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-1747_5,TotalVariants=13586530,VariantsNotRead=0,HarmonisedVariants=13586530,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-1747_5/ukb-d-1747_5_data.json --ref /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/QC/genomes/b37/human_g1k_v37.fasta; 1.1.1",
"file_date": "2019-11-25T15:33:28.852980",
"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-1747_5/ukb-d-1747_5.vcf.gz -O z /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-1747_5/ukb-d-1747_5_data.vcf.gz; Date=Mon Nov 25 16:24:24 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-1747_5/ukb-d-1747_5.vcf.gz; Date=Sun May 10 09:17:55 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-1747_5/ukb-d-1747_5.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-1747_5/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 16:55:09 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-1747_5/ukb-d-1747_5.vcf.gz ...
Read summary statistics for 13586530 SNPs.
Dropped 12711 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, 1283504 SNPs remain.
After merging with regression SNP LD, 1283504 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0586 (0.0148)
Lambda GC: 1.1349
Mean Chi^2: 1.4218
Intercept: 1.0401 (0.0098)
Ratio: 0.095 (0.0232)
Analysis finished at Mon Nov 25 16:57:27 2019
Total time elapsed: 2.0m:18.27sQC metrics
Metrics
Metrics
{
"af_correlation": 0.9521,
"inflation_factor": 1.0916,
"mean_EFFECT": 6.8972e-06,
"n": 360270,
"n_snps": 13586530,
"n_clumped_hits": 67,
"n_p_sig": 13698,
"n_mono": 0,
"n_ns": 1251807,
"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": 569284,
"n_est": 361644.1047,
"ratio_se_n": 1.0019,
"mean_diff": 0,
"ratio_diff": 106.0413,
"sd_y_est1": 0.2026,
"sd_y_est2": 0.203,
"r2_sum1": 0.0017,
"r2_sum2": 0.0407,
"r2_sum3": 0.0405,
"r2_sum4": 0.0397,
"ldsc_nsnp_merge_refpanel_ld": 1283504,
"ldsc_nsnp_merge_regression_ld": 1283504,
"ldsc_observed_scale_h2_beta": 0.0586,
"ldsc_observed_scale_h2_se": 0.0148,
"ldsc_intercept_beta": 1.0401,
"ldsc_intercept_se": 0.0098,
"ldsc_lambda_gc": 1.1349,
"ldsc_mean_chisq": 1.4218,
"ldsc_ratio": 0.0951
}
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 | 13574483 | 0 | NA | NA | NA | NA | NA | NA | NA | NA |
| character | REF | 0 | 1.0000000 | 1 | 100 | 0 | 57082 | 0 | NA | NA | NA | NA | NA | NA | NA | NA |
| character | ALT | 0 | 1.0000000 | 1 | 342 | 0 | 33336 | 0 | NA | NA | NA | NA | NA | NA | NA | NA |
| numeric | CHROM | 0 | 1.0000000 | NA | NA | NA | NA | NA | 9.051332e+00 | 6.184976e+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 | 7.902492e+07 | 5.591479e+07 | 3.02000e+02 | 3.293086e+07 | 7.013828e+07 | 1.148589e+08 | 2.492309e+08 | ▇▆▅▂▁ |
| numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | 6.900000e-06 | 2.847800e-03 | -8.41459e-02 | -7.873000e-04 | -4.800000e-06 | 7.738000e-04 | 1.069690e-01 | ▁▁▇▁▁ |
| numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | 2.005800e-03 | 1.934800e-03 | 3.92500e-04 | 5.710000e-04 | 1.052300e-03 | 2.882600e-03 | 9.732500e-03 | ▇▂▁▁▁ |
| numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | 4.852622e-01 | 2.935717e-01 | 0.00000e+00 | 2.279570e-01 | 4.809988e-01 | 7.396087e-01 | 1.000000e+00 | ▇▇▇▇▇ |
| numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | 4.852618e-01 | 2.935719e-01 | 0.00000e+00 | 2.279563e-01 | 4.809988e-01 | 7.396081e-01 | 9.999998e-01 | ▇▇▇▇▇ |
| numeric | AF | 0 | 1.0000000 | NA | NA | NA | NA | NA | 1.908023e-01 | 2.544021e-01 | 1.00000e-03 | 7.429300e-03 | 6.003020e-02 | 2.953080e-01 | 9.989990e-01 | ▇▂▁▁▁ |
| numeric | AF_reference | 569284 | 0.9580994 | NA | NA | NA | NA | NA | 1.963336e-01 | 2.471006e-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 | 3.602700e+05 | 0.000000e+00 | 3.60270e+05 | 3.602700e+05 | 3.602700e+05 | 3.602700e+05 | 3.602700e+05 | ▁▁▇▁▁ |
Head and tail
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 692794 | rs530212009 | CA | C | -0.0009932 | 0.0008358 | 0.2347351 | 0.2347342 | 0.1106500 | 0.1894970 | 360270 |
| 1 | 693731 | rs12238997 | A | G | -0.0000698 | 0.0007898 | 0.9295411 | 0.9295408 | 0.1158380 | 0.1417730 | 360270 |
| 1 | 707522 | rs371890604 | G | C | 0.0004109 | 0.0008880 | 0.6435585 | 0.6435578 | 0.0972910 | 0.1293930 | 360270 |
| 1 | 717587 | rs144155419 | G | A | -0.0019896 | 0.0021178 | 0.3475042 | 0.3475032 | 0.0157019 | 0.0045926 | 360270 |
| 1 | 723329 | rs189787166 | A | T | -0.0008386 | 0.0062575 | 0.8933929 | 0.8933929 | 0.0017308 | 0.0003994 | 360270 |
| 1 | 730087 | rs148120343 | T | C | -0.0009629 | 0.0011004 | 0.3815566 | 0.3815572 | 0.0564472 | 0.0127796 | 360270 |
| 1 | 731718 | rs142557973 | T | C | 0.0002762 | 0.0007490 | 0.7122837 | 0.7122824 | 0.1217410 | 0.1543530 | 360270 |
| 1 | 732032 | rs61770163 | A | C | 0.0000129 | 0.0007990 | 0.9871170 | 0.9871171 | 0.1211730 | 0.1555510 | 360270 |
| 1 | 734349 | rs141242758 | T | C | 0.0002038 | 0.0007494 | 0.7857077 | 0.7857079 | 0.1209690 | 0.1525560 | 360270 |
| 1 | 740284 | rs61770167 | C | T | 0.0019973 | 0.0034271 | 0.5600335 | 0.5600341 | 0.0057907 | 0.0023962 | 360270 |
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 23 | 154923311 | rs141127553 | C | T | -0.0010943 | 0.0008658 | 0.2062719 | 0.2062704 | 0.0561460 | 0.0309934 | 360270 |
| 23 | 154923374 | rs111332691 | T | A | -0.0020233 | 0.0009513 | 0.0334357 | 0.0334346 | 0.0447845 | 0.0116556 | 360270 |
| 23 | 154925045 | rs509981 | C | T | -0.0000174 | 0.0004577 | 0.9696181 | 0.9696179 | 0.2456300 | 0.3634440 | 360270 |
| 23 | 154925895 | rs538470 | C | T | -0.0001036 | 0.0004682 | 0.8249380 | 0.8249385 | 0.2419380 | 0.3634440 | 360270 |
| 23 | 154927581 | rs644138 | G | A | -0.0002914 | 0.0004304 | 0.4984332 | 0.4984334 | 0.3021610 | 0.4635760 | 360270 |
| 23 | 154929412 | rs557132 | C | T | -0.0000246 | 0.0004578 | 0.9570810 | 0.9570808 | 0.2454820 | 0.3568210 | 360270 |
| 23 | 154929637 | rs35185538 | CT | C | -0.0002834 | 0.0004778 | 0.5530444 | 0.5530437 | 0.2297100 | 0.3011920 | 360270 |
| 23 | 154929952 | rs4012982 | CAA | C | 0.0000250 | 0.0004815 | 0.9585611 | 0.9585613 | 0.2394580 | 0.3165560 | 360270 |
| 23 | 154930230 | rs781880 | A | G | -0.0000292 | 0.0004578 | 0.9490990 | 0.9490986 | 0.2458930 | 0.3618540 | 360270 |
| 23 | 154930487 | rs781879 | T | A | -0.0015964 | 0.0015696 | 0.3091320 | 0.3091304 | 0.0195732 | 0.1263580 | 360270 |
bcf preview
1 692794 rs530212009 CA C . PASS AF=0.11065 ES:SE:LP:AF:SS:ID -0.000993186:0.000835838:0.629422:0.11065:360270:1_692794_CA_C
1 693731 rs12238997 A G . PASS AF=0.115838 ES:SE:LP:AF:SS:ID -6.98354e-05:0.000789791:0.0317314:0.115838:360270:rs12238997
1 707522 rs371890604 G C . PASS AF=0.097291 ES:SE:LP:AF:SS:ID 0.000410903:0.000887997:0.191412:0.097291:360270:rs371890604
1 717587 rs144155419 G A . PASS AF=0.0157019 ES:SE:LP:AF:SS:ID -0.0019896:0.00211785:0.45904:0.0157019:360270:rs144155419
1 723329 rs189787166 A T . PASS AF=0.00173076 ES:SE:LP:AF:SS:ID -0.000838587:0.00625754:0.0489575:0.00173076:360270:rs189787166
1 730087 rs148120343 T C . PASS AF=0.0564472 ES:SE:LP:AF:SS:ID -0.00096291:0.00110043:0.418441:0.0564472:360270:rs148120343
1 731718 rs58276399 T C . PASS AF=0.121741 ES:SE:LP:AF:SS:ID 0.00027624:0.000749039:0.147347:0.121741:360270:rs58276399
1 732032 rs61770163 A C . PASS AF=0.121173 ES:SE:LP:AF:SS:ID 1.29017e-05:0.000799017:0.00563137:0.121173:360270:rs61770163
1 734349 rs141242758 T C . PASS AF=0.120969 ES:SE:LP:AF:SS:ID 0.000203764:0.00074944:0.104739:0.120969:360270:rs141242758
1 740284 rs61770167 C T . PASS AF=0.00579066 ES:SE:LP:AF:SS:ID 0.0019973:0.00342713:0.251786:0.00579066:360270:rs61770167
1 742813 rs112573343 C T . PASS AF=0.00187672 ES:SE:LP:AF:SS:ID -0.00500031:0.00647832:0.356348:0.00187672:360270:rs112573343
1 749963 rs529266287 T TAA . PASS AF=0.869737 ES:SE:LP:AF:SS:ID 4.23876e-05:0.000738827:0.0203383:0.869737:360270:rs529266287
1 750230 rs190826124 G C . PASS AF=0.00153102 ES:SE:LP:AF:SS:ID -0.000463873:0.00668715:0.0247075:0.00153102:360270:rs190826124
1 751343 rs28544273 T A . PASS AF=0.122922 ES:SE:LP:AF:SS:ID 0.000123675:0.000731721:0.0625914:0.122922:360270:rs28544273
1 751488 rs200141114 G GA . PASS AF=0.142717 ES:SE:LP:AF:SS:ID -8.48591e-05:0.000723257:0.0425848:0.142717:360270:rs200141114
1 751756 rs28527770 T C . PASS AF=0.123037 ES:SE:LP:AF:SS:ID 0.000132136:0.000730703:0.0672736:0.123037:360270:rs28527770
1 753405 rs3115860 C A . PASS AF=0.87088 ES:SE:LP:AF:SS:ID -0.000126186:0.000712044:0.0658355:0.87088:360270:rs3115860
1 753425 rs3131970 T C . PASS AF=0.875466 ES:SE:LP:AF:SS:ID -1.21282e-05:0.000723858:0.0058448:0.875466:360270:rs3131970
1 753541 rs2073813 G A . PASS AF=0.128643 ES:SE:LP:AF:SS:ID 0.000112325:0.00071382:0.0580098:0.128643:360270:rs2073813
1 754105 rs12184325 C T . PASS AF=0.0363464 ES:SE:LP:AF:SS:ID -0.000106407:0.00129531:0.0294072:0.0363464:360270:rs12184325
1 754182 rs3131969 A G . PASS AF=0.870474 ES:SE:LP:AF:SS:ID -6.1467e-05:0.000711305:0.0309864:0.870474:360270:rs3131969
1 754192 rs3131968 A G . PASS AF=0.870579 ES:SE:LP:AF:SS:ID -4.2198e-05:0.00071163:0.021037:0.870579:360270:rs3131968
1 754334 rs3131967 T C . PASS AF=0.870471 ES:SE:LP:AF:SS:ID -5.80071e-05:0.000711278:0.0291875:0.870471:360270:rs3131967
1 754433 rs150578204 G A . PASS AF=0.00505041 ES:SE:LP:AF:SS:ID 0.00174836:0.0036491:0.199384:0.00505041:360270:rs150578204
1 754458 rs142682604 G T . PASS AF=0.00501736 ES:SE:LP:AF:SS:ID 0.00180326:0.00365886:0.206125:0.00501736:360270:rs142682604
1 755435 rs184270342 T G . PASS AF=0.00558719 ES:SE:LP:AF:SS:ID 0.0018518:0.00353633:0.22147:0.00558719:360270:rs184270342
1 755890 rs3115858 A T . PASS AF=0.870552 ES:SE:LP:AF:SS:ID -0.000103978:0.000710022:0.0537585:0.870552:360270:rs3115858
1 756434 rs61768170 G C . PASS AF=0.125993 ES:SE:LP:AF:SS:ID 0.000212823:0.000724485:0.114105:0.125993:360270:rs61768170
1 756604 rs3131962 A G . PASS AF=0.870117 ES:SE:LP:AF:SS:ID -8.15171e-05:0.000708314:0.0417339:0.870117:360270:rs3131962
1 757640 rs3115853 G A . PASS AF=0.869406 ES:SE:LP:AF:SS:ID -1.41252e-05:0.00070767:0.0069718:0.869406:360270:rs3115853
1 757734 rs4951929 C T . PASS AF=0.870272 ES:SE:LP:AF:SS:ID -9.30555e-05:0.000708925:0.0479019:0.870272:360270:rs4951929
1 757936 rs4951862 C A . PASS AF=0.870278 ES:SE:LP:AF:SS:ID -9.22637e-05:0.000708976:0.0474701:0.870278:360270:rs4951862
1 758144 rs3131956 A G . PASS AF=0.870287 ES:SE:LP:AF:SS:ID -9.39034e-05:0.000708998:0.0483556:0.870287:360270:rs3131956
1 758626 rs3131954 C T . PASS AF=0.870728 ES:SE:LP:AF:SS:ID -0.000112187:0.000710802:0.0581955:0.870728:360270:rs3131954
1 759293 rs10157329 T A . PASS AF=0.0988323 ES:SE:LP:AF:SS:ID 0.000373514:0.000826053:0.18632:0.0988323:360270:rs10157329
1 759600 rs545998451 AGT A . PASS AF=0.00647755 ES:SE:LP:AF:SS:ID 0.00345561:0.00319471:0.55377:0.00647755:360270:1_759600_AGT_A
1 759837 rs3115851 T A . PASS AF=0.874628 ES:SE:LP:AF:SS:ID -7.31853e-05:0.000721406:0.0365923:0.874628:360270:rs3115851
1 761732 rs2286139 C T . PASS AF=0.864021 ES:SE:LP:AF:SS:ID -8.17207e-05:0.00070744:0.0418969:0.864021:360270:rs2286139
1 761752 rs1057213 C T . PASS AF=0.869415 ES:SE:LP:AF:SS:ID -7.55224e-05:0.000714307:0.0382003:0.869415:360270:rs1057213
1 762273 rs3115849 G A . PASS AF=0.866359 ES:SE:LP:AF:SS:ID 7.50333e-05:0.000714447:0.0379348:0.866359:360270:rs3115849
1 762485 rs12095200 C A . PASS AF=0.0987912 ES:SE:LP:AF:SS:ID 0.000345916:0.000855327:0.163739:0.0987912:360270:rs12095200
1 762589 rs3115848 G C . PASS AF=0.871548 ES:SE:LP:AF:SS:ID 8.52385e-05:0.000722598:0.0428248:0.871548:360270:rs3115848
1 762592 rs3131950 C G . PASS AF=0.871548 ES:SE:LP:AF:SS:ID 8.52111e-05:0.000722598:0.04281:0.871548:360270:rs3131950
1 762601 rs3131949 T C . PASS AF=0.871547 ES:SE:LP:AF:SS:ID 8.44096e-05:0.000722611:0.0423884:0.871547:360270:rs3131949
1 762632 rs3131948 T A . PASS AF=0.871922 ES:SE:LP:AF:SS:ID 4.10579e-05:0.000723025:0.0201263:0.871922:360270:rs3131948
1 764191 rs7515915 T G . PASS AF=0.12557 ES:SE:LP:AF:SS:ID 0.000140474:0.000723584:0.0725937:0.12557:360270:rs7515915
1 766007 rs61768174 A C . PASS AF=0.105413 ES:SE:LP:AF:SS:ID 0.000391042:0.000787785:0.20787:0.105413:360270:rs61768174
1 766105 rs2519015 T A . PASS AF=0.855359 ES:SE:LP:AF:SS:ID -5.56737e-05:0.000707165:0.028145:0.855359:360270:rs2519015
1 767393 rs538667473 A C . PASS AF=0.00165156 ES:SE:LP:AF:SS:ID -0.0036876:0.00627104:0.254529:0.00165156:360270:rs538667473
1 768116 rs376645387 A AGTTTT . PASS AF=0.838382 ES:SE:LP:AF:SS:ID 0.000617917:0.000696831:0.425722:0.838382:360270:rs376645387