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-16,TotalVariants=4988035,VariantsNotRead=0,HarmonisedVariants=4988035,VariantsNotHarmonised=0,SwitchedAlleles=1212274,NormalisedVariants=0,TotalControls=29677,TotalCases=228,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/453395e0-6f38-4be6-aae2-4db382f30cef/call-vcf/inputs/562856131/upload.txt.gz --id ieu-b-16 --json /data/cromwell-executions/qc/453395e0-6f38-4be6-aae2-4db382f30cef/call-vcf/inputs/562856131/ieu-b-16_data.json --ref /data/cromwell-executions/qc/453395e0-6f38-4be6-aae2-4db382f30cef/call-vcf/inputs/1899004205/human_g1k_v37.fasta --dbsnp /data/cromwell-executions/qc/453395e0-6f38-4be6-aae2-4db382f30cef/call-vcf/inputs/-307190728/dbsnp.v153.b37.vcf.gz --out /data/igd/ieu-b-16/ieu-b-16.vcf.gz --rm_chr_prefix --cohort_cases 228 --cohort_controls 29677; 1.2.1",
"file_date": "2020-06-26T15:37:18.944023",
"bcftools_viewVersion": "1.9+htslib-1.9",
"bcftools_viewCommand": "view -h /data/igd/ieu-b-16/ieu-b-16.vcf.gz; Date=Wed Feb 24 16:30:25 2021"
}
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/453395e0-6f38-4be6-aae2-4db382f30cef/call-ldsc/inputs/562856131/ieu-b-16.vcf.gz \
--ref-ld-chr /data/ref/eur_w_ld_chr/ \
--out /data/igd/ieu-b-16/ldsc.txt \
--w-ld-chr /data/ref/eur_w_ld_chr/
Beginning analysis at Fri Jun 26 15:43:26 2020
Reading summary statistics from /data/cromwell-executions/qc/453395e0-6f38-4be6-aae2-4db382f30cef/call-ldsc/inputs/562856131/ieu-b-16.vcf.gz ...
Read summary statistics for 4988022 SNPs.
Dropped 11911 SNPs with duplicated rs numbers.
Reading reference panel LD Score from /data/ref/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 /data/ref/eur_w_ld_chr/[1-22] ...
Read regression weight LD Scores for 1290028 SNPs.
After merging with reference panel LD, 951632 SNPs remain.
After merging with regression SNP LD, 951632 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0604 (0.017)
Lambda GC: 1.0741
Mean Chi^2: 1.0638
Intercept: 1.0244 (0.009)
Ratio: 0.3828 (0.1406)
Analysis finished at Fri Jun 26 15:44:19 2020
Total time elapsed: 52.15sQC metrics
Metrics
Metrics
{
"af_correlation": 0.9303,
"inflation_factor": 1.0475,
"mean_EFFECT": -0,
"n": "-Inf",
"n_snps": 4988035,
"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": 29960,
"n_est": "NA",
"ratio_se_n": "NA",
"mean_diff": "NaN",
"ratio_diff": "NaN",
"sd_y_est1": "NA",
"sd_y_est2": "NA",
"r2_sum1": 0,
"r2_sum2": 0,
"r2_sum3": 0,
"r2_sum4": 0,
"ldsc_nsnp_merge_refpanel_ld": 951632,
"ldsc_nsnp_merge_regression_ld": 951632,
"ldsc_observed_scale_h2_beta": 0.0604,
"ldsc_observed_scale_h2_se": 0.017,
"ldsc_intercept_beta": 1.0244,
"ldsc_intercept_se": 0.009,
"ldsc_lambda_gc": 1.0741,
"ldsc_mean_chisq": 1.0638,
"ldsc_ratio": 0.3824
}
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 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 | 1 | 0.9999998 | 3 | 35 | 0 | 4988031 | 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 | 4988035 | 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 | 8.645840e+00 | 5.873062e+00 | 1.00000e+00 | 4.000000e+00 | 8.000000e+00 | 1.300000e+01 | 2.300000e+01 | ▇▅▅▂▂ |
| numeric | POS | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 7.978591e+07 | 5.501378e+07 | 3.30120e+04 | 3.475994e+07 | 7.128113e+07 | 1.143919e+08 | 2.492190e+08 | ▇▇▅▂▁ |
| numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | -2.410000e-05 | 1.545800e-03 | -1.40138e-02 | -8.746000e-04 | -3.410000e-05 | 8.064000e-04 | 1.888890e-02 | ▁▃▇▁▁ |
| numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 1.370800e-03 | 6.541000e-04 | 7.01500e-04 | 9.186000e-04 | 1.106100e-03 | 1.565900e-03 | 4.458100e-03 | ▇▂▁▁▁ |
| numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.909730e-01 | 2.907902e-01 | 1.00000e-07 | 2.399999e-01 | 4.899999e-01 | 7.400005e-01 | 1.000000e+00 | ▇▇▇▇▇ |
| numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.909728e-01 | 2.907656e-01 | 2.00000e-07 | 2.363494e-01 | 4.866900e-01 | 7.431217e-01 | 9.999998e-01 | ▇▇▇▇▇ |
| numeric | AF | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 3.075557e-01 | 2.582576e-01 | 1.00004e-02 | 8.994690e-02 | 2.269840e-01 | 4.776830e-01 | 9.900000e-01 | ▇▃▂▂▁ |
| numeric | AF_reference | 29960 | 0.9939936 | NA | NA | NA | NA | NA | NA | NA | 3.087950e-01 | 2.468717e-01 | 1.99700e-04 | 1.046330e-01 | 2.384190e-01 | 4.696490e-01 | 1.000000e+00 | ▇▅▃▂▁ |
Head and tail
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 1029805 | rs6689308 | A | G | -0.0008992 | 0.0011739 | 0.4400003 | 0.4437209 | 0.1636420 | 0.3156950 | NA |
| 1 | 1030565 | rs6687776 | C | T | -0.0003071 | 0.0011761 | 0.7899998 | 0.7939803 | 0.1635740 | 0.3067090 | NA |
| 1 | 1030633 | rs6678318 | G | A | -0.0003060 | 0.0011761 | 0.7899998 | 0.7947158 | 0.1635810 | 0.3065100 | NA |
| 1 | 1031973 | rs9651270 | C | T | -0.0007131 | 0.0011916 | 0.5500004 | 0.5495671 | 0.1602210 | 0.3107030 | NA |
| 1 | 1033596 | rs6604964 | T | C | -0.0007057 | 0.0011926 | 0.5500004 | 0.5540327 | 0.1600850 | 0.3117010 | NA |
| 1 | 1033670 | rs6604966 | T | C | -0.0007021 | 0.0011930 | 0.5600000 | 0.5561980 | 0.1600370 | 0.3158950 | NA |
| 1 | 1033680 | rs6604967 | T | A | -0.0007014 | 0.0011930 | 0.5600000 | 0.5565672 | 0.1600240 | 0.3117010 | NA |
| 1 | 1033994 | rs6698368 | C | T | -0.0007033 | 0.0011927 | 0.5600000 | 0.5553980 | 0.1600870 | 0.3115020 | NA |
| 1 | 1034200 | rs77977351 | T | C | -0.0007013 | 0.0011928 | 0.5600000 | 0.5565489 | 0.1600930 | 0.3115020 | NA |
| 1 | 1036601 | rs72910156 | C | T | 0.0026229 | 0.0028572 | 0.3599996 | 0.3586275 | 0.0236873 | 0.0399361 | NA |
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 23 | 139314056 | rs5955415 | C | G | 0.0006665 | 0.0012189 | 0.5800000 | 0.5845020 | 0.096722 | 0.125033 | NA |
| 23 | 139314798 | rs62609008 | C | A | 0.0006675 | 0.0012241 | 0.5900000 | 0.5855313 | 0.095806 | 0.106755 | NA |
| 23 | 139315107 | rs62609010 | T | A | 0.0006635 | 0.0012234 | 0.5900000 | 0.5875828 | 0.095896 | 0.107020 | NA |
| 23 | 139316769 | rs73230748 | T | C | 0.0006603 | 0.0012211 | 0.5900000 | 0.5886683 | 0.096294 | 0.121060 | NA |
| 23 | 139317055 | rs62609011 | C | A | 0.0005371 | 0.0012210 | 0.6600001 | 0.6600145 | 0.096320 | 0.116026 | NA |
| 23 | 139317165 | rs28877369 | C | G | 0.0006692 | 0.0012213 | 0.5800000 | 0.5837269 | 0.096261 | 0.116291 | NA |
| 23 | 139317337 | rs55757628 | A | G | 0.0006660 | 0.0012230 | 0.5900000 | 0.5860814 | 0.095968 | 0.107285 | NA |
| 23 | 139319949 | rs140616281 | A | G | 0.0005309 | 0.0012241 | 0.6600001 | 0.6645072 | 0.095872 | 0.116291 | NA |
| 23 | 139320136 | rs76621315 | C | G | 0.0006621 | 0.0012203 | 0.5900000 | 0.5874056 | 0.096460 | 0.114437 | NA |
| 23 | 139325995 | rs62609013 | G | A | 0.0006700 | 0.0012216 | 0.5800000 | 0.5834018 | 0.096270 | 0.101987 | NA |
bcf preview
1 1029805 rs891281851 A G . PASS AF=0.163642 ES:SE:LP:AF:ID -0.00089915:0.00117394:0.356547:0.163642:rs891281851
1 1030565 rs6687776 C T . PASS AF=0.163574 ES:SE:LP:AF:ID -0.000307141:0.00117613:0.102373:0.163574:rs6687776
1 1030633 rs6678318 G A . PASS AF=0.163581 ES:SE:LP:AF:ID -0.000306022:0.00117614:0.102373:0.163581:rs6678318
1 1031973 rs9651270 C T . PASS AF=0.160221 ES:SE:LP:AF:ID -0.000713094:0.00119165:0.259637:0.160221:rs9651270
1 1033596 rs6604964 T C . PASS AF=0.160085 ES:SE:LP:AF:ID -0.000705683:0.00119258:0.259637:0.160085:rs6604964
1 1033670 rs1370950991 T C . PASS AF=0.160037 ES:SE:LP:AF:ID -0.00070209:0.00119302:0.251812:0.160037:rs1370950991
1 1033680 rs1370950991 T A . PASS AF=0.160024 ES:SE:LP:AF:ID -0.000701422:0.001193:0.251812:0.160024:rs1370950991
1 1033994 rs6698368 C T . PASS AF=0.160087 ES:SE:LP:AF:ID -0.000703336:0.00119272:0.251812:0.160087:rs6698368
1 1034200 rs77977351 T C . PASS AF=0.160093 ES:SE:LP:AF:ID -0.000701331:0.00119279:0.251812:0.160093:rs77977351
1 1036601 rs72910156 C T . PASS AF=0.0236873 ES:SE:LP:AF:ID 0.00262289:0.00285723:0.443698:0.0236873:rs72910156
1 1036860 rs11579922 A C . PASS AF=0.126829 ES:SE:LP:AF:ID -0.000634943:0.00130622:0.200659:0.126829:rs11579922
1 1036959 rs1162868282 T C . PASS AF=0.112898 ES:SE:LP:AF:ID -0.00191261:0.00136224:0.79588:0.112898:rs1162868282
1 1037303 rs11260592 T C . PASS AF=0.140083 ES:SE:LP:AF:ID -0.000467394:0.00123858:0.148742:0.140083:rs11260592
1 1037313 rs11260593 A G . PASS AF=0.140165 ES:SE:LP:AF:ID -0.000471873:0.00123861:0.154902:0.140165:rs11260593
1 1037367 rs11260594 G A . PASS AF=0.140082 ES:SE:LP:AF:ID -0.000470189:0.00123873:0.154902:0.140082:rs11260594
1 1038088 rs66622470 G C . PASS AF=0.140153 ES:SE:LP:AF:ID -0.000471628:0.00123796:0.154902:0.140153:rs66622470
1 1039098 rs11260595 C A . PASS AF=0.0240233 ES:SE:LP:AF:ID 0.0026:0.00283265:0.443698:0.0240233:rs11260595
1 1039268 rs9329410 T C . PASS AF=0.140321 ES:SE:LP:AF:ID -0.000474292:0.00123675:0.154902:0.140321:rs9329410
1 1039817 rs1205065516 A G . PASS AF=0.140221 ES:SE:LP:AF:ID -0.000472465:0.00123747:0.154902:0.140221:rs1205065516
1 1040026 rs6671356 T C . PASS AF=0.140613 ES:SE:LP:AF:ID -0.000498036:0.00123497:0.161151:0.140613:rs6671356
1 1040472 rs6664124 C T . PASS AF=0.140514 ES:SE:LP:AF:ID -0.00049625:0.00123569:0.161151:0.140514:rs6664124
1 1040794 rs6687681 G A . PASS AF=0.14049 ES:SE:LP:AF:ID -0.000495237:0.0012358:0.161151:0.14049:rs6687681
1 1040824 rs6656379 T C . PASS AF=0.140637 ES:SE:LP:AF:ID -0.000505593:0.00123521:0.167491:0.140637:rs6656379
1 1040985 rs6697379 C G . PASS AF=0.140464 ES:SE:LP:AF:ID -0.000494974:0.00123584:0.161151:0.140464:rs6697379
1 1041700 rs6604968 A G . PASS AF=0.140606 ES:SE:LP:AF:ID -0.000504978:0.00123541:0.167491:0.140606:rs6604968
1 1041786 rs6604969 T C . PASS AF=0.140618 ES:SE:LP:AF:ID -0.000504964:0.00123528:0.167491:0.140618:rs6604969
1 1042483 rs12733365 C T . PASS AF=0.140487 ES:SE:LP:AF:ID -0.000492477:0.00123567:0.161151:0.140487:rs12733365
1 1042527 rs1486993720 G C . PASS AF=0.112699 ES:SE:LP:AF:ID -0.00186336:0.00136268:0.769551:0.112699:rs1486993720
1 1042673 rs897825316 C T . PASS AF=0.141593 ES:SE:LP:AF:ID -0.000545297:0.00123926:0.180456:0.141593:rs897825316
1 1042927 rs4970354 G T . PASS AF=0.140473 ES:SE:LP:AF:ID -0.000491823:0.00123557:0.161151:0.140473:rs4970354
1 1043053 rs4970355 A G . PASS AF=0.140399 ES:SE:LP:AF:ID -0.00048697:0.00123585:0.161151:0.140399:rs4970355
1 1045473 rs11586034 G A . PASS AF=0.111905 ES:SE:LP:AF:ID -0.0017909:0.0013677:0.721246:0.111905:rs11586034
1 1046073 rs11590188 C A . PASS AF=0.138803 ES:SE:LP:AF:ID -0.000783606:0.00124343:0.275724:0.138803:rs11590188
1 1046164 rs386627439 C T . PASS AF=0.140449 ES:SE:LP:AF:ID -0.000488534:0.00123569:0.161151:0.140449:rs386627439
1 1046717 rs34820586 G C . PASS AF=0.112762 ES:SE:LP:AF:ID -0.00186346:0.00136235:0.769551:0.112762:rs34820586
1 1046861 rs12723165 G A . PASS AF=0.112753 ES:SE:LP:AF:ID -0.00186275:0.00136233:0.769551:0.112753:rs12723165
1 1047374 rs12743678 T A . PASS AF=0.140066 ES:SE:LP:AF:ID -0.000461178:0.0012371:0.148742:0.140066:rs12743678
1 1048501 rs7518814 G A . PASS AF=0.138809 ES:SE:LP:AF:ID -0.00078344:0.00124344:0.275724:0.138809:rs7518814
1 1048955 rs4970405 A G . PASS AF=0.104547 ES:SE:LP:AF:ID -0.00198494:0.00140812:0.79588:0.104547:rs4970405
1 1048989 rs4970406 A G . PASS AF=0.113456 ES:SE:LP:AF:ID -0.00217616:0.00136046:0.958607:0.113456:rs4970406
1 1049083 rs4970407 C A . PASS AF=0.112673 ES:SE:LP:AF:ID -0.00200319:0.00136328:0.853872:0.112673:rs4970407
1 1049950 rs12726255 A G . PASS AF=0.138796 ES:SE:LP:AF:ID -0.00164697:0.0012459:0.721246:0.138796:rs12726255
1 1052946 rs12755848 G T . PASS AF=0.111675 ES:SE:LP:AF:ID -0.00195003:0.00137198:0.79588:0.111675:rs12755848
1 1053452 rs4970409 G A . PASS AF=0.111677 ES:SE:LP:AF:ID -0.00194947:0.00137187:0.79588:0.111677:rs4970409
1 1053670 rs4970410 G A . PASS AF=0.137678 ES:SE:LP:AF:ID -0.00154575:0.00125251:0.657577:0.137678:rs4970410
1 1053724 rs4970411 A G . PASS AF=0.13729 ES:SE:LP:AF:ID -0.00152789:0.00125448:0.657577:0.13729:rs4970411
1 1054552 rs12567697 G A . PASS AF=0.110694 ES:SE:LP:AF:ID -0.00187676:0.00137803:0.769551:0.110694:rs12567697
1 1054893 rs4970412 T C . PASS AF=0.13749 ES:SE:LP:AF:ID -0.00152344:0.00125333:0.657577:0.13749:rs4970412
1 1055653 rs34808604 C G . PASS AF=0.110838 ES:SE:LP:AF:ID -0.00188808:0.00137689:0.769551:0.110838:rs34808604
1 1055797 rs76744376 A G . PASS AF=0.111311 ES:SE:LP:AF:ID -0.00203643:0.00137504:0.853872:0.111311:rs76744376