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-a-972,TotalVariants=123626,VariantsNotRead=9,HarmonisedVariants=123617,VariantsNotHarmonised=0,SwitchedAlleles=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>",
"gwas_harmonisation_command": "--json /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-972/ieu-a-972_data.json --ref /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/QC/genomes/b37/human_g1k_v37.fasta; 1.1.1",
"file_date": "2020-02-04T08:29:33.302657",
"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/ieu-a-import/processed/ieu-a-972/ieu-a-972.vcf.gz -O z /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-972/ieu-a-972_data.vcf.gz; Date=Tue Feb 4 09:00:30 2020",
"bcftools_viewVersion": "1.9-74-g6af271c+htslib-1.9-64-g226b4a8",
"bcftools_viewCommand": "view -h /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ieu-a-972/ieu-a-972.vcf.gz; Date=Sat May 9 19:52:11 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/ieu-a-import/processed/ieu-a-972/ieu-a-972.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/ieu-a-import/processed/ieu-a-972/ldsc.txt \
--w-ld-chr /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/reference/eur_w_ld_chr/
Beginning analysis at Tue Feb 4 10:11:12 2020
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-972/ieu-a-972.vcf.gz ...
Read summary statistics for 123617 SNPs.
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, 50534 SNPs remain.
After merging with regression SNP LD, 50534 SNPs remain.
WARNING: number of SNPs less than 200k; this is almost always bad.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 2.7077 (1.9525)
Lambda GC: 1.1168
Mean Chi^2: 1.1214
Intercept: 1.0783 (0.0214)
Ratio: 0.6446 (0.1761)
Analysis finished at Tue Feb 4 10:11:27 2020
Total time elapsed: 15.09sQC metrics
Metrics
Metrics
{
"af_correlation": 0.7839,
"inflation_factor": 1.1837,
"mean_EFFECT": 0.0055,
"n": 739,
"n_snps": 123617,
"n_clumped_hits": 0,
"n_p_sig": 0,
"n_mono": 0,
"n_ns": 0,
"n_mac": 3169,
"is_snpid_unique": true,
"n_miss_EFFECT": 0,
"n_miss_SE": 0,
"n_miss_PVAL": 0,
"n_miss_AF": 1184,
"n_miss_AF_reference": 827,
"n_est": 739.7228,
"ratio_se_n": 1.0005,
"mean_diff": 0.0205,
"ratio_diff": 1.82,
"sd_y_est1": 1.9638,
"sd_y_est2": 1.9647,
"r2_sum1": 0,
"r2_sum2": 0,
"r2_sum3": 0,
"r2_sum4": 0,
"ldsc_nsnp_merge_refpanel_ld": 50534,
"ldsc_nsnp_merge_regression_ld": 50534,
"ldsc_observed_scale_h2_beta": 2.7077,
"ldsc_observed_scale_h2_se": 1.9525,
"ldsc_intercept_beta": 1.0783,
"ldsc_intercept_se": 0.0214,
"ldsc_lambda_gc": 1.1168,
"ldsc_mean_chisq": 1.1214,
"ldsc_ratio": 0.645
}
Flags
| name | value |
|---|---|
| af_correlation | FALSE |
| inflation_factor | FALSE |
| n | TRUE |
| is_snpid_non_unique | FALSE |
| mean_EFFECT_nonfinite | FALSE |
| mean_EFFECT_05 | FALSE |
| mean_EFFECT_01 | FALSE |
| mean_chisq | FALSE |
| n_p_sig | FALSE |
| miss_EFFECT | FALSE |
| miss_SE | FALSE |
| miss_PVAL | FALSE |
| ldsc_ratio | TRUE |
| 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 | 1.000000 | 5 | 25 | 0 | 123617 | 0 | NA | NA | NA | NA | NA | NA | NA | NA |
| character | REF | 0 | 1.000000 | 1 | 1 | 0 | 4 | 0 | NA | NA | NA | NA | NA | NA | NA | NA |
| character | ALT | 0 | 1.000000 | 1 | 1 | 0 | 4 | 0 | NA | NA | NA | NA | NA | NA | NA | NA |
| numeric | CHROM | 0 | 1.000000 | NA | NA | NA | NA | NA | 8.087464e+00 | 5.769597e+00 | 1.00000e+00 | 3.000000e+00 | 6.000000e+00 | 1.200000e+01 | 2.200000e+01 | ▇▅▃▂▂ |
| numeric | POS | 0 | 1.000000 | NA | NA | NA | NA | NA | 7.901125e+07 | 5.778993e+07 | 6.34110e+04 | 3.290726e+07 | 6.220920e+07 | 1.176363e+08 | 2.492107e+08 | ▇▅▃▂▁ |
| numeric | EFFECT | 0 | 1.000000 | NA | NA | NA | NA | NA | 5.500200e-03 | 6.938452e-01 | -1.95340e+01 | -1.138260e-01 | 3.518000e-04 | 1.164190e-01 | 1.548690e+02 | ▇▁▁▁▁ |
| numeric | SE | 0 | 1.000000 | NA | NA | NA | NA | NA | 2.437835e-01 | 4.665800e-01 | 9.57113e-02 | 1.102960e-01 | 1.359580e-01 | 2.144680e-01 | 9.428900e+01 | ▇▁▁▁▁ |
| numeric | PVAL | 0 | 1.000000 | NA | NA | NA | NA | NA | 4.733697e-01 | 2.941426e-01 | 1.00000e-07 | 2.126949e-01 | 4.630565e-01 | 7.282458e-01 | 9.999980e-01 | ▇▇▆▆▆ |
| numeric | PVAL_ztest | 0 | 1.000000 | NA | NA | NA | NA | NA | 4.732529e-01 | 2.942450e-01 | 1.00000e-07 | 2.124584e-01 | 4.629811e-01 | 7.282426e-01 | 9.999978e-01 | ▇▇▆▆▆ |
| numeric | AF | 1184 | 0.990422 | NA | NA | NA | NA | NA | 3.178954e-01 | 2.829672e-01 | 1.46200e-03 | 7.749000e-02 | 2.295000e-01 | 5.088000e-01 | 9.985380e-01 | ▇▃▂▂▂ |
| numeric | AF_reference | 827 | 0.993310 | NA | NA | NA | NA | NA | 2.882265e-01 | 2.573936e-01 | 1.99700e-04 | 7.567890e-02 | 2.082670e-01 | 4.482830e-01 | 1.000000e+00 | ▇▃▂▂▁ |
| numeric | N | 0 | 1.000000 | NA | NA | NA | NA | NA | 7.390000e+02 | 0.000000e+00 | 7.39000e+02 | 7.390000e+02 | 7.390000e+02 | 7.390000e+02 | 7.390000e+02 | ▁▁▇▁▁ |
Head and tail
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 1118275 | rs61733845 | C | T | 0.1415570 | 0.167431 | 0.3979550 | 0.3978514 | 0.09795 | 0.185703 | 739 |
| 1 | 1120431 | rs1320571 | G | A | 0.1374490 | 0.165435 | 0.4061730 | 0.4060675 | 0.10820 | 0.185304 | 739 |
| 1 | 1135242 | rs9729550 | A | C | -0.0057612 | 0.105540 | 0.9564670 | 0.9564670 | 0.34500 | 0.551917 | 739 |
| 1 | 1140435 | rs1815606 | G | T | 0.0212465 | 0.100075 | 0.8318760 | 0.8318685 | 0.43860 | 0.712061 | 739 |
| 1 | 1163804 | rs7515488 | C | T | 0.1651840 | 0.143657 | 0.2503427 | 0.2502057 | 0.14470 | 0.186901 | 739 |
| 1 | 1165310 | rs11260562 | G | A | -0.1996060 | 0.203532 | 0.3268820 | 0.3267355 | 0.07310 | 0.101837 | 739 |
| 1 | 1173611 | rs6697886 | G | A | 0.1418880 | 0.148717 | 0.3401308 | 0.3400429 | 0.13160 | 0.220647 | 739 |
| 1 | 1186502 | rs6603785 | A | T | 0.0831447 | 0.160051 | 0.6034607 | 0.6034199 | 0.11400 | 0.246206 | 739 |
| 1 | 1194804 | rs11804831 | T | C | -0.0893148 | 0.104467 | 0.3926748 | 0.3925749 | 0.35230 | 0.685903 | 739 |
| 1 | 1218086 | rs6603788 | C | T | -0.1403310 | 0.140918 | 0.3194596 | 0.3193306 | 0.16520 | 0.469449 | 739 |
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 22 | 50966914 | rs470119 | T | C | 0.0129330 | 0.110443 | 0.9067791 | 0.9067799 | 0.6857 | 0.5547120 | 739 |
| 22 | 50971752 | rs131794 | A | C | -0.0654140 | 0.129740 | 0.6141974 | 0.6141258 | 0.8056 | 0.8326680 | 739 |
| 22 | 50988193 | rs131779 | A | G | -0.0525105 | 0.110398 | 0.6343574 | 0.6343257 | 0.6477 | 0.5802720 | 739 |
| 22 | 50999182 | rs140518 | C | T | -0.1261830 | 0.115017 | 0.2728048 | 0.2726059 | 0.7251 | 0.7655750 | 739 |
| 22 | 51078251 | rs4040041 | C | T | -0.1030630 | 0.105613 | 0.3293002 | 0.3291362 | 0.4386 | 0.4666530 | 739 |
| 22 | 51094926 | rs9616810 | C | T | -0.1089090 | 0.123591 | 0.3783337 | 0.3782069 | 0.2456 | 0.2224440 | 739 |
| 22 | 51105556 | rs9616812 | C | T | 0.0255733 | 0.101460 | 0.8010011 | 0.8010001 | 0.4430 | 0.3628190 | 739 |
| 22 | 51109992 | rs9628185 | T | C | -0.0112981 | 0.100978 | 0.9109140 | 0.9109132 | 0.4561 | 0.4053510 | 739 |
| 22 | 51134186 | rs8135777 | A | G | 1.1448100 | 2.231460 | 0.6078816 | 0.6079291 | NA | 0.0273562 | 739 |
| 22 | 51156666 | rs9628187 | C | T | -0.0178030 | 0.142856 | 0.9008239 | 0.9008228 | 0.1652 | 0.1299920 | 739 |
bcf preview
1 1118275 rs61733845 C T . PASS AF=0.09795 ES:SE:LP:AF:SS:ID 0.141557:0.167431:0.400166:0.09795:739:rs61733845
1 1120431 rs1320571 G A . PASS AF=0.1082 ES:SE:LP:AF:SS:ID 0.137449:0.165435:0.391289:0.1082:739:rs1320571
1 1135242 rs9729550 A C . PASS AF=0.345 ES:SE:LP:AF:SS:ID -0.00576118:0.10554:0.01933:0.345:739:rs9729550
1 1140435 rs1815606 G T . PASS AF=0.4386 ES:SE:LP:AF:SS:ID 0.0212465:0.100075:0.0799414:0.4386:739:rs1815606
1 1163804 rs7515488 C T . PASS AF=0.1447 ES:SE:LP:AF:SS:ID 0.165184:0.143657:0.601465:0.1447:739:rs7515488
1 1165310 rs11260562 G A . PASS AF=0.0731 ES:SE:LP:AF:SS:ID -0.199606:0.203532:0.485609:0.0731:739:rs11260562
1 1173611 rs6697886 G A . PASS AF=0.1316 ES:SE:LP:AF:SS:ID 0.141888:0.148717:0.468354:0.1316:739:rs6697886
1 1186502 rs6603785 A T . PASS AF=0.114 ES:SE:LP:AF:SS:ID 0.0831447:0.160051:0.219351:0.114:739:rs6603785
1 1194804 rs11804831 T C . PASS AF=0.3523 ES:SE:LP:AF:SS:ID -0.0893148:0.104467:0.405967:0.3523:739:rs11804831
1 1218086 rs6603788 C T . PASS AF=0.1652 ES:SE:LP:AF:SS:ID -0.140331:0.140918:0.495584:0.1652:739:rs6603788
1 1227897 rs3737721 A G . PASS AF=0.06871 ES:SE:LP:AF:SS:ID -0.505912:0.225901:1.59598:0.06871:739:rs3737721
1 1231656 rs1749951 G A . PASS AF=0.05848 ES:SE:LP:AF:SS:ID 0.272591:0.192521:0.804419:0.05848:739:rs1749951
1 1233941 rs1739855 T C . PASS AF=0.1827 ES:SE:LP:AF:SS:ID -0.118439:0.132957:0.42812:0.1827:739:rs1739855
1 1241529 rs1536168 A G . PASS AF=0.91228 ES:SE:LP:AF:SS:ID -0.124313:0.165371:0.34464:0.91228:739:rs1536168
1 1242468 rs2274264 G A . PASS AF=0.06433 ES:SE:LP:AF:SS:ID -0.45324:0.228873:1.31922:0.06433:739:rs2274264
1 1247494 rs12103 T C . PASS AF=0.6857 ES:SE:LP:AF:SS:ID 0.0722188:0.108585:0.295807:0.6857:739:rs12103
1 1249187 rs12142199 G A . PASS AF=0.6769 ES:SE:LP:AF:SS:ID 0.0954124:0.108258:0.422235:0.6769:739:rs12142199
1 1254255 rs62623580 G A . PASS AF=0.04386 ES:SE:LP:AF:SS:ID -0.0712077:0.255415:0.107687:0.04386:739:rs62623580
1 1335790 rs1240708 A G . PASS AF=0.3114 ES:SE:LP:AF:SS:ID -0.0972809:0.111502:0.416765:0.3114:739:rs1240708
1 1493727 rs880051 G A . PASS AF=0.3816 ES:SE:LP:AF:SS:ID 0.0375228:0.105793:0.140955:0.3816:739:rs880051
1 1497824 rs2296716 C T . PASS AF=0.1784 ES:SE:LP:AF:SS:ID 0.0155512:0.141171:0.0398699:0.1784:739:rs2296716
1 1611995 rs4074196 A G . PASS AF=0.3713 ES:SE:LP:AF:SS:ID 0.0413063:0.105586:0.157602:0.3713:739:rs4074196
1 1706160 rs7531583 A G . PASS AF=0.5673 ES:SE:LP:AF:SS:ID 0.0501823:0.103882:0.201287:0.5673:739:rs7531583
1 1721479 rs2272908 C T . PASS AF=0.348 ES:SE:LP:AF:SS:ID -0.0983152:0.106556:0.448238:0.348:739:rs2272908
1 1723031 rs9660180 G A . PASS AF=0.348 ES:SE:LP:AF:SS:ID -0.0983152:0.106556:0.448238:0.348:739:rs9660180
1 1781220 rs6681938 T C . PASS AF=0.2135 ES:SE:LP:AF:SS:ID -0.0300645:0.125244:0.0913558:0.2135:739:rs6681938
1 1838516 rs2377037 C A . PASS AF=0.2222 ES:SE:LP:AF:SS:ID 0.175046:0.120002:0.838998:0.2222:739:rs2377037
1 1840038 rs2474461 T C . PASS AF=0.8874 ES:SE:LP:AF:SS:ID 0.128774:0.164037:0.363959:0.8874:739:rs2474461
1 1853288 rs1884454 G T . PASS AF=0.2339 ES:SE:LP:AF:SS:ID 0.109188:0.118817:0.44586:0.2339:739:rs1884454
1 1855319 rs2295362 C T . PASS AF=0.1155 ES:SE:LP:AF:SS:ID -0.0936867:0.162319:0.248826:0.1155:739:rs2295362
1 1871337 rs16824543 G A . PASS AF=0.117 ES:SE:LP:AF:SS:ID -0.108677:0.161063:0.301117:0.117:739:rs16824543
1 1873625 rs12758705 G A . PASS AF=0.2266 ES:SE:LP:AF:SS:ID 0.115545:0.119998:0.474007:0.2266:739:rs12758705
1 1881070 rs4648596 G A . PASS AF=0.08626 ES:SE:LP:AF:SS:ID -0.0466509:0.188122:0.0946619:0.08626:739:rs4648596
1 1888193 rs3820011 C A . PASS AF=0.2442 ES:SE:LP:AF:SS:ID 0.156525:0.119102:0.723729:0.2442:739:rs3820011
1 2024064 rs2459994 C T . PASS AF=0.2991 ES:SE:LP:AF:SS:ID 0.0926666:0.113568:0.382337:0.2991:739:rs2459994
1 2146966 rs7512482 T C . PASS AF=0.2295 ES:SE:LP:AF:SS:ID 0.112949:0.120078:0.459652:0.2295:739:rs7512482
1 2202774 rs6673129 C T . PASS AF=0.1681 ES:SE:LP:AF:SS:ID 0.186699:0.134568:0.780861:0.1681:739:rs6673129
1 2229478 rs12562937 C T . PASS AF=0.1711 ES:SE:LP:AF:SS:ID 0.0433926:0.137758:0.123331:0.1711:739:rs12562937
1 2283896 rs2840528 A G . PASS AF=0.3421 ES:SE:LP:AF:SS:ID -0.0844577:0.109352:0.356549:0.3421:739:rs2840528
1 2290143 rs34587196 G A . PASS AF=0.01023 ES:SE:LP:AF:SS:ID 0.677579:0.445052:0.892183:0.01023:739:rs34587196
1 2404256 rs2494626 C T . PASS AF=0.3202 ES:SE:LP:AF:SS:ID 0.0311582:0.11127:0.1082:0.3202:739:rs2494626
1 2407781 rs78504402 C T . PASS AF=0.04386 ES:SE:LP:AF:SS:ID 0.100874:0.247804:0.164964:0.04386:739:rs78504402
1 2408471 rs115996655 G A . PASS AF=0.001462 ES:SE:LP:AF:SS:ID -3.13999:2.81636:0.576666:0.001462:739:rs115996655
1 2408834 rs11588930 G A . PASS AF=0.09064 ES:SE:LP:AF:SS:ID 0.184741:0.165781:0.576197:0.09064:739:rs11588930
1 2409892 rs12727342 A G . PASS AF=0.6477 ES:SE:LP:AF:SS:ID -0.162962:0.104181:0.928059:0.6477:739:rs12727342
1 2410789 rs11799501 C T . PASS AF=0.636 ES:SE:LP:AF:SS:ID -0.134846:0.104284:0.707372:0.636:739:rs11799501
1 2412279 rs4648638 A T . PASS AF=0.3567 ES:SE:LP:AF:SS:ID 0.171336:0.103517:1.00807:0.3567:739:rs4648638
1 2412293 rs12731186 C T . PASS AF=0.08918 ES:SE:LP:AF:SS:ID -0.0335033:0.178417:0.0700449:0.08918:739:rs12731186
1 2413166 rs115810747 A G . PASS AF=0.004386 ES:SE:LP:AF:SS:ID 0.646944:0.689703:0.457827:0.004386:739:rs115810747
1 2413464 rs114424485 G C . PASS AF=0.001462 ES:SE:LP:AF:SS:ID -3.13999:2.81636:0.576666:0.001462:739:rs114424485