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=ukb-d-30850_irnt,TotalVariants=13585068,VariantsNotRead=0,HarmonisedVariants=13585068,VariantsNotHarmonised=0,SwitchedAlleles=229,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>",
"gwas_harmonisation_command": "--json /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-30850_irnt/ukb-d-30850_irnt_data.json --ref /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/QC/genomes/b37/human_g1k_v37.fasta; 1.1.1",
"file_date": "2019-11-25T13:37:52.186152",
"bcftools_annotateVersion": "1.9-74-g6af271c+htslib-1.9-64-g226b4a8",
"bcftools_annotateCommand": "annotate -a /mnt/storage/home/gh13047/mr-eve/vcf-reference-datasets/dbsnp/dbsnp.v153.b37.vcf.gz -c ID -o /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-30850_irnt/ukb-d-30850_irnt.vcf.gz -O z /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-30850_irnt/ukb-d-30850_irnt_data.vcf.gz; Date=Mon Nov 25 14:31:01 2019",
"bcftools_viewVersion": "1.9-74-g6af271c+htslib-1.9-64-g226b4a8",
"bcftools_viewCommand": "view -h /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukb-d-30850_irnt/ukb-d-30850_irnt.vcf.gz; Date=Sat May 9 19:18:56 2020"
}
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 /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-30850_irnt/ukb-d-30850_irnt.vcf.gz \
--ref-ld-chr /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-30850_irnt/ldsc.txt \
--w-ld-chr /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/reference/eur_w_ld_chr/
Beginning analysis at Mon Nov 25 15:00:24 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-30850_irnt/ukb-d-30850_irnt.vcf.gz ...
Read summary statistics for 13585068 SNPs.
Dropped 12707 SNPs with duplicated rs numbers.
Reading reference panel LD Score from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/reference/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 /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/reference/eur_w_ld_chr/[1-22] ...
Read regression weight LD Scores for 1290028 SNPs.
After merging with reference panel LD, 1283501 SNPs remain.
After merging with regression SNP LD, 1283501 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0725 (0.0108)
Lambda GC: 1.2584
Mean Chi^2: 1.4895
Intercept: 1.0455 (0.0108)
Ratio: 0.0929 (0.022)
Analysis finished at Mon Nov 25 15:03:15 2019
Total time elapsed: 2.0m:50.85sQC metrics
Metrics
Metrics
{
"af_correlation": 0.9521,
"inflation_factor": 1.1668,
"mean_EFFECT": 7.6881e-07,
"n": 312102,
"n_snps": 13585068,
"n_clumped_hits": 100,
"n_p_sig": 17462,
"n_mono": 0,
"n_ns": 1251749,
"n_mac": 0,
"is_snpid_unique": false,
"n_miss_EFFECT": 0,
"n_miss_SE": 0,
"n_miss_PVAL": 0,
"n_miss_AF": 0,
"n_miss_AF_reference": 568966,
"n_est": 313518.5109,
"ratio_se_n": 1.0023,
"mean_diff": 1.7719e-06,
"ratio_diff": 1.3929,
"sd_y_est1": 0.6046,
"sd_y_est2": 0.606,
"r2_sum1": 0.0099,
"r2_sum2": 0.0271,
"r2_sum3": 0.027,
"r2_sum4": 0.027,
"ldsc_nsnp_merge_refpanel_ld": 1283501,
"ldsc_nsnp_merge_regression_ld": 1283501,
"ldsc_observed_scale_h2_beta": 0.0725,
"ldsc_observed_scale_h2_se": 0.0108,
"ldsc_intercept_beta": 1.0455,
"ldsc_intercept_se": 0.0108,
"ldsc_lambda_gc": 1.2584,
"ldsc_mean_chisq": 1.4895,
"ldsc_ratio": 0.093
}
Flags
| name | value |
|---|---|
| af_correlation | FALSE |
| inflation_factor | FALSE |
| 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 | numeric.mean | numeric.sd | numeric.p0 | numeric.p25 | numeric.p50 | numeric.p75 | numeric.p100 | numeric.hist |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| character | ID | 0 | 1.0000000 | 3 | 94 | 0 | 13573025 | 0 | NA | NA | NA | NA | NA | NA | NA | NA |
| character | REF | 0 | 1.0000000 | 1 | 100 | 0 | 57081 | 0 | NA | NA | NA | NA | NA | NA | NA | NA |
| character | ALT | 0 | 1.0000000 | 1 | 342 | 0 | 33337 | 0 | NA | NA | NA | NA | NA | NA | NA | NA |
| numeric | CHROM | 0 | 1.0000000 | NA | NA | NA | NA | NA | 9.051273e+00 | 6.184938e+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 | 7.902581e+07 | 5.591529e+07 | 3.02000e+02 | 3.293089e+07 | 7.013920e+07 | 1.148611e+08 | 2.492309e+08 | ▇▆▅▂▁ |
| numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | 8.000000e-07 | 9.153500e-03 | -2.36230e-01 | -2.628900e-03 | -1.740000e-05 | 2.601800e-03 | 1.539200e-01 | ▁▁▃▇▁ |
| numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | 6.429400e-03 | 6.202400e-03 | 1.24080e-03 | 1.831000e-03 | 3.373600e-03 | 9.237400e-03 | 3.147200e-02 | ▇▂▁▁▁ |
| numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | 4.738794e-01 | 2.969519e-01 | 0.00000e+00 | 2.101701e-01 | 4.662598e-01 | 7.315803e-01 | 1.000000e+00 | ▇▆▆▆▆ |
| numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | 4.738789e-01 | 2.969521e-01 | 0.00000e+00 | 2.101743e-01 | 4.662623e-01 | 7.315826e-01 | 1.000000e+00 | ▇▆▆▆▆ |
| numeric | AF | 0 | 1.0000000 | NA | NA | NA | NA | NA | 1.908226e-01 | 2.544084e-01 | 1.00000e-03 | 7.433500e-03 | 6.005700e-02 | 2.953400e-01 | 9.990000e-01 | ▇▂▁▁▁ |
| numeric | AF_reference | 568966 | 0.9581183 | NA | NA | NA | NA | NA | 1.963496e-01 | 2.471053e-01 | 0.00000e+00 | 5.591000e-03 | 8.426520e-02 | 3.081070e-01 | 1.000000e+00 | ▇▂▁▁▁ |
| numeric | N | 0 | 1.0000000 | NA | NA | NA | NA | NA | 3.121020e+05 | 0.000000e+00 | 3.12102e+05 | 3.121020e+05 | 3.121020e+05 | 3.121020e+05 | 3.121020e+05 | ▁▁▇▁▁ |
Head and tail
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 692794 | rs530212009 | CA | C | -0.0017549 | 0.0026812 | 0.5127705 | 0.5127766 | 0.1105700 | 0.1894970 | 312102 |
| 1 | 693731 | rs12238997 | A | G | -0.0033314 | 0.0025331 | 0.1884799 | 0.1884604 | 0.1157900 | 0.1417730 | 312102 |
| 1 | 707522 | rs371890604 | G | C | -0.0023829 | 0.0028490 | 0.4029304 | 0.4029306 | 0.0972050 | 0.1293930 | 312102 |
| 1 | 717587 | rs144155419 | G | A | -0.0089468 | 0.0068035 | 0.1884998 | 0.1885001 | 0.0156560 | 0.0045926 | 312102 |
| 1 | 723329 | rs189787166 | A | T | 0.0283040 | 0.0201950 | 0.1610601 | 0.1610541 | 0.0017138 | 0.0003994 | 312102 |
| 1 | 730087 | rs148120343 | T | C | 0.0027032 | 0.0035281 | 0.4435596 | 0.4435624 | 0.0565080 | 0.0127796 | 312102 |
| 1 | 731718 | rs142557973 | T | C | -0.0024313 | 0.0024019 | 0.3114204 | 0.3114232 | 0.1217200 | 0.1543530 | 312102 |
| 1 | 732032 | rs61770163 | A | C | -0.0030546 | 0.0025630 | 0.2333399 | 0.2333371 | 0.1211100 | 0.1555510 | 312102 |
| 1 | 734349 | rs141242758 | T | C | -0.0024159 | 0.0024031 | 0.3147502 | 0.3147397 | 0.1209500 | 0.1525560 | 312102 |
| 1 | 740284 | rs61770167 | C | T | -0.0109680 | 0.0110340 | 0.3201998 | 0.3202139 | 0.0057506 | 0.0023962 | 312102 |
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 23 | 154923311 | rs141127553 | C | T | 0.0022680 | 0.0027370 | 0.4073099 | 0.4073056 | 0.056136 | 0.0309934 | 312102 |
| 23 | 154923374 | rs111332691 | T | A | -0.0011677 | 0.0030096 | 0.6980299 | 0.6980221 | 0.044702 | 0.0116556 | 312102 |
| 23 | 154925045 | rs509981 | C | T | 0.0036232 | 0.0014462 | 0.0122360 | 0.0122339 | 0.245850 | 0.3634440 | 312102 |
| 23 | 154925895 | rs538470 | C | T | 0.0039164 | 0.0014794 | 0.0081130 | 0.0081140 | 0.242170 | 0.3634440 | 312102 |
| 23 | 154927581 | rs644138 | G | A | 0.0036977 | 0.0013601 | 0.0065544 | 0.0065540 | 0.302350 | 0.4635760 | 312102 |
| 23 | 154929412 | rs557132 | C | T | 0.0035871 | 0.0014466 | 0.0131519 | 0.0131502 | 0.245700 | 0.3568210 | 312102 |
| 23 | 154929637 | rs35185538 | CT | C | 0.0034802 | 0.0015094 | 0.0211329 | 0.0211283 | 0.230090 | 0.3011920 | 312102 |
| 23 | 154929952 | rs4012982 | CAA | C | 0.0041165 | 0.0015212 | 0.0068097 | 0.0068081 | 0.239690 | 0.3165560 | 312102 |
| 23 | 154930230 | rs781880 | A | G | 0.0035981 | 0.0014464 | 0.0128609 | 0.0128599 | 0.246100 | 0.3618540 | 312102 |
| 23 | 154930487 | rs781879 | T | A | -0.0006308 | 0.0049571 | 0.8987500 | 0.8987459 | 0.019591 | 0.1263580 | 312102 |
bcf preview
1 692794 rs530212009 CA C . PASS AF=0.11057 ES:SE:LP:AF:SS:ID -0.0017549:0.0026812:0.290077:0.11057:312102:1_692794_CA_C
1 693731 rs12238997 A G . PASS AF=0.11579 ES:SE:LP:AF:SS:ID -0.0033314:0.0025331:0.724735:0.11579:312102:rs12238997
1 707522 rs371890604 G C . PASS AF=0.097205 ES:SE:LP:AF:SS:ID -0.0023829:0.002849:0.39477:0.097205:312102:rs371890604
1 717587 rs144155419 G A . PASS AF=0.015656 ES:SE:LP:AF:SS:ID -0.0089468:0.0068035:0.724689:0.015656:312102:rs144155419
1 723329 rs189787166 A T . PASS AF=0.0017138 ES:SE:LP:AF:SS:ID 0.028304:0.020195:0.793012:0.0017138:312102:rs189787166
1 730087 rs148120343 T C . PASS AF=0.056508 ES:SE:LP:AF:SS:ID 0.0027032:0.0035281:0.353048:0.056508:312102:rs148120343
1 731718 rs58276399 T C . PASS AF=0.12172 ES:SE:LP:AF:SS:ID -0.0024313:0.0024019:0.506653:0.12172:312102:rs58276399
1 732032 rs61770163 A C . PASS AF=0.12111 ES:SE:LP:AF:SS:ID -0.0030546:0.002563:0.632011:0.12111:312102:rs61770163
1 734349 rs141242758 T C . PASS AF=0.12095 ES:SE:LP:AF:SS:ID -0.0024159:0.0024031:0.502034:0.12095:312102:rs141242758
1 740284 rs61770167 C T . PASS AF=0.0057506 ES:SE:LP:AF:SS:ID -0.010968:0.011034:0.494579:0.0057506:312102:rs61770167
1 742813 rs112573343 C T . PASS AF=0.0018642 ES:SE:LP:AF:SS:ID -0.003128:0.020892:0.055034:0.0018642:312102:rs112573343
1 749963 rs529266287 T TAA . PASS AF=0.86987 ES:SE:LP:AF:SS:ID 0.0023833:0.0023698:0.502297:0.86987:312102:rs529266287
1 750230 rs190826124 G C . PASS AF=0.0015184 ES:SE:LP:AF:SS:ID -0.0011049:0.021524:0.0181542:0.0015184:312102:rs190826124
1 751343 rs28544273 T A . PASS AF=0.12283 ES:SE:LP:AF:SS:ID -0.001904:0.0023466:0.379718:0.12283:312102:rs28544273
1 751488 rs200141114 G GA . PASS AF=0.14265 ES:SE:LP:AF:SS:ID -0.0021154:0.0023195:0.441591:0.14265:312102:rs200141114
1 751756 rs28527770 T C . PASS AF=0.12294 ES:SE:LP:AF:SS:ID -0.0018768:0.0023434:0.373454:0.12294:312102:rs28527770
1 753405 rs3115860 C A . PASS AF=0.87099 ES:SE:LP:AF:SS:ID 0.0018315:0.0022836:0.374142:0.87099:312102:rs3115860
1 753425 rs3131970 T C . PASS AF=0.87559 ES:SE:LP:AF:SS:ID 0.0017244:0.0023217:0.339457:0.87559:312102:rs3131970
1 753541 rs2073813 G A . PASS AF=0.12856 ES:SE:LP:AF:SS:ID -0.0018593:0.0022891:0.380229:0.12856:312102:rs2073813
1 754105 rs12184325 C T . PASS AF=0.036378 ES:SE:LP:AF:SS:ID 0.00035823:0.0041532:0.0309291:0.036378:312102:rs12184325
1 754182 rs3131969 A G . PASS AF=0.87058 ES:SE:LP:AF:SS:ID 0.0018996:0.0022812:0.392545:0.87058:312102:rs3131969
1 754192 rs3131968 A G . PASS AF=0.87069 ES:SE:LP:AF:SS:ID 0.0018261:0.0022823:0.373013:0.87069:312102:rs3131968
1 754334 rs3131967 T C . PASS AF=0.87058 ES:SE:LP:AF:SS:ID 0.0019594:0.0022811:0.408524:0.87058:312102:rs3131967
1 754433 rs150578204 G A . PASS AF=0.0050665 ES:SE:LP:AF:SS:ID -0.0019225:0.011682:0.0608403:0.0050665:312102:rs150578204
1 754458 rs142682604 G T . PASS AF=0.0050345 ES:SE:LP:AF:SS:ID -0.0015086:0.011713:0.0469607:0.0050345:312102:rs142682604
1 755435 rs184270342 T G . PASS AF=0.0055257 ES:SE:LP:AF:SS:ID 0.0096566:0.011407:0.400925:0.0055257:312102:rs184270342
1 755890 rs3115858 A T . PASS AF=0.87067 ES:SE:LP:AF:SS:ID 0.0020369:0.0022772:0.430556:0.87067:312102:rs3115858
1 756434 rs61768170 G C . PASS AF=0.12589 ES:SE:LP:AF:SS:ID -0.002111:0.0023235:0.4394:0.12589:312102:rs61768170
1 756604 rs3131962 A G . PASS AF=0.87024 ES:SE:LP:AF:SS:ID 0.0019515:0.0022718:0.408568:0.87024:312102:rs3131962
1 757640 rs3115853 G A . PASS AF=0.86952 ES:SE:LP:AF:SS:ID 0.0020397:0.0022696:0.433186:0.86952:312102:rs3115853
1 757734 rs4951929 C T . PASS AF=0.87039 ES:SE:LP:AF:SS:ID 0.001956:0.0022737:0.409359:0.87039:312102:rs4951929
1 757936 rs4951862 C A . PASS AF=0.8704 ES:SE:LP:AF:SS:ID 0.0019565:0.0022738:0.409437:0.8704:312102:rs4951862
1 758144 rs3131956 A G . PASS AF=0.87041 ES:SE:LP:AF:SS:ID 0.0019554:0.0022739:0.409125:0.87041:312102:rs3131956
1 758626 rs3131954 C T . PASS AF=0.87085 ES:SE:LP:AF:SS:ID 0.0021521:0.0022797:0.461992:0.87085:312102:rs3131954
1 759293 rs10157329 T A . PASS AF=0.098704 ES:SE:LP:AF:SS:ID -0.001747:0.0026505:0.292583:0.098704:312102:rs10157329
1 759600 rs545998451 AGT A . PASS AF=0.0064042 ES:SE:LP:AF:SS:ID 0.0080825:0.01031:0.363422:0.0064042:312102:1_759600_AGT_A
1 759837 rs3115851 T A . PASS AF=0.87478 ES:SE:LP:AF:SS:ID 0.001918:0.0023141:0.390182:0.87478:312102:rs3115851
1 761732 rs2286139 C T . PASS AF=0.86413 ES:SE:LP:AF:SS:ID 0.0018329:0.0022692:0.377537:0.86413:312102:rs2286139
1 761752 rs1057213 C T . PASS AF=0.86954 ES:SE:LP:AF:SS:ID 0.0022803:0.002291:0.495434:0.86954:312102:rs1057213
1 762273 rs3115849 G A . PASS AF=0.86646 ES:SE:LP:AF:SS:ID 0.0021233:0.0022914:0.450862:0.86646:312102:rs3115849
1 762485 rs12095200 C A . PASS AF=0.098633 ES:SE:LP:AF:SS:ID -0.0019081:0.0027439:0.312641:0.098633:312102:rs12095200
1 762589 rs3115848 G C . PASS AF=0.87167 ES:SE:LP:AF:SS:ID 0.0017615:0.0023178:0.34943:0.87167:312102:rs3115848
1 762592 rs3131950 C G . PASS AF=0.87167 ES:SE:LP:AF:SS:ID 0.0017614:0.0023178:0.349411:0.87167:312102:rs3131950
1 762601 rs3131949 T C . PASS AF=0.87167 ES:SE:LP:AF:SS:ID 0.0017497:0.0023179:0.346459:0.87167:312102:rs3131949
1 762632 rs3131948 T A . PASS AF=0.87205 ES:SE:LP:AF:SS:ID 0.0017658:0.0023192:0.350256:0.87205:312102:rs3131948
1 764191 rs7515915 T G . PASS AF=0.12545 ES:SE:LP:AF:SS:ID -0.0019857:0.0023208:0.40647:0.12545:312102:rs7515915
1 766007 rs61768174 A C . PASS AF=0.10535 ES:SE:LP:AF:SS:ID -0.0016832:0.0025272:0.296382:0.10535:312102:rs61768174
1 766105 rs2519015 T A . PASS AF=0.85548 ES:SE:LP:AF:SS:ID 0.0019828:0.0022684:0.41788:0.85548:312102:rs2519015
1 767393 rs538667473 A C . PASS AF=0.0016292 ES:SE:LP:AF:SS:ID 0.026145:0.020261:0.705754:0.0016292:312102:rs538667473
1 768116 rs376645387 A AGTTTT . PASS AF=0.83851 ES:SE:LP:AF:SS:ID -0.00044722:0.0022345:0.075013:0.83851:312102:rs376645387