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-118,TotalVariants=2455342,VariantsNotRead=0,HarmonisedVariants=2455342,VariantsNotHarmonised=0,SwitchedAlleles=0,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/7efb0b10-a5ae-4c37-bf31-4fee89ca1526/call-vcf/inputs/268670778/upload.txt.gz --id ieu-b-118 --json /data/cromwell-executions/qc/7efb0b10-a5ae-4c37-bf31-4fee89ca1526/call-vcf/inputs/268670778/ieu-b-118_data.json --ref /data/cromwell-executions/qc/7efb0b10-a5ae-4c37-bf31-4fee89ca1526/call-vcf/inputs/1899004205/human_g1k_v37.fasta --dbsnp /data/cromwell-executions/qc/7efb0b10-a5ae-4c37-bf31-4fee89ca1526/call-vcf/inputs/-307190728/dbsnp.v153.b37.vcf.gz --out /data/igd/ieu-b-118/ieu-b-118.vcf.gz --alias alias.txt; 1.3.0",
"file_date": "2021-04-01T16:36:38.464344",
"bcftools_viewVersion": "1.9+htslib-1.9",
"bcftools_viewCommand": "view -h /data/cromwell-executions/qc/7efb0b10-a5ae-4c37-bf31-4fee89ca1526/call-report/inputs/268670778/ieu-b-118.vcf.gz; Date=Thu Apr 1 16:43:31 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/7efb0b10-a5ae-4c37-bf31-4fee89ca1526/call-ldsc/inputs/268670778/ieu-b-118.vcf.gz \
--ref-ld-chr /data/ref/eur_w_ld_chr/ \
--out /data/igd/ieu-b-118/ldsc.txt \
--w-ld-chr /data/ref/eur_w_ld_chr/
Beginning analysis at Thu Apr 1 16:39:36 2021
Reading summary statistics from /data/cromwell-executions/qc/7efb0b10-a5ae-4c37-bf31-4fee89ca1526/call-ldsc/inputs/268670778/ieu-b-118.vcf.gz ...
Read summary statistics for 2455342 SNPs.
Dropped 835 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, 1095698 SNPs remain.
After merging with regression SNP LD, 1095698 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0717 (0.0128)
Lambda GC: 1.048
Mean Chi^2: 1.0534
Intercept: 1.0013 (0.0067)
Ratio: 0.0253 (0.1253)
Analysis finished at Thu Apr 1 16:40:27 2021
Total time elapsed: 51.37sQC metrics
Metrics
Metrics
{
"af_correlation": "NA",
"inflation_factor": 1.0402,
"mean_EFFECT": 0,
"n": 37037,
"n_snps": 2455342,
"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": 2455342,
"n_miss_AF_reference": 20711,
"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": 1095698,
"ldsc_nsnp_merge_regression_ld": 1095698,
"ldsc_observed_scale_h2_beta": 0.0717,
"ldsc_observed_scale_h2_se": 0.0128,
"ldsc_intercept_beta": 1.0013,
"ldsc_intercept_se": 0.0067,
"ldsc_lambda_gc": 1.048,
"ldsc_mean_chisq": 1.0534,
"ldsc_ratio": 0.0243
}
Flags
| name | value |
|---|---|
| af_correlation | NA |
| inflation_factor | FALSE |
| n | FALSE |
| 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 | 0 | 1.0000000 | 3 | 42 | 0 | 2455337 | 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 | 2455342 | 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 | 8.592001e+00 | 5.660516e+00 | 1.0000e+00 | 4.000000e+00 | 8.000000e+00 | 1.200000e+01 | 2.30000e+01 | ▇▅▅▂▂ |
| numeric | POS | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 7.882337e+07 | 5.568264e+07 | 1.2994e+04 | 3.263644e+07 | 7.023235e+07 | 1.143364e+08 | 2.49219e+08 | ▇▆▅▂▁ |
| numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 2.500000e-05 | 7.897700e-03 | -1.5000e-01 | -3.800000e-03 | 0.000000e+00 | 3.900000e-03 | 1.30000e-01 | ▁▁▇▁▁ |
| numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 6.572000e-03 | 4.187000e-03 | 3.9000e-03 | 4.300000e-03 | 5.000000e-03 | 7.000000e-03 | 6.70000e-02 | ▇▁▁▁▁ |
| numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.936142e-01 | 2.905548e-01 | 1.0000e-07 | 2.405000e-01 | 4.915005e-01 | 7.455006e-01 | 1.00000e+00 | ▇▇▇▇▇ |
| numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.936468e-01 | 2.905790e-01 | 1.0000e-07 | 2.399947e-01 | 4.917677e-01 | 7.451811e-01 | 1.00000e+00 | ▇▇▇▇▇ |
| numeric | AF_reference | 20711 | 0.9915649 | NA | NA | NA | NA | NA | NA | NA | 3.616178e-01 | 2.556344e-01 | 0.0000e+00 | 1.467650e-01 | 2.995210e-01 | 5.459270e-01 | 1.00000e+00 | ▇▆▃▃▂ |
| numeric | N | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 3.703700e+04 | 0.000000e+00 | 3.7037e+04 | 3.703700e+04 | 3.703700e+04 | 3.703700e+04 | 3.70370e+04 | ▁▁▇▁▁ |
Head and tail
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 721290 | rs12565286 | G | C | 0.0310 | 0.0190 | 0.1028999 | 0.1027682 | NA | 0.0371406 | 37037 |
| 1 | 723819 | rs11804171 | T | A | 0.0300 | 0.0190 | 0.1046001 | 0.1143481 | NA | 0.1345850 | 37037 |
| 1 | 723891 | rs2977670 | G | C | -0.0340 | 0.0210 | 0.1082999 | 0.1054370 | NA | 0.7799520 | 37037 |
| 1 | 752566 | rs3094315 | G | A | -0.0110 | 0.0079 | 0.1797000 | 0.1637998 | NA | 0.7182510 | 37037 |
| 1 | 754192 | rs3131968 | A | G | 0.0038 | 0.0110 | 0.7370993 | 0.7297527 | NA | 0.6785140 | 37037 |
| 1 | 775659 | rs2905035 | A | G | -0.0059 | 0.0083 | 0.4767997 | 0.4771813 | NA | 0.7450080 | 37037 |
| 1 | 776546 | rs12124819 | A | G | 0.0023 | 0.0084 | 0.7808992 | 0.7842310 | NA | 0.0756789 | 37037 |
| 1 | 777122 | rs2980319 | A | T | -0.0060 | 0.0083 | 0.4715003 | 0.4697465 | NA | 0.7472040 | 37037 |
| 1 | 779322 | rs4040617 | A | G | 0.0067 | 0.0084 | 0.4285998 | 0.4250916 | NA | 0.2264380 | 37037 |
| 1 | 780785 | rs2977612 | T | A | -0.0066 | 0.0083 | 0.4303997 | 0.4265084 | NA | 0.6693290 | 37037 |
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 22 | 51216564 | rs9616970 | T | C | 0.0072 | 0.0091 | 0.4258003 | 0.4288222 | NA | 0.1563500 | 37037 |
| 22 | 51217134 | rs117417021 | A | G | 0.0025 | 0.0089 | 0.7818006 | 0.7787880 | NA | 0.2671730 | 37037 |
| 22 | 51222100 | rs114553188 | G | T | 0.0037 | 0.0110 | 0.7290998 | 0.7365967 | NA | 0.0880591 | 37037 |
| 22 | 51223637 | rs375798137 | G | A | 0.0027 | 0.0110 | 0.7968000 | 0.8061045 | NA | 0.0788738 | 37037 |
| 22 | 51229805 | rs9616985 | T | C | 0.0310 | 0.0140 | 0.0268102 | 0.0268091 | NA | 0.0730831 | 37037 |
| 23 | 35921591 | rs2204667 | C | G | 0.0029 | 0.0054 | 0.5951001 | 0.5912420 | NA | NA | 37037 |
| 23 | 51666786 | rs14115 | A | G | -0.0038 | 0.0090 | 0.6704000 | 0.6728628 | NA | NA | 37037 |
| 23 | 70163799 | rs1626496 | A | C | 0.0049 | 0.0081 | 0.5485005 | 0.5452200 | NA | NA | 37037 |
| 23 | 91415872 | rs6562597 | G | A | -0.0072 | 0.0160 | 0.6533998 | 0.6527104 | NA | 0.0021192 | 37037 |
| 23 | 118495837 | rs12882977 | G | A | 0.0021 | 0.0040 | 0.6032995 | 0.5995832 | NA | 0.2307280 | 37037 |
bcf preview
1 721290 rs12565286 G C . PASS . ES:SE:LP:SS:ID 0.031:0.019:0.987585:37037:rs12565286
1 723819 rs11804171 T A . PASS . ES:SE:LP:SS:ID 0.03:0.019:0.980468:37037:rs11804171
1 723891 rs2977670 G C . PASS . ES:SE:LP:SS:ID -0.034:0.021:0.965372:37037:rs2977670
1 752566 rs3094315 G A . PASS . ES:SE:LP:SS:ID -0.011:0.0079:0.745452:37037:rs3094315
1 754192 rs3131968 A G . PASS . ES:SE:LP:SS:ID 0.0038:0.011:0.132474:37037:rs3131968
1 775659 rs2905035 A G . PASS . ES:SE:LP:SS:ID -0.0059:0.0083:0.321664:37037:rs2905035
1 776546 rs12124819 A G . PASS . ES:SE:LP:SS:ID 0.0023:0.0084:0.107405:37037:rs12124819
1 777122 rs2980319 A T . PASS . ES:SE:LP:SS:ID -0.006:0.0083:0.326518:37037:rs2980319
1 779322 rs4040617 A G . PASS . ES:SE:LP:SS:ID 0.0067:0.0084:0.367948:37037:rs4040617
1 780785 rs2977612 T A . PASS . ES:SE:LP:SS:ID -0.0066:0.0083:0.366128:37037:rs2977612
1 785050 rs2905062 G A . PASS . ES:SE:LP:SS:ID -0.0082:0.0083:0.486383:37037:rs2905062
1 785989 rs2980300 T C . PASS . ES:SE:LP:SS:ID -0.011:0.008:0.788612:37037:rs2980300
1 990380 rs3121561 C T . PASS . ES:SE:LP:SS:ID -0.0018:0.0078:0.090337:37037:rs3121561
1 998501 rs3813193 G C . PASS . ES:SE:LP:SS:ID -0.0038:0.0072:0.221994:37037:rs3813193
1 1003629 rs4075116 C T . PASS . ES:SE:LP:SS:ID -0.01:0.0051:1.36291:37037:rs4075116
1 1005806 rs3934834 C T . PASS . ES:SE:LP:SS:ID -0.0021:0.007:0.11413:37037:rs3934834
1 1017170 rs3766193 C G . PASS . ES:SE:LP:SS:ID -0.011:0.0053:1.32855:37037:rs3766193
1 1017197 rs3766192 C T . PASS . ES:SE:LP:SS:ID -0.0088:0.005:1.10155:37037:rs3766192
1 1017587 rs3766191 C T . PASS . ES:SE:LP:SS:ID -0.0019:0.0073:0.101878:37037:rs3766191
1 1018562 rs9442371 C T . PASS . ES:SE:LP:SS:ID -0.0092:0.0049:1.22105:37037:rs9442371
1 1018704 rs9442372 A G . PASS . ES:SE:LP:SS:ID -0.009:0.0049:1.19199:37037:rs9442372
1 1021346 rs10907177 A G . PASS . ES:SE:LP:SS:ID -0.0011:0.0073:0.0542853:37037:rs10907177
1 1021415 rs386627436 A G . PASS . ES:SE:LP:SS:ID -0.012:0.005:1.79102:37037:rs386627436
1 1021583 rs10907178 A C . PASS . ES:SE:LP:SS:ID -0.0012:0.0074:0.0614803:37037:rs10907178
1 1021695 rs9442398 A G . PASS . ES:SE:LP:SS:ID -0.01:0.0051:1.3535:37037:rs9442398
1 1022037 rs6701114 C T . PASS . ES:SE:LP:SS:ID -0.0063:0.0055:0.60415:37037:rs6701114
1 1025301 rs9442400 T C . PASS . ES:SE:LP:SS:ID -0.0016:0.022:0.0259491:37037:rs9442400
1 1026707 rs4074137 C A . PASS . ES:SE:LP:SS:ID -0.006:0.006:0.494172:37037:rs4074137
1 1030565 rs6687776 C T . PASS . ES:SE:LP:SS:ID -0.0029:0.0069:0.170632:37037:rs6687776
1 1031540 rs776599533 A G . PASS . ES:SE:LP:SS:ID -0.0072:0.0062:0.607655:37037:rs776599533
1 1036959 rs1162868282 T C . PASS . ES:SE:LP:SS:ID -0.0056:0.0087:0.286846:37037:rs1162868282
1 1040026 rs6671356 T C . PASS . ES:SE:LP:SS:ID -0.0077:0.0077:0.502794:37037:rs6671356
1 1046164 rs386627439 C T . PASS . ES:SE:LP:SS:ID -0.0087:0.0075:0.604499:37037:rs386627439
1 1048955 rs4970405 A G . PASS . ES:SE:LP:SS:ID -0.007:0.0076:0.44636:37037:rs4970405
1 1049950 rs12726255 A G . PASS . ES:SE:LP:SS:ID -0.0052:0.0074:0.315065:37037:rs12726255
1 1053452 rs4970409 G A . PASS . ES:SE:LP:SS:ID -0.0075:0.0086:0.417937:37037:rs4970409
1 1060235 rs7540009 G A . PASS . ES:SE:LP:SS:ID -0.019:0.016:0.632458:37037:rs7540009
1 1060608 rs17160824 G A . PASS . ES:SE:LP:SS:ID -0.0076:0.0088:0.412738:37037:rs17160824
1 1061115 rs17160826 T C . PASS . ES:SE:LP:SS:ID -0.0069:0.0088:0.367138:37037:rs17160826
1 1061152 rs12748370 T C . PASS . ES:SE:LP:SS:ID -0.0068:0.0088:0.357338:37037:rs12748370
1 1061166 rs11807848 T C . PASS . ES:SE:LP:SS:ID -0.0006:0.0063:0.034375:37037:rs11807848
1 1062015 rs1557446446 C T . PASS . ES:SE:LP:SS:ID -0.02:0.016:0.66374:37037:rs1557446446
1 1062638 rs9442373 C A . PASS . ES:SE:LP:SS:ID -0.0001:0.0063:0.00445255:37037:rs9442373
1 1064535 rs6682475 G C . PASS . ES:SE:LP:SS:ID -0.0004:0.0079:0.0193604:37037:rs6682475
1 1064979 rs2298217 C T . PASS . ES:SE:LP:SS:ID -0.0045:0.0075:0.259479:37037:rs2298217
1 1066403 rs10907182 T C . PASS . ES:SE:LP:SS:ID 0.0044:0.0064:0.310602:37037:rs10907182
1 1071118 rs10907183 G C . PASS . ES:SE:LP:SS:ID 0.0042:0.0067:0.269864:37037:rs10907183
1 1077064 rs4970357 C A . PASS . ES:SE:LP:SS:ID -0.009:0.0088:0.508778:37037:rs4970357
1 1080925 rs911335568 G C . PASS . ES:SE:LP:SS:ID -0.0082:0.011:0.331707:37037:rs911335568
1 1087683 rs9442380 T C . PASS . ES:SE:LP:SS:ID -0.0051:0.0083:0.268814:37037:rs9442380