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-4832,TotalVariants=7892788,VariantsNotRead=0,HarmonisedVariants=7892788,VariantsNotHarmonised=0,SwitchedAlleles=3496041,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/215c1327-7aef-468d-ae36-ab303651184e/call-vcf/inputs/-261044479/upload.txt.gz --id ieu-b-4832 --json /data/cromwell-executions/qc/215c1327-7aef-468d-ae36-ab303651184e/call-vcf/inputs/-261044479/ieu-b-4832_data.json --ref /data/cromwell-executions/qc/215c1327-7aef-468d-ae36-ab303651184e/call-vcf/inputs/1899004205/human_g1k_v37.fasta --dbsnp /data/cromwell-executions/qc/215c1327-7aef-468d-ae36-ab303651184e/call-vcf/inputs/-307190728/dbsnp.v153.b37.vcf.gz --out /data/igd/ieu-b-4832/ieu-b-4832.vcf.gz --alias alias.txt; 1.3.0",
"file_date": "2022-01-05T09:46:56.009717",
"bcftools_viewVersion": "1.9+htslib-1.9",
"bcftools_viewCommand": "view -h /data/cromwell-executions/qc/215c1327-7aef-468d-ae36-ab303651184e/call-report/inputs/-261044479/ieu-b-4832.vcf.gz; Date=Wed Jan 5 10:07:36 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/215c1327-7aef-468d-ae36-ab303651184e/call-ldsc/inputs/-261044479/ieu-b-4832.vcf.gz \
--ref-ld-chr /data/ref/eur_w_ld_chr/ \
--out /data/igd/ieu-b-4832/ldsc.txt \
--w-ld-chr /data/ref/eur_w_ld_chr/
Beginning analysis at Wed Jan 5 09:59:06 2022
Reading summary statistics from /data/cromwell-executions/qc/215c1327-7aef-468d-ae36-ab303651184e/call-ldsc/inputs/-261044479/ieu-b-4832.vcf.gz ...
Read summary statistics for 7892730 SNPs.
Dropped 38590 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, 1196616 SNPs remain.
After merging with regression SNP LD, 1196616 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.1701 (0.0146)
Lambda GC: 1.3239
Mean Chi^2: 1.4158
Intercept: 1.1489 (0.0099)
Ratio: 0.3581 (0.0239)
Analysis finished at Wed Jan 5 10:00:56 2022
Total time elapsed: 1.0m:49.77sQC metrics
Metrics
Metrics
{
"af_correlation": "NA",
"inflation_factor": 1.2998,
"mean_EFFECT": -0.0002,
"n": 76511,
"n_snps": 7892788,
"n_clumped_hits": 47,
"n_p_sig": 3403,
"n_mono": 0,
"n_ns": 285919,
"n_mac": 0,
"is_snpid_unique": false,
"n_miss_EFFECT": 0,
"n_miss_SE": 0,
"n_miss_PVAL": 0,
"n_miss_AF": 7892788,
"n_miss_AF_reference": 161488,
"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": 1196616,
"ldsc_nsnp_merge_regression_ld": 1196616,
"ldsc_observed_scale_h2_beta": 0.1701,
"ldsc_observed_scale_h2_se": 0.0146,
"ldsc_intercept_beta": 1.1489,
"ldsc_intercept_se": 0.0099,
"ldsc_lambda_gc": 1.3239,
"ldsc_mean_chisq": 1.4158,
"ldsc_ratio": 0.3581
}
Flags
| name | value |
|---|---|
| af_correlation | NA |
| inflation_factor | TRUE |
| n | FALSE |
| is_snpid_non_unique | TRUE |
| mean_EFFECT_nonfinite | FALSE |
| mean_EFFECT_05 | FALSE |
| mean_EFFECT_01 | FALSE |
| mean_chisq | TRUE |
| n_p_sig | TRUE |
| 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 | 14 | 0.9999982 | 3 | 58 | 0 | 7892661 | 0 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| character | REF | 0 | 1.0000000 | 1 | 43 | 0 | 16674 | 0 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| character | ALT | 0 | 1.0000000 | 1 | 44 | 0 | 6032 | 0 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| logical | AF | 7892788 | 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 | 8.643539e+00 | 5.753999e+00 | 1.0000e+00 | 4.000000e+00 | 8.000000e+00 | 1.300000e+01 | 2.200000e+01 | ▇▅▅▂▂ |
| numeric | POS | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 7.907661e+07 | 5.635413e+07 | 3.0200e+02 | 3.279860e+07 | 6.985354e+07 | 1.148346e+08 | 2.492223e+08 | ▇▆▅▂▁ |
| numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | -1.542000e-04 | 1.682437e-01 | -2.3393e+00 | -8.610000e-02 | -2.000000e-04 | 8.560000e-02 | 2.111800e+00 | ▁▁▇▁▁ |
| numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 1.320464e-01 | 6.971580e-02 | 6.6500e-02 | 7.720000e-02 | 1.017000e-01 | 1.685000e-01 | 4.116000e-01 | ▇▂▂▁▁ |
| numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.579604e-01 | 2.998504e-01 | 0.0000e+00 | 1.873001e-01 | 4.419000e-01 | 7.185004e-01 | 1.000000e+00 | ▇▆▆▆▆ |
| numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.579605e-01 | 2.998505e-01 | 0.0000e+00 | 1.872960e-01 | 4.419355e-01 | 7.185489e-01 | 1.000000e+00 | ▇▆▆▆▆ |
| numeric | AF_reference | 161488 | 0.9795398 | NA | NA | NA | NA | NA | NA | NA | 2.649183e-01 | 2.521992e-01 | 1.9970e-04 | 5.750800e-02 | 1.795130e-01 | 4.137380e-01 | 1.000000e+00 | ▇▃▂▁▁ |
| numeric | N | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 7.518967e+04 | 2.877990e+03 | 6.6631e+04 | 7.561800e+04 | 7.651100e+04 | 7.651100e+04 | 7.651100e+04 | ▁▁▁▁▇ |
Head and tail
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 797440 | rs58013264 | T | C | 0.1528 | 0.1068 | 0.1525001 | 0.1525129 | NA | 0.189497 | 75618 |
| 1 | 798400 | rs10900604 | A | G | 0.0901 | 0.0873 | 0.3020000 | 0.3020378 | NA | 0.410543 | 76511 |
| 1 | 798959 | rs11240777 | G | A | 0.0889 | 0.0874 | 0.3089997 | 0.3090761 | NA | 0.409944 | 76511 |
| 1 | 801467 | rs61768212 | G | C | 0.1161 | 0.1067 | 0.2764999 | 0.2765521 | NA | 0.193091 | 75618 |
| 1 | 804759 | rs7526310 | C | T | 0.1137 | 0.1068 | 0.2870999 | 0.2870539 | NA | 0.193890 | 75618 |
| 1 | 808223 | rs4951933 | G | C | -0.1084 | 0.0890 | 0.2229000 | 0.2232325 | NA | 0.452077 | 66631 |
| 1 | 808631 | rs11240779 | G | A | -0.1043 | 0.0850 | 0.2198999 | 0.2198005 | NA | 0.453474 | 75618 |
| 1 | 808928 | rs11240780 | C | T | -0.1062 | 0.0850 | 0.2116002 | 0.2115145 | NA | 0.452276 | 75618 |
| 1 | 845274 | rs112856858 | G | T | 0.0883 | 0.0931 | 0.3428996 | 0.3429042 | NA | 0.374002 | 66631 |
| 1 | 845635 | rs117086422 | C | T | 0.0971 | 0.0891 | 0.2757998 | 0.2758071 | NA | 0.158546 | 75618 |
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 22 | 51177257 | rs73174437 | C | T | -0.1976 | 0.1921 | 0.3036002 | 0.3036531 | NA | 0.0091853 | 75618 |
| 22 | 51178607 | rs6010067 | G | C | -0.3472 | 0.2544 | 0.1722999 | 0.1723222 | NA | 0.0814696 | 75618 |
| 22 | 51180878 | rs6010069 | A | G | 0.0170 | 0.0961 | 0.8599001 | 0.8595877 | NA | 0.1589460 | 66631 |
| 22 | 51180959 | rs6010070 | A | G | 0.0185 | 0.0960 | 0.8471999 | 0.8471874 | NA | 0.2056710 | 66631 |
| 22 | 51181685 | rs34756634 | G | A | 0.0408 | 0.1093 | 0.7090992 | 0.7089367 | NA | 0.7118610 | 66631 |
| 22 | 51181687 | rs9616955 | A | T | 0.0268 | 0.1557 | 0.8631000 | 0.8633386 | NA | 0.0485224 | 66631 |
| 22 | 51181759 | rs13056621 | A | G | -0.0734 | 0.1073 | 0.4935998 | 0.4939351 | NA | 0.6761180 | 75618 |
| 22 | 51182090 | rs28516879 | G | A | 0.1728 | 0.1393 | 0.2148998 | 0.2147949 | NA | 0.0467252 | 75618 |
| 22 | 51185848 | rs3865764 | G | A | 0.0413 | 0.1820 | 0.8206999 | 0.8204836 | NA | 0.9776360 | 75618 |
| 22 | 51188319 | rs139620215 | T | C | 0.4048 | 0.3157 | 0.1999001 | 0.1997620 | NA | 0.0037939 | 75618 |
bcf preview
1 797440 rs58013264 T C . PASS . ES:SE:LP:SS:ID 0.1528:0.1068:0.81673:75618:rs58013264
1 798400 rs10900604 A G . PASS . ES:SE:LP:SS:ID 0.0901:0.0873:0.519993:76511:rs10900604
1 798959 rs11240777 G A . PASS . ES:SE:LP:SS:ID 0.0889:0.0874:0.510042:76511:rs11240777
1 801467 rs61768212 G C . PASS . ES:SE:LP:SS:ID 0.1161:0.1067:0.558305:75618:rs61768212
1 804759 rs7526310 C T . PASS . ES:SE:LP:SS:ID 0.1137:0.1068:0.541967:75618:rs7526310
1 808223 rs1557576983 G C . PASS . ES:SE:LP:SS:ID -0.1084:0.089:0.65189:66631:rs1557576983
1 808631 rs11240779 G A . PASS . ES:SE:LP:SS:ID -0.1043:0.085:0.657775:75618:rs11240779
1 808928 rs1247187939 C T . PASS . ES:SE:LP:SS:ID -0.1062:0.085:0.674484:75618:rs1247187939
1 845274 rs1324283754 G T . PASS . ES:SE:LP:SS:ID 0.0883:0.0931:0.464833:66631:rs1324283754
1 845635 rs117086422 C T . PASS . ES:SE:LP:SS:ID 0.0971:0.0891:0.559406:75618:rs117086422
1 845938 rs57760052 G A . PASS . ES:SE:LP:SS:ID 0.1037:0.0885:0.616723:75618:rs57760052
1 846078 rs778265812 C T . PASS . ES:SE:LP:SS:ID 0.055:0.0917:0.260665:75618:rs778265812
1 846398 rs58781670 G A . PASS . ES:SE:LP:SS:ID 0.11:0.0896:0.658763:75618:rs58781670
1 846465 rs60454217 C T . PASS . ES:SE:LP:SS:ID 0.48:0.2732:1.10276:75618:rs60454217
1 846543 rs79396034 G T . PASS . ES:SE:LP:SS:ID 0.5618:0.2902:1.27704:66631:rs79396034
1 846808 rs4475691 C T . PASS . ES:SE:LP:SS:ID 0.055:0.0915:0.261457:75618:rs4475691
1 846864 rs1269142199 G C . PASS . ES:SE:LP:SS:ID 0.0395:0.0916:0.176461:75618:rs1269142199
1 847228 rs3905286 C T . PASS . ES:SE:LP:SS:ID 0.0645:0.0903:0.323306:75618:rs3905286
1 847491 rs1158719307 G A . PASS . ES:SE:LP:SS:ID 0.0705:0.0892:0.367138:75618:rs1158719307
1 848090 rs4246505 G A . PASS . ES:SE:LP:SS:ID 0.0644:0.0895:0.326058:75618:rs4246505
1 848445 rs1156895099 G A . PASS . ES:SE:LP:SS:ID 0.066:0.0896:0.336111:75618:rs1156895099
1 848456 rs11507767 A G . PASS . ES:SE:LP:SS:ID 0.067:0.0896:0.342466:75618:rs11507767
1 848738 rs3829741 C T . PASS . ES:SE:LP:SS:ID 0.0642:0.0895:0.324955:75618:rs3829741
1 850062 rs28723578 A T . PASS . ES:SE:LP:SS:ID 0.0699:0.0892:0.363011:75618:rs28723578
1 850123 rs28622257 C T . PASS . ES:SE:LP:SS:ID 0.0609:0.0895:0.304781:75618:rs28622257
1 851190 rs28609852 G A . PASS . ES:SE:LP:SS:ID 0.0701:0.0892:0.364818:75618:rs28609852
1 851204 rs28552953 G C . PASS . ES:SE:LP:SS:ID 0.0699:0.0883:0.367847:75618:rs28552953
1 852664 rs28605311 C T . PASS . ES:SE:LP:SS:ID 0.0364:0.0902:0.163296:75618:rs28605311
1 852758 rs4970462 G C . PASS . ES:SE:LP:SS:ID 0.036:0.0902:0.161214:75618:rs4970462
1 853239 rs4970380 A G . PASS . ES:SE:LP:SS:ID 0.0367:0.0902:0.165134:75618:rs4970380
1 853805 rs3748591 C T . PASS . ES:SE:LP:SS:ID 0.5211:0.2418:1.5064:75618:rs3748591
1 854250 rs7537756 A G . PASS . ES:SE:LP:SS:ID 0.0489:0.09:0.231362:75618:rs7537756
1 854429 rs72902552 G A . PASS . ES:SE:LP:SS:ID 0.5097:0.2418:1.45506:75618:rs72902552
1 856436 rs34105146 TG T . PASS . ES:SE:LP:SS:ID 0.003:0.0953:0.0110399:66631:rs34105146
1 856476 rs4040605 A G . PASS . ES:SE:LP:SS:ID 0.0016:0.075:0.00762324:75618:rs4040605
1 857177 rs386627408 T C . PASS . ES:SE:LP:SS:ID 0.6512:0.2406:2.16768:75618:rs386627408
1 858040 rs4970460 C A . PASS . ES:SE:LP:SS:ID 0.026:0.0883:0.114243:75618:rs4970460
1 858051 rs4970459 C T . PASS . ES:SE:LP:SS:ID 0.027:0.0883:0.119415:75618:rs4970459
1 858801 rs7418179 A G . PASS . ES:SE:LP:SS:ID -0.1244:0.0856:0.835647:75618:rs7418179
1 859404 rs71509444 C G . PASS . ES:SE:LP:SS:ID -0.5385:0.2465:1.53895:66631:rs71509444
1 859685 rs111572704 G A . PASS . ES:SE:LP:SS:ID 0.0238:0.0929:0.0983238:66631:rs111572704
1 859690 rs71509445 C G . PASS . ES:SE:LP:SS:ID -0.5717:0.2674:1.48812:66631:rs71509445
1 859701 rs71509446 C G . PASS . ES:SE:LP:SS:ID -0.5717:0.2674:1.48812:66631:rs71509446
1 859913 rs1187056171 A G . PASS . ES:SE:LP:SS:ID -0.4905:0.2609:1.22113:75618:rs1187056171
1 860416 rs61464428 G A . PASS . ES:SE:LP:SS:ID -0.1242:0.0857:0.831797:75618:rs61464428
1 860461 rs57465118 G A . PASS . ES:SE:LP:SS:ID -0.5647:0.2339:1.80272:75618:rs57465118
1 860521 rs57924093 C A . PASS . ES:SE:LP:SS:ID -0.5647:0.2339:1.80272:75618:rs57924093
1 860688 rs60837925 G A . PASS . ES:SE:LP:SS:ID -0.1262:0.0857:0.851706:75618:rs60837925
1 860854 rs57816555 T C . PASS . ES:SE:LP:SS:ID -0.5685:0.2887:1.30989:66631:rs57816555
1 861008 rs28521172 G C . PASS . ES:SE:LP:SS:ID -0.5621:0.234:1.78808:75618:rs28521172