19/GRCh37>",
"contig.72": "<ID=GL000205.1,length=174588,assembly=HG19/GRCh37>",
"contig.73": "<ID=GL000219.1,length=179198,assembly=HG19/GRCh37>",
"contig.74": "<ID=GL000224.1,length=179693,assembly=HG19/GRCh37>",
"contig.75": "<ID=GL000223.1,length=180455,assembly=HG19/GRCh37>",
"contig.76": "<ID=GL000195.1,length=182896,assembly=HG19/GRCh37>",
"contig.77": "<ID=GL000212.1,length=186858,assembly=HG19/GRCh37>",
"contig.78": "<ID=GL000222.1,length=186861,assembly=HG19/GRCh37>",
"contig.79": "<ID=GL000200.1,length=187035,assembly=HG19/GRCh37>",
"contig.80": "<ID=GL000193.1,length=189789,assembly=HG19/GRCh37>",
"contig.81": "<ID=GL000194.1,length=191469,assembly=HG19/GRCh37>",
"contig.82": "<ID=GL000225.1,length=211173,assembly=HG19/GRCh37>",
"contig.83": "<ID=GL000192.1,length=547496,assembly=HG19/GRCh37>",
"Gwas2VCF_command": "--data /data/cromwell-executions/qc/629d3aa6-36f7-404c-a6b1-f32ed3dd46d6/call-vcf/inputs/-261044504/upload.txt.gz --id ieu-b-4828 --json /data/cromwell-executions/qc/629d3aa6-36f7-404c-a6b1-f32ed3dd46d6/call-vcf/inputs/-261044504/ieu-b-4828_data.json --ref /data/cromwell-executions/qc/629d3aa6-36f7-404c-a6b1-f32ed3dd46d6/call-vcf/inputs/1899004205/human_g1k_v37.fasta --dbsnp /data/cromwell-executions/qc/629d3aa6-36f7-404c-a6b1-f32ed3dd46d6/call-vcf/inputs/-307190728/dbsnp.v153.b37.vcf.gz --out /data/igd/ieu-b-4828/ieu-b-4828.vcf.gz --alias alias.txt; 1.3.0",
"file_date": "2022-01-05T09:11:21.611779",
"bcftools_viewVersion": "1.9+htslib-1.9",
"bcftools_viewCommand": "view -h /data/cromwell-executions/qc/629d3aa6-36f7-404c-a6b1-f32ed3dd46d6/call-report/inputs/-261044504/ieu-b-4828.vcf.gz; Date=Wed Jan 5 09:31:15 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/629d3aa6-36f7-404c-a6b1-f32ed3dd46d6/call-ldsc/inputs/-261044504/ieu-b-4828.vcf.gz \
--ref-ld-chr /data/ref/eur_w_ld_chr/ \
--out /data/igd/ieu-b-4828/ldsc.txt \
--w-ld-chr /data/ref/eur_w_ld_chr/
Beginning analysis at Wed Jan 5 09:22:41 2022
Reading summary statistics from /data/cromwell-executions/qc/629d3aa6-36f7-404c-a6b1-f32ed3dd46d6/call-ldsc/inputs/-261044504/ieu-b-4828.vcf.gz ...
Read summary statistics for 7974332 SNPs.
Dropped 39132 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, 1202624 SNPs remain.
After merging with regression SNP LD, 1202624 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0347 (0.0085)
Lambda GC: 1.07
Mean Chi^2: 1.0661
Intercept: 1.0258 (0.0063)
Ratio: 0.3899 (0.0952)
Analysis finished at Wed Jan 5 09:24:21 2022
Total time elapsed: 1.0m:39.78sQC metrics
Metrics
Metrics
{
"af_correlation": "NA",
"inflation_factor": 1.0654,
"mean_EFFECT": -0.0003,
"n": 60430,
"n_snps": 7974403,
"n_clumped_hits": 1,
"n_p_sig": 2,
"n_mono": 0,
"n_ns": 285241,
"n_mac": 0,
"is_snpid_unique": false,
"n_miss_EFFECT": 0,
"n_miss_SE": 0,
"n_miss_PVAL": 0,
"n_miss_AF": 7974403,
"n_miss_AF_reference": 164849,
"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": 1202624,
"ldsc_nsnp_merge_regression_ld": 1202624,
"ldsc_observed_scale_h2_beta": 0.0347,
"ldsc_observed_scale_h2_se": 0.0085,
"ldsc_intercept_beta": 1.0258,
"ldsc_intercept_se": 0.0063,
"ldsc_lambda_gc": 1.07,
"ldsc_mean_chisq": 1.0661,
"ldsc_ratio": 0.3903
}
Flags
| name | value |
|---|---|
| af_correlation | NA |
| inflation_factor | FALSE |
| n | FALSE |
| is_snpid_non_unique | TRUE |
| mean_EFFECT_nonfinite | FALSE |
| mean_EFFECT_05 | FALSE |
| mean_EFFECT_01 | FALSE |
| mean_chisq | FALSE |
| n_p_sig | FALSE |
| miss_EFFECT | FALSE |
| miss_SE | FALSE |
| miss_PVAL | FALSE |
| ldsc_ratio | FALSE |
| ldsc_intercept_beta | FALSE |
| n_clumped_hits | FALSE |
| r2_sum1 | FALSE |
| r2_sum2 | FALSE |
| r2_sum3 | FALSE |
| r2_sum4 | FALSE |
Definitions
General metrics
af_correlation: Correlation coefficient 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 | 22 | 0.9999972 | 3 | 58 | 0 | 7974245 | 0 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| character | REF | 0 | 1.0000000 | 1 | 43 | 0 | 16634 | 0 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| character | ALT | 0 | 1.0000000 | 1 | 44 | 0 | 6013 | 0 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| logical | AF | 7974403 | 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 | 8.648259e+00 | 5.755412e+00 | 1.0000 | 4.000000e+00 | 8.000000e+00 | 1.300000e+01 | 2.200000e+01 | ▇▅▅▂▂ |
| numeric | POS | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 7.879905e+07 | 5.636303e+07 | 302.0000 | 3.242980e+07 | 6.934579e+07 | 1.145649e+08 | 2.492223e+08 | ▇▆▅▂▁ |
| numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | -3.377000e-04 | 1.630110e-02 | -0.1816 | -7.900000e-03 | -2.000000e-04 | 7.300000e-03 | 1.650000e-01 | ▁▁▇▁▁ |
| numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 1.361820e-02 | 8.325100e-03 | 0.0065 | 7.600000e-03 | 1.000000e-02 | 1.700000e-02 | 5.510000e-02 | ▇▂▁▁▁ |
| numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.902853e-01 | 2.911220e-01 | 0.0000 | 2.355998e-01 | 4.862997e-01 | 7.424992e-01 | 1.000000e+00 | ▇▇▇▇▇ |
| numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.902863e-01 | 2.911333e-01 | 0.0000 | 2.355139e-01 | 4.864288e-01 | 7.424796e-01 | 1.000000e+00 | ▇▇▇▇▇ |
| numeric | AF_reference | 164849 | 0.9793277 | NA | NA | NA | NA | NA | NA | NA | 2.646304e-01 | 2.521037e-01 | 0.0000 | 5.730830e-02 | 1.791130e-01 | 4.131390e-01 | 1.000000e+00 | ▇▃▂▁▁ |
| numeric | N | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 5.457145e+04 | 7.630339e+03 | 36259.0000 | 4.920500e+04 | 5.946500e+04 | 6.043000e+04 | 6.043000e+04 | ▂▁▁▁▇ |
Head and tail
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 693731 | rs12238997 | A | G | -0.0090 | 0.0128 | 0.4826997 | 0.4819779 | NA | 0.141773 | 39183 |
| 1 | 729679 | rs4951859 | C | G | -0.0047 | 0.0121 | 0.6952004 | 0.6976980 | NA | 0.639976 | 36665 |
| 1 | 731718 | rs142557973 | T | C | -0.0084 | 0.0126 | 0.5073995 | 0.5049851 | NA | 0.154353 | 39183 |
| 1 | 734349 | rs141242758 | T | C | -0.0095 | 0.0126 | 0.4497001 | 0.4508683 | NA | 0.152556 | 39183 |
| 1 | 736289 | rs79010578 | T | A | -0.0011 | 0.0127 | 0.9315001 | 0.9309782 | NA | 0.139577 | 37559 |
| 1 | 752566 | rs3094315 | G | A | -0.0068 | 0.0120 | 0.5715997 | 0.5709407 | NA | 0.718251 | 36665 |
| 1 | 752721 | rs3131972 | A | G | -0.0058 | 0.0120 | 0.6324002 | 0.6288591 | NA | 0.653355 | 36665 |
| 1 | 753405 | rs3115860 | C | A | 0.0039 | 0.0127 | 0.7621001 | 0.7587774 | NA | 0.751797 | 36665 |
| 1 | 753541 | rs2073813 | G | A | -0.0090 | 0.0123 | 0.4649005 | 0.4643472 | NA | 0.301917 | 39183 |
| 1 | 754182 | rs3131969 | A | G | 0.0046 | 0.0127 | 0.7197008 | 0.7171990 | NA | 0.678514 | 36665 |
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 22 | 51218377 | rs2519461 | G | C | 0.0077 | 0.0152 | 0.6124999 | 0.6124503 | NA | 0.0826677 | 42446 |
| 22 | 51219006 | rs28729663 | G | A | 0.0052 | 0.0125 | 0.6754995 | 0.6774100 | NA | 0.2052720 | 38585 |
| 22 | 51219387 | rs9616832 | T | C | 0.0096 | 0.0152 | 0.5292002 | 0.5276620 | NA | 0.0654952 | 42446 |
| 22 | 51219704 | rs147475742 | G | A | 0.0074 | 0.0196 | 0.7055000 | 0.7057642 | NA | 0.0473243 | 40473 |
| 22 | 51221190 | rs369304721 | G | A | 0.0105 | 0.0179 | 0.5596004 | 0.5574776 | NA | NA | 41367 |
| 22 | 51221731 | rs115055839 | T | C | 0.0091 | 0.0153 | 0.5518004 | 0.5519964 | NA | 0.0625000 | 42446 |
| 22 | 51222100 | rs114553188 | G | T | 0.0013 | 0.0169 | 0.9402999 | 0.9386847 | NA | 0.0880591 | 42393 |
| 22 | 51223637 | rs375798137 | G | A | -0.0068 | 0.0171 | 0.6906993 | 0.6908802 | NA | 0.0788738 | 41367 |
| 22 | 51229805 | rs9616985 | T | C | 0.0096 | 0.0153 | 0.5311999 | 0.5303637 | NA | 0.0730831 | 42446 |
| 22 | 51237063 | rs3896457 | T | C | -0.0041 | 0.0093 | 0.6581002 | 0.6593142 | NA | 0.2050720 | 37559 |
bcf preview
1 693731 rs12238997 A G . PASS . ES:SE:LP:SS:ID -0.009:0.0128:0.316323:39183:rs12238997
1 729679 rs4951859 C G . PASS . ES:SE:LP:SS:ID -0.0047:0.0121:0.15789:36665:rs4951859
1 731718 rs58276399 T C . PASS . ES:SE:LP:SS:ID -0.0084:0.0126:0.29465:39183:rs58276399
1 734349 rs141242758 T C . PASS . ES:SE:LP:SS:ID -0.0095:0.0126:0.347077:39183:rs141242758
1 736289 rs1254887344 T A . PASS . ES:SE:LP:SS:ID -0.0011:0.0127:0.0308171:37559:rs1254887344
1 752566 rs3094315 G A . PASS . ES:SE:LP:SS:ID -0.0068:0.012:0.242908:36665:rs3094315
1 752721 rs3131972 A G . PASS . ES:SE:LP:SS:ID -0.0058:0.012:0.199008:36665:rs3131972
1 753405 rs3115860 C A . PASS . ES:SE:LP:SS:ID 0.0039:0.0127:0.117988:36665:rs3115860
1 753541 rs1388595942 G A . PASS . ES:SE:LP:SS:ID -0.009:0.0123:0.33264:39183:rs1388595942
1 754182 rs3131969 A G . PASS . ES:SE:LP:SS:ID 0.0046:0.0127:0.142848:36665:rs3131969
1 754192 rs3131968 A G . PASS . ES:SE:LP:SS:ID 0.0042:0.0127:0.128485:36665:rs3131968
1 754334 rs3131967 T C . PASS . ES:SE:LP:SS:ID 0.0031:0.0127:0.0933418:36665:rs3131967
1 754503 rs3115859 G A . PASS . ES:SE:LP:SS:ID -0.0071:0.012:0.254769:36665:rs3115859
1 754964 rs3131966 C T . PASS . ES:SE:LP:SS:ID -0.0071:0.012:0.25516:36665:rs3131966
1 755775 rs3131965 A G . PASS . ES:SE:LP:SS:ID -0.01:0.012:0.390406:36665:rs3131965
1 755890 rs1280367067 A T . PASS . ES:SE:LP:SS:ID 0.0021:0.0127:0.0600317:36665:rs1280367067
1 756604 rs3131962 A G . PASS . ES:SE:LP:SS:ID 0.0024:0.0127:0.0700194:36665:rs3131962
1 757640 rs3115853 G A . PASS . ES:SE:LP:SS:ID 0.0036:0.0127:0.108295:36665:rs3115853
1 757734 rs1557551770 C T . PASS . ES:SE:LP:SS:ID 0.0021:0.0127:0.0622314:36665:rs1557551770
1 757936 rs1360886751 C A . PASS . ES:SE:LP:SS:ID 0.0021:0.0127:0.0622314:36665:rs1360886751
1 758144 rs3131956 A G . PASS . ES:SE:LP:SS:ID 0.0022:0.0127:0.0625824:36665:rs3131956
1 758626 rs3131954 C T . PASS . ES:SE:LP:SS:ID 0.0021:0.0127:0.0596828:36665:rs3131954
1 760912 rs1048488 C T . PASS . ES:SE:LP:SS:ID -0.0091:0.012:0.346402:36665:rs1048488
1 761147 rs3115850 T C . PASS . ES:SE:LP:SS:ID -0.0087:0.012:0.32994:36665:rs3115850
1 761732 rs2286139 C T . PASS . ES:SE:LP:SS:ID 0.0022:0.0126:0.0654006:36665:rs2286139
1 766007 rs61768174 A C . PASS . ES:SE:LP:SS:ID -0.0081:0.0132:0.268734:39183:rs61768174
1 768253 rs2977608 A C . PASS . ES:SE:LP:SS:ID 0.0068:0.0099:0.309893:39183:rs2977608
1 768448 rs12562034 G A . PASS . ES:SE:LP:SS:ID -0.0067:0.0142:0.195111:37559:rs12562034
1 769223 rs60320384 C G . PASS . ES:SE:LP:SS:ID -0.0085:0.0124:0.307682:39183:rs60320384
1 771823 rs2977605 T C . PASS . ES:SE:LP:SS:ID 0.0016:0.0127:0.0448416:36665:rs2977605
1 771967 rs59066358 G A . PASS . ES:SE:LP:SS:ID -0.0077:0.0124:0.271809:39183:rs59066358
1 772755 rs2905039 A C . PASS . ES:SE:LP:SS:ID 0.0024:0.0127:0.0695094:36665:rs2905039
1 777122 rs2980319 A T . PASS . ES:SE:LP:SS:ID 0.0077:0.0127:0.264321:36665:rs2980319
1 777232 rs112618790 C T . PASS . ES:SE:LP:SS:ID -0.0055:0.0148:0.147825:39183:rs112618790
1 778745 rs1055606 A G . PASS . ES:SE:LP:SS:ID -0.0118:0.0124:0.467628:39183:rs1055606
1 779322 rs4040617 A G . PASS . ES:SE:LP:SS:ID -0.0119:0.0123:0.476384:39183:rs4040617
1 780785 rs2977612 T A . PASS . ES:SE:LP:SS:ID 0.0083:0.0127:0.289037:36665:rs2977612
1 781845 rs1391043716 A G . PASS . ES:SE:LP:SS:ID -0.0085:0.0134:0.278932:39183:rs1391043716
1 782981 rs6594026 C T . PASS . ES:SE:LP:SS:ID -0.012:0.0123:0.484391:39183:rs6594026
1 785050 rs2905062 G A . PASS . ES:SE:LP:SS:ID 0.0079:0.0127:0.271646:36665:rs2905062
1 785989 rs2980300 T C . PASS . ES:SE:LP:SS:ID 0.0081:0.0127:0.282662:36665:rs2980300
1 787399 rs2905055 G T . PASS . ES:SE:LP:SS:ID 0.0104:0.0126:0.388702:36665:rs2905055
1 787606 rs3863622 G T . PASS . ES:SE:LP:SS:ID -0.0111:0.0123:0.431798:39183:rs3863622
1 787685 rs2905054 G T . PASS . ES:SE:LP:SS:ID 0.0109:0.0126:0.411392:36665:rs2905054
1 787844 rs2905053 C T . PASS . ES:SE:LP:SS:ID 0.0079:0.0127:0.270916:36665:rs2905053
1 790465 rs61768207 G A . PASS . ES:SE:LP:SS:ID -0.0105:0.0136:0.355069:39183:rs61768207
1 791191 rs111818025 G A . PASS . ES:SE:LP:SS:ID -0.0121:0.0124:0.484656:39183:rs111818025
1 791853 rs6684487 G A . PASS . ES:SE:LP:SS:ID -0.0045:0.0148:0.117589:39183:rs6684487
1 794332 rs12127425 G A . PASS . ES:SE:LP:SS:ID -0.0081:0.016:0.21169:39183:rs12127425
1 795222 rs12131377 C G . PASS . ES:SE:LP:SS:ID -0.0092:0.016:0.248413:39183:rs12131377