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-5106,TotalVariants=10562208,VariantsNotRead=0,HarmonisedVariants=10548750,VariantsNotHarmonised=13458,SwitchedAlleles=4720098,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/c9066f65-4f6d-4687-95a5-b00c4ae279aa/call-vcf/inputs/-261021504/upload.txt.gz --id ieu-b-5106 --json /data/cromwell-executions/qc/c9066f65-4f6d-4687-95a5-b00c4ae279aa/call-vcf/inputs/-261021504/ieu-b-5106_data.json --ref /data/cromwell-executions/qc/c9066f65-4f6d-4687-95a5-b00c4ae279aa/call-vcf/inputs/1899004205/human_g1k_v37.fasta --dbsnp /data/cromwell-executions/qc/c9066f65-4f6d-4687-95a5-b00c4ae279aa/call-vcf/inputs/-307190728/dbsnp.v153.b37.vcf.gz --out /data/igd/ieu-b-5106/ieu-b-5106.vcf.gz --alias alias.txt; 1.3.0",
"file_date": "2023-08-11T17:31:42.763406",
"bcftools_viewVersion": "1.9+htslib-1.9",
"bcftools_viewCommand": "view -h /data/cromwell-executions/qc/c9066f65-4f6d-4687-95a5-b00c4ae279aa/call-report/inputs/-261021504/ieu-b-5106.vcf.gz; Date=Fri Aug 11 17:54:42 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/c9066f65-4f6d-4687-95a5-b00c4ae279aa/call-ldsc/inputs/-261021504/ieu-b-5106.vcf.gz \
--ref-ld-chr /data/ref/eur_w_ld_chr/ \
--out /data/igd/ieu-b-5106/ldsc.txt \
--w-ld-chr /data/ref/eur_w_ld_chr/
Beginning analysis at Fri Aug 11 17:46:11 2023
Reading summary statistics from /data/cromwell-executions/qc/c9066f65-4f6d-4687-95a5-b00c4ae279aa/call-ldsc/inputs/-261021504/ieu-b-5106.vcf.gz ...
Traceback (most recent call last):
File "./ldsc/ldsc.py", line 647, in <module>
sumstats.estimate_h2(args, log)
File "/ldsc/ldscore/sumstats.py", line 330, in estimate_h2
args, log, args.h2)
File "/ldsc/ldscore/sumstats.py", line 246, in _read_ld_sumstats
sumstats = _read_sumstats(args, log, fh, alleles=alleles, dropna=dropna)
File "/ldsc/ldscore/sumstats.py", line 167, in _read_sumstats
sumstats = ps.sumstats(fh, alleles=alleles, dropna=dropna)
File "/ldsc/ldscore/parse.py", line 97, in sumstats
x = read_vcf(fh, alleles, slh)
File "/ldsc/ldscore/parse.py", line 152, in read_vcf
o = [[rec.id, rec.samples[sample]['ES'][0]/rec.samples[sample]['SE'][0]] for rec in vcf_in.fetch()]
ZeroDivisionError: float division by zero
Analysis finished at Fri Aug 11 17:46:11 2023
Total time elapsed: 0.08sQC metrics
Metrics
Metrics
{
"af_correlation": "NA",
"inflation_factor": 1.399,
"mean_EFFECT": 7.3787e-06,
"n": "-Inf",
"n_snps": 10548750,
"n_clumped_hits": 207,
"n_p_sig": 24438,
"n_mono": 0,
"n_ns": 34387,
"n_mac": 0,
"is_snpid_unique": false,
"n_miss_EFFECT": 0,
"n_miss_SE": 0,
"n_miss_PVAL": 0,
"n_miss_AF": 10548750,
"n_miss_AF_reference": 192266,
"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": "NA",
"ldsc_nsnp_merge_regression_ld": "NA",
"ldsc_observed_scale_h2_beta": "NA",
"ldsc_observed_scale_h2_se": "NA",
"ldsc_intercept_beta": "NA",
"ldsc_intercept_se": "NA",
"ldsc_lambda_gc": "NA",
"ldsc_mean_chisq": "NA",
"ldsc_ratio": "NA"
}
Flags
| name | value |
|---|---|
| af_correlation | NA |
| inflation_factor | TRUE |
| n | TRUE |
| is_snpid_non_unique | TRUE |
| mean_EFFECT_nonfinite | FALSE |
| mean_EFFECT_05 | FALSE |
| mean_EFFECT_01 | FALSE |
| mean_chisq | NA |
| n_p_sig | TRUE |
| miss_EFFECT | FALSE |
| miss_SE | FALSE |
| miss_PVAL | FALSE |
| ldsc_ratio | NA |
| ldsc_intercept_beta | NA |
| 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 | 2 | 0.9999998 | 3 | 58 | 0 | 10540100 | 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 | AF | 10548750 | 0.0000000 | NA | NA | NA | NA | NA | NaN | : | NA | NA | NA | NA | NA | NA | NA | NA |
| logical | N | 10548750 | 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 | 8.814771e+00 | 5.948963e+00 | 1.00 | 4.000000e+00 | 8.000000e+00 | 1.300000e+01 | 2.30000e+01 | ▇▅▅▂▂ |
| numeric | POS | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 7.883270e+07 | 5.597013e+07 | 828.00 | 3.269335e+07 | 6.976533e+07 | 1.145490e+08 | 2.49219e+08 | ▇▆▅▂▁ |
| numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 7.400000e-06 | 2.969690e-02 | -0.68 | -7.800000e-03 | 0.000000e+00 | 7.900000e-03 | 6.10000e-01 | ▁▁▇▁▁ |
| numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | Inf | NaN | 0.00 | 5.184300e-03 | 8.648200e-03 | 2.164670e-02 | Inf | ▇▁▁▁▁ |
| numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.447016e-01 | 3.040950e-01 | 0.00 | 1.669998e-01 | 4.250001e-01 | 7.079996e-01 | 1.00000e+00 | ▇▆▅▅▅ |
| numeric | PVAL_ztest | 34345 | 0.9967442 | NA | NA | NA | NA | NA | NA | NA | 4.428997e-01 | 3.029497e-01 | 0.00 | 1.660002e-01 | 4.239998e-01 | 7.050003e-01 | 1.00000e+00 | ▇▆▅▅▅ |
| numeric | AF_reference | 192266 | 0.9817736 | NA | NA | NA | NA | NA | NA | NA | 2.110611e-01 | 2.497486e-01 | 0.00 | 1.317890e-02 | 1.044330e-01 | 3.298720e-01 | 1.00000e+00 | ▇▂▁▁▁ |
Head and tail
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 751756 | rs143225517 | T | C | -0.0074 | 0.0083940 | 0.3780002 | 0.3780000 | NA | 0.2422120 | NA |
| 1 | 752478 | rs146277091 | G | A | -0.0071 | 0.0238566 | 0.7660004 | 0.7659996 | NA | 0.0277556 | NA |
| 1 | 752566 | rs3094315 | G | A | 0.0017 | 0.0073875 | 0.8180000 | 0.8180000 | NA | 0.7182510 | NA |
| 1 | 752617 | rs149886465 | C | A | -0.0100 | 0.0232413 | 0.6670003 | 0.6670003 | NA | 0.0275559 | NA |
| 1 | 752721 | rs3131972 | A | G | 0.0033 | 0.0075488 | 0.6620000 | 0.6620002 | NA | 0.6533550 | NA |
| 1 | 752894 | rs3131971 | T | C | 0.0038 | 0.0078424 | 0.6280005 | 0.6280001 | NA | 0.7531950 | NA |
| 1 | 753405 | rs3115860 | C | A | 0.0079 | 0.0082282 | 0.3370001 | 0.3370002 | NA | 0.7517970 | NA |
| 1 | 753474 | rs2073814 | C | G | 0.0026 | 0.0077420 | 0.7369992 | 0.7370000 | NA | 0.6114220 | NA |
| 1 | 753541 | rs2073813 | G | A | -0.0081 | 0.0083670 | 0.3329998 | 0.3330000 | NA | 0.3019170 | NA |
| 1 | 754063 | rs12184312 | G | T | -0.0099 | 0.0242426 | 0.6830005 | 0.6830006 | NA | 0.0229633 | NA |
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 23 | 154908749 | rs601837 | G | C | -0.023 | 0.0079028 | 0.0036100 | 0.0036100 | NA | 0.363974 | NA |
| 23 | 154909055 | rs473529 | C | G | -0.018 | 0.0073928 | 0.0149001 | 0.0149000 | NA | 0.463046 | NA |
| 23 | 154909877 | rs586454 | G | T | -0.025 | 0.0081687 | 0.0022100 | 0.0022100 | NA | 0.355762 | NA |
| 23 | 154913799 | rs622581 | T | C | -0.023 | 0.0077338 | 0.0029400 | 0.0029400 | NA | 0.356821 | NA |
| 23 | 154915619 | rs571421 | G | A | -0.023 | 0.0077659 | 0.0030600 | 0.0030600 | NA | 0.356556 | NA |
| 23 | 154915975 | rs672932 | G | A | -0.023 | 0.0077338 | 0.0029400 | 0.0029400 | NA | 0.363709 | NA |
| 23 | 154916845 | rs669237 | G | T | -0.023 | 0.0076667 | 0.0027000 | 0.0027000 | NA | 0.416689 | NA |
| 23 | 154918266 | rs642043 | C | T | -0.018 | 0.0072390 | 0.0129000 | 0.0129000 | NA | 0.478675 | NA |
| 23 | 154918383 | rs641588 | G | T | -0.023 | 0.0077659 | 0.0030600 | 0.0030600 | NA | 0.356556 | NA |
| 23 | 154918624 | rs5940558 | A | G | 0.021 | 0.0184100 | 0.2540002 | 0.2540013 | NA | 0.129007 | NA |
bcf preview
1 751756 rs28527770 T C . PASS . ES:SE:LP:ID -0.0074:0.00839395:0.422508:rs28527770
1 752478 rs146277091 G A . PASS . ES:SE:LP:ID -0.0071:0.0238566:0.115771:rs146277091
1 752566 rs3094315 G A . PASS . ES:SE:LP:ID 0.0017:0.00738751:0.0872467:rs3094315
1 752617 rs149886465 C A . PASS . ES:SE:LP:ID -0.01:0.0232413:0.175874:rs149886465
1 752721 rs3131972 A G . PASS . ES:SE:LP:ID 0.0033:0.00754884:0.179142:rs3131972
1 752894 rs3131971 T C . PASS . ES:SE:LP:ID 0.0038:0.00784243:0.20204:rs3131971
1 753405 rs3115860 C A . PASS . ES:SE:LP:ID 0.0079:0.00822823:0.47237:rs3115860
1 753474 rs2073814 C G . PASS . ES:SE:LP:ID 0.0026:0.00774204:0.132533:rs2073814
1 753541 rs1388595942 G A . PASS . ES:SE:LP:ID -0.0081:0.008367:0.477556:rs1388595942
1 754063 rs12184312 G T . PASS . ES:SE:LP:ID -0.0099:0.0242426:0.165579:rs12184312
1 754105 rs12184325 C T . PASS . ES:SE:LP:ID -0.014:0.0220245:0.279841:rs12184325
1 754182 rs3131969 A G . PASS . ES:SE:LP:ID 0.0097:0.00820283:0.625252:rs3131969
1 754192 rs3131968 A G . PASS . ES:SE:LP:ID 0.0095:0.00820616:0.607303:rs3131968
1 754211 rs12184313 G A . PASS . ES:SE:LP:ID -0.0004:0.0245492:0.00568285:rs12184313
1 754334 rs3131967 T C . PASS . ES:SE:LP:ID 0.0078:0.00827695:0.460924:rs3131967
1 754503 rs3115859 G A . PASS . ES:SE:LP:ID 0.0039:0.00773239:0.211832:rs3115859
1 754629 rs10454459 A G . PASS . ES:SE:LP:ID -0.0075:0.0260008:0.111821:rs10454459
1 754964 rs3131966 C T . PASS . ES:SE:LP:ID 0.0055:0.00802281:0.307153:rs3131966
1 755364 rs1557550576 G C . PASS . ES:SE:LP:ID 0.022:0.0406101:0.230623:rs1557550576
1 755775 rs3131965 A G . PASS . ES:SE:LP:ID 0.0003:0.0140793:0.00744648:rs3131965
1 755890 rs1280367067 A T . PASS . ES:SE:LP:ID 0.0078:0.00843303:0.449772:rs1280367067
1 756604 rs3131962 A G . PASS . ES:SE:LP:ID 0.0066:0.00832683:0.368556:rs3131962
1 757640 rs3115853 G A . PASS . ES:SE:LP:ID 0.0095:0.00845173:0.583359:rs3115853
1 757734 rs1557551770 C T . PASS . ES:SE:LP:ID 0.0075:0.00838362:0.430626:rs1557551770
1 757936 rs1360886751 C A . PASS . ES:SE:LP:ID 0.007:0.00842406:0.391474:rs1360886751
1 758144 rs3131956 A G . PASS . ES:SE:LP:ID 0.0054:0.00821566:0.291579:rs3131956
1 758626 rs3131954 C T . PASS . ES:SE:LP:ID 0.0075:0.00845407:0.425969:rs3131954
1 758841 rs1557552299 T C . PASS . ES:SE:LP:ID 0.038:0.0411695:0.44855:rs1557552299
1 759036 rs114525117 G A . PASS . ES:SE:LP:ID 0.049:0.0421476:0.610834:rs114525117
1 759700 rs989694037 T C . PASS . ES:SE:LP:ID -0.0029:0.014364:0.0757207:rs989694037
1 759837 rs3115851 T A . PASS . ES:SE:LP:ID 0.0068:0.00846871:0.374688:rs3115851
1 759970 rs145098582 A G . PASS . ES:SE:LP:ID 0.043:0.0417467:0.518557:rs145098582
1 760912 rs1048488 C T . PASS . ES:SE:LP:ID -0.0012:0.00815399:0.0540393:rs1048488
1 760998 rs148828841 C A . PASS . ES:SE:LP:ID 0.057:0.042611:0.742321:rs148828841
1 761147 rs3115850 T C . PASS . ES:SE:LP:ID -0.0003:0.00725143:0.0145735:rs3115850
1 761752 rs1057213 C T . PASS . ES:SE:LP:ID 0.0062:0.00862035:0.326058:rs1057213
1 768253 rs2977608 A C . PASS . ES:SE:LP:ID 0.0081:0.00689369:0.619789:rs2977608
1 768448 rs12562034 G A . PASS . ES:SE:LP:ID -0.011:0.0088328:0.67162:rs12562034
1 769963 rs7518545 G A . PASS . ES:SE:LP:ID -0.01:0.00891523:0.581699:rs7518545
1 776546 rs12124819 A G . PASS . ES:SE:LP:ID 0.02:0.00797987:1.91364:rs12124819
1 796767 rs12076540 G A . PASS . ES:SE:LP:ID 0.0048:0.010202:0.195179:rs12076540
1 797440 rs58013264 T C . PASS . ES:SE:LP:ID -0.0035:0.00962041:0.145087:rs58013264
1 798400 rs10900604 A G . PASS . ES:SE:LP:ID -0.0014:0.00740277:0.0705811:rs10900604
1 798959 rs11240777 G A . PASS . ES:SE:LP:ID -0.0011:0.00722558:0.0560111:rs11240777
1 800007 rs1329349395 T C . PASS . ES:SE:LP:ID -0.016:0.10872:0.0540393:rs1329349395
1 801467 rs61768212 G C . PASS . ES:SE:LP:ID -0.0083:0.0126878:0.289883:rs61768212
1 802026 rs1557574948 G A . PASS . ES:SE:LP:ID -0.0052:0.0103099:0.211832:rs1557574948
1 802496 rs1557575256 C T . PASS . ES:SE:LP:ID -0.0072:0.0127741:0.241845:rs1557575256
1 824357 rs80134645 C T . PASS . ES:SE:LP:ID -0.07:0.0501773:0.787812:rs80134645
1 830791 rs184031231 C T . PASS . ES:SE:LP:ID 0.0077:0.0510038:0.0555173:rs184031231