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-b:7196,TotalVariants=9851866,VariantsNotRead=0,HarmonisedVariants=9851866,VariantsNotHarmonised=0,SwitchedAlleles=9851866,TotalControls=9009,TotalCases=1478,StudyType=CaseControl>",
"contig": "<ID=1,length=249250621,assembly=GRCh37>",
"contig.1": "<ID=2,length=243199373,assembly=GRCh37>",
"contig.2": "<ID=3,length=198022430,assembly=GRCh37>",
"contig.3": "<ID=4,length=191154276,assembly=GRCh37>",
"contig.4": "<ID=5,length=180915260,assembly=GRCh37>",
"contig.5": "<ID=6,length=171115067,assembly=GRCh37>",
"contig.6": "<ID=7,length=159138663,assembly=GRCh37>",
"contig.7": "<ID=8,length=146364022,assembly=GRCh37>",
"contig.8": "<ID=9,length=141213431,assembly=GRCh37>",
"contig.9": "<ID=10,length=135534747,assembly=GRCh37>",
"contig.10": "<ID=11,length=135006516,assembly=GRCh37>",
"contig.11": "<ID=12,length=133851895,assembly=GRCh37>",
"contig.12": "<ID=13,length=115169878,assembly=GRCh37>",
"contig.13": "<ID=14,length=107349540,assembly=GRCh37>",
"contig.14": "<ID=15,length=102531392,assembly=GRCh37>",
"contig.15": "<ID=16,length=90354753,assembly=GRCh37>",
"contig.16": "<ID=17,length=81195210,assembly=GRCh37>",
"contig.17": "<ID=18,length=78077248,assembly=GRCh37>",
"contig.18": "<ID=19,length=59128983,assembly=GRCh37>",
"contig.19": "<ID=20,length=63025520,assembly=GRCh37>",
"contig.20": "<ID=21,length=48129895,assembly=GRCh37>",
"contig.21": "<ID=22,length=51304566,assembly=GRCh37>",
"contig.22": "<ID=X,length=155270560,assembly=GRCh37>",
"contig.23": "<ID=Y,length=59373566,assembly=GRCh37>",
"contig.24": "<ID=MT,length=16569,assembly=GRCh37>",
"contig.25": "<ID=GL000207.1,length=4262,assembly=GRCh37>",
"contig.26": "<ID=GL000226.1,length=15008,assembly=GRCh37>",
"contig.27": "<ID=GL000229.1,length=19913,assembly=GRCh37>",
"contig.28": "<ID=GL000231.1,length=27386,assembly=GRCh37>",
"contig.29": "<ID=GL000210.1,length=27682,assembly=GRCh37>",
"contig.30": "<ID=GL000239.1,length=33824,assembly=GRCh37>",
"contig.31": "<ID=GL000235.1,length=34474,assembly=GRCh37>",
"contig.32": "<ID=GL000201.1,length=36148,assembly=GRCh37>",
"contig.33": "<ID=GL000247.1,length=36422,assembly=GRCh37>",
"contig.34": "<ID=GL000245.1,length=36651,assembly=GRCh37>",
"contig.35": "<ID=GL000197.1,length=37175,assembly=GRCh37>",
"contig.36": "<ID=GL000203.1,length=37498,assembly=GRCh37>",
"contig.37": "<ID=GL000246.1,length=38154,assembly=GRCh37>",
"contig.38": "<ID=GL000249.1,length=38502,assembly=GRCh37>",
"contig.39": "<ID=GL000196.1,length=38914,assembly=GRCh37>",
"contig.40": "<ID=GL000248.1,length=39786,assembly=GRCh37>",
"contig.41": "<ID=GL000244.1,length=39929,assembly=GRCh37>",
"contig.42": "<ID=GL000238.1,length=39939,assembly=GRCh37>",
"contig.43": "<ID=GL000202.1,length=40103,assembly=GRCh37>",
"contig.44": "<ID=GL000234.1,length=40531,assembly=GRCh37>",
"contig.45": "<ID=GL000232.1,length=40652,assembly=GRCh37>",
"contig.46": "<ID=GL000206.1,length=41001,assembly=GRCh37>",
"contig.47": "<ID=GL000240.1,length=41933,assembly=GRCh37>",
"contig.48": "<ID=GL000236.1,length=41934,assembly=GRCh37>",
"contig.49": "<ID=GL000241.1,length=42152,assembly=GRCh37>",
"contig.50": "<ID=GL000243.1,length=43341,assembly=GRCh37>",
"contig.51": "<ID=GL000242.1,length=43523,assembly=GRCh37>",
"contig.52": "<ID=GL000230.1,length=43691,assembly=GRCh37>",
"contig.53": "<ID=GL000237.1,length=45867,assembly=GRCh37>",
"contig.54": "<ID=GL000233.1,length=45941,assembly=GRCh37>",
"contig.55": "<ID=GL000204.1,length=81310,assembly=GRCh37>",
"contig.56": "<ID=GL000198.1,length=90085,assembly=GRCh37>",
"contig.57": "<ID=GL000208.1,length=92689,assembly=GRCh37>",
"contig.58": "<ID=GL000191.1,length=106433,assembly=GRCh37>",
"contig.59": "<ID=GL000227.1,length=128374,assembly=GRCh37>",
"contig.60": "<ID=GL000228.1,length=129120,assembly=GRCh37>",
"contig.61": "<ID=GL000214.1,length=137718,assembly=GRCh37>",
"contig.62": "<ID=GL000221.1,length=155397,assembly=GRCh37>",
"contig.63": "<ID=GL000209.1,length=159169,assembly=GRCh37>",
"contig.64": "<ID=GL000218.1,length=161147,assembly=GRCh37>",
"contig.65": "<ID=GL000220.1,length=161802,assembly=GRCh37>",
"contig.66": "<ID=GL000213.1,length=164239,assembly=GRCh37>",
"contig.67": "<ID=GL000211.1,length=166566,assembly=GRCh37>",
"contig.68": "<ID=GL000199.1,length=169874,assembly=GRCh37>",
"contig.69": "<ID=GL000217.1,length=172149,assembly=GRCh37>",
"contig.70": "<ID=GL000216.1,length=172294,assembly=GRCh37>",
"contig.71": "<ID=GL000215.1,length=172545,assembly=GRCh37>",
"contig.72": "<ID=GL000205.1,length=174588,assembly=GRCh37>",
"contig.73": "<ID=GL000219.1,length=179198,assembly=GRCh37>",
"contig.74": "<ID=GL000224.1,length=179693,assembly=GRCh37>",
"contig.75": "<ID=GL000223.1,length=180455,assembly=GRCh37>",
"contig.76": "<ID=GL000195.1,length=182896,assembly=GRCh37>",
"contig.77": "<ID=GL000212.1,length=186858,assembly=GRCh37>",
"contig.78": "<ID=GL000222.1,length=186861,assembly=GRCh37>",
"contig.79": "<ID=GL000200.1,length=187035,assembly=GRCh37>",
"contig.80": "<ID=GL000193.1,length=189789,assembly=GRCh37>",
"contig.81": "<ID=GL000194.1,length=191469,assembly=GRCh37>",
"contig.82": "<ID=GL000225.1,length=211173,assembly=GRCh37>",
"contig.83": "<ID=GL000192.1,length=547496,assembly=GRCh37>",
"gwas_harmonisation_command": "--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/vcf_09_19b/bgzip_vcf/data.batch_41221_7.vcf.gz --id UKB-b:7196 --data /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/raw-output/data.batch_41221_7.txt.gz --cohort_cases 1478 --cohort_controls 9009 --ref /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/human_g1k_v37.fasta --json /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/ukb_gwas.json; 1.1.1",
"file_date": "2019-09-13T01:35:03.134045",
"bcftools_viewVersion": "1.9-74-g6af271c+htslib-1.9-64-g226b4a8",
"bcftools_viewCommand": "view -T ^/mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-7196/mac_discard.txt -Oz /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-7196/UKB-b-7196_raw.vcf.gz; Date=Thu Oct 17 12:18:00 2019",
"bcftools_viewCommand.1": "view -h /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukb-b-7196/ukb-b-7196.vcf.gz; Date=Sun May 10 03:50:04 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/public/UKB-b-7196/UKB-b-7196_data.vcf.gz \
--ref-ld-chr ../reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-7196/ldsc.txt \
--w-ld-chr ../reference/eur_w_ld_chr/
Beginning analysis at Thu Oct 17 14:40:18 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-7196/UKB-b-7196_data.vcf.gz ...
Read summary statistics for 2462879 SNPs.
Dropped 286 SNPs with duplicated rs numbers.
Reading reference panel LD Score from ../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 ../reference/eur_w_ld_chr/[1-22] ...
Read regression weight LD Scores for 1290028 SNPs.
After merging with reference panel LD, 624098 SNPs remain.
After merging with regression SNP LD, 624098 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0073 (0.0518)
Lambda GC: 1.0232
Mean Chi^2: 1.0142
Intercept: 1.0125 (0.0093)
Ratio: 0.8757 (0.6566)
Analysis finished at Thu Oct 17 14:40:44 2019
Total time elapsed: 26.7sQC metrics
Metrics
Metrics
{
"af_correlation": 0.7654,
"inflation_factor": 1,
"mean_EFFECT": 5.6358e-06,
"n": "-Inf",
"n_snps": 9851866,
"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": 0,
"n_miss_AF_reference": 19488,
"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": 624098,
"ldsc_nsnp_merge_regression_ld": 624098,
"ldsc_observed_scale_h2_beta": 0.0073,
"ldsc_observed_scale_h2_se": 0.0518,
"ldsc_intercept_beta": 1.0125,
"ldsc_intercept_se": 0.0093,
"ldsc_lambda_gc": 1.0232,
"ldsc_mean_chisq": 1.0142,
"ldsc_ratio": 0.8803
}
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 | 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 | 4 | 58 | 0 | 2462596 | 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 | N | 2462879 | 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 | 8.651892e+00 | 5.767147e+00 | 1.0000000 | 4.000000e+00 | 8.000000e+00 | 1.300000e+01 | 2.200000e+01 | ▇▅▃▂▂ |
| numeric | POS | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 7.856278e+07 | 5.662764e+07 | 5687.0000000 | 3.169560e+07 | 6.896363e+07 | 1.147691e+08 | 2.491917e+08 | ▇▆▅▂▁ |
| numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 5.600000e-06 | 5.130300e-03 | -0.0266253 | -3.473600e-03 | -6.800000e-06 | 3.468500e-03 | 3.279630e-02 | ▁▃▇▁▁ |
| numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 5.101800e-03 | 2.704000e-04 | 0.0046065 | 4.876000e-03 | 5.025800e-03 | 5.287000e-03 | 1.008480e-02 | ▇▁▁▁▁ |
| numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.971808e-01 | 2.880443e-01 | 0.0000017 | 2.500000e-01 | 5.000000e-01 | 7.499995e-01 | 1.000000e+00 | ▇▇▇▇▇ |
| numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.971785e-01 | 2.880181e-01 | 0.0000017 | 2.472596e-01 | 4.954617e-01 | 7.453920e-01 | 9.999998e-01 | ▇▇▇▇▇ |
| numeric | AF | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.547402e-01 | 1.497274e-01 | 0.2368070 | 3.230790e-01 | 4.329840e-01 | 5.749475e-01 | 7.631910e-01 | ▇▆▅▅▃ |
| numeric | AF_reference | 19488 | 0.9920873 | NA | NA | NA | NA | NA | NA | NA | 4.363352e-01 | 1.751417e-01 | 0.0001997 | 2.983230e-01 | 4.213260e-01 | 5.643970e-01 | 1.000000e+00 | ▂▇▇▃▁ |
Head and tail
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 49298 | rs200943160 | T | C | -0.0017323 | 0.0086226 | 0.8400000 | 0.8407777 | 0.625501 | 0.7821490 | NA |
| 1 | 54676 | rs2462492 | C | T | -0.0083270 | 0.0085232 | 0.3300000 | 0.3285748 | 0.398443 | NA | NA |
| 1 | 91536 | rs6702460 | G | T | 0.0000351 | 0.0083938 | 1.0000000 | 0.9966629 | 0.458861 | 0.4207270 | NA |
| 1 | 534192 | rs6680723 | C | T | 0.0016210 | 0.0095845 | 0.8700001 | 0.8656927 | 0.239151 | NA | NA |
| 1 | 706368 | rs55727773 | A | G | 0.0056821 | 0.0058664 | 0.3300000 | 0.3327555 | 0.513615 | 0.2751600 | NA |
| 1 | 763394 | rs369924889 | G | A | 0.0052825 | 0.0068946 | 0.4400003 | 0.4435628 | 0.706796 | 0.6176120 | NA |
| 1 | 768253 | rs2977608 | A | C | -0.0028338 | 0.0055880 | 0.6100002 | 0.6120695 | 0.758130 | 0.4894170 | NA |
| 1 | 776546 | rs12124819 | A | G | 0.0001710 | 0.0063195 | 0.9800000 | 0.9784144 | 0.266808 | 0.0756789 | NA |
| 1 | 814495 | rs74461805 | C | A | -0.0101426 | 0.0081638 | 0.2099999 | 0.2140938 | 0.340789 | NA | NA |
| 1 | 830181 | rs28444699 | A | G | 0.0048749 | 0.0054234 | 0.3700002 | 0.3687175 | 0.696950 | 0.6912940 | NA |
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 22 | 51180501 | rs5770999 | T | C | -0.0035044 | 0.0055042 | 0.5199996 | 0.5243283 | 0.711773 | 0.6369810 | NA |
| 22 | 51181919 | rs9616825 | G | C | -0.0051679 | 0.0054858 | 0.3500000 | 0.3461668 | 0.693011 | 0.6194090 | NA |
| 22 | 51182485 | rs6009961 | A | G | -0.0038697 | 0.0055296 | 0.4799997 | 0.4840435 | 0.713594 | 0.6383790 | NA |
| 22 | 51186143 | rs2879914 | T | C | 0.0002873 | 0.0051612 | 0.9599999 | 0.9556029 | 0.378583 | 0.2733630 | NA |
| 22 | 51186228 | rs3865766 | C | T | -0.0000448 | 0.0050355 | 0.9900000 | 0.9928996 | 0.450005 | 0.4532750 | NA |
| 22 | 51197266 | rs61290853 | A | G | 0.0006877 | 0.0052094 | 0.8900000 | 0.8949747 | 0.384827 | 0.4229230 | NA |
| 22 | 51198027 | rs34939255 | A | G | -0.0051870 | 0.0059205 | 0.3800004 | 0.3809641 | 0.254195 | 0.0984425 | NA |
| 22 | 51211106 | rs9628250 | T | C | -0.0047682 | 0.0058662 | 0.4199997 | 0.4163174 | 0.271092 | 0.1671330 | NA |
| 22 | 51212875 | rs2238837 | A | C | 0.0008221 | 0.0055688 | 0.8800001 | 0.8826416 | 0.325868 | 0.3724040 | NA |
| 22 | 51237063 | rs3896457 | T | C | 0.0048985 | 0.0056798 | 0.3900004 | 0.3884444 | 0.293888 | 0.2050720 | NA |
bcf preview
1 49298 rs10399793 T C . PASS AF=0.625501 ES:SE:LP:AF:ID -0.00173227:0.0086226:0.0757207:0.625501:rs10399793
1 54676 rs2462492 C T . PASS AF=0.398443 ES:SE:LP:AF:ID -0.00832704:0.00852317:0.481486:0.398443:rs2462492
1 91536 rs6702460 G T . PASS AF=0.458861 ES:SE:LP:AF:ID 3.51069e-05:0.00839379:-0:0.458861:rs6702460
1 534192 rs6680723 C T . PASS AF=0.239151 ES:SE:LP:AF:ID 0.00162105:0.00958452:0.0604807:0.239151:rs6680723
1 706368 rs12029736 A G . PASS AF=0.513615 ES:SE:LP:AF:ID 0.00568206:0.00586639:0.481486:0.513615:rs12029736
1 763394 rs3115847 G A . PASS AF=0.706796 ES:SE:LP:AF:ID 0.00528254:0.00689455:0.356547:0.706796:rs3115847
1 768253 rs2977608 A C . PASS AF=0.75813 ES:SE:LP:AF:ID -0.00283377:0.00558795:0.21467:0.75813:rs2977608
1 776546 rs12124819 A G . PASS AF=0.266808 ES:SE:LP:AF:ID 0.000170986:0.00631952:0.00877392:0.266808:rs12124819
1 814495 rs74461805 C A . PASS AF=0.340789 ES:SE:LP:AF:ID -0.0101426:0.0081638:0.677781:0.340789:rs74461805
1 830181 rs28444699 A G . PASS AF=0.69695 ES:SE:LP:AF:ID 0.00487494:0.00542336:0.431798:0.69695:rs28444699
1 831489 rs4970385 C T . PASS AF=0.706945 ES:SE:LP:AF:ID 0.00247208:0.00534488:0.19382:0.706945:rs4970385
1 831909 rs9697642 C T . PASS AF=0.707015 ES:SE:LP:AF:ID 0.00242086:0.0053447:0.187087:0.707015:rs9697642
1 832066 rs9697380 G C . PASS AF=0.707305 ES:SE:LP:AF:ID 0.00247591:0.00534362:0.19382:0.707305:rs9697380
1 832318 rs4500250 C A . PASS AF=0.707356 ES:SE:LP:AF:ID 0.00244381:0.00534423:0.187087:0.707356:rs4500250
1 832398 rs4553118 T C . PASS AF=0.732285 ES:SE:LP:AF:ID 0.00445021:0.00547614:0.376751:0.732285:rs4553118
1 832918 rs28765502 T C . PASS AF=0.29274 ES:SE:LP:AF:ID -0.00227928:0.00534442:0.173925:0.29274:rs28765502
1 833641 rs28594623 T C . PASS AF=0.239099 ES:SE:LP:AF:ID -0.00591388:0.00565489:0.522879:0.239099:rs28594623
1 835499 rs4422948 A G . PASS AF=0.240154 ES:SE:LP:AF:ID -0.00604706:0.00563146:0.552842:0.240154:rs4422948
1 836896 rs28705752 T C . PASS AF=0.265707 ES:SE:LP:AF:ID -0.00502149:0.00546108:0.443698:0.265707:rs28705752
1 838555 rs4970383 C A . PASS AF=0.242586 ES:SE:LP:AF:ID -0.00738651:0.0056069:0.721246:0.242586:rs4970383
1 839103 rs28562941 A G . PASS AF=0.265966 ES:SE:LP:AF:ID -0.00514167:0.00546629:0.455932:0.265966:rs28562941
1 840753 rs4970382 T C . PASS AF=0.400114 ES:SE:LP:AF:ID 0.00614985:0.00491594:0.677781:0.400114:rs4970382
1 843405 rs11516185 A G . PASS AF=0.359026 ES:SE:LP:AF:ID -0.00507002:0.00610767:0.387216:0.359026:rs11516185
1 850218 rs6664536 T A . PASS AF=0.591615 ES:SE:LP:AF:ID 0.00315681:0.00490281:0.283997:0.591615:rs6664536
1 850371 rs6679046 G T . PASS AF=0.604429 ES:SE:LP:AF:ID 0.00383861:0.00492727:0.356547:0.604429:rs6679046
1 850780 rs6657440 C T . PASS AF=0.604939 ES:SE:LP:AF:ID 0.00386304:0.00492348:0.366532:0.604939:rs6657440
1 852037 rs4970463 G A . PASS AF=0.59093 ES:SE:LP:AF:ID 0.00366313:0.00490903:0.337242:0.59093:rs4970463
1 852063 rs28436996 G A . PASS AF=0.590923 ES:SE:LP:AF:ID 0.00370267:0.00490589:0.346787:0.590923:rs28436996
1 852875 rs13303369 C T . PASS AF=0.607555 ES:SE:LP:AF:ID 0.00425104:0.00493789:0.408935:0.607555:rs13303369
1 853954 rs1806509 C A . PASS AF=0.607748 ES:SE:LP:AF:ID 0.00440964:0.00493707:0.431798:0.607748:rs1806509
1 854777 rs13303019 A G . PASS AF=0.611232 ES:SE:LP:AF:ID 0.00366967:0.00494462:0.337242:0.611232:rs13303019
1 854978 rs13303057 A C . PASS AF=0.603997 ES:SE:LP:AF:ID 0.00377934:0.00492418:0.356547:0.603997:rs13303057
1 855075 rs6673914 C G . PASS AF=0.611231 ES:SE:LP:AF:ID 0.00358242:0.00494504:0.327902:0.611231:rs6673914
1 856099 rs28534711 T G . PASS AF=0.388963 ES:SE:LP:AF:ID -0.00367471:0.00494654:0.337242:0.388963:rs28534711
1 856108 rs28742275 A G . PASS AF=0.388954 ES:SE:LP:AF:ID -0.00366317:0.00494656:0.337242:0.388954:rs28742275
1 856476 rs4040605 A G . PASS AF=0.350591 ES:SE:LP:AF:ID -0.00156902:0.00506262:0.119186:0.350591:rs4040605
1 862866 rs3892970 C T . PASS AF=0.763028 ES:SE:LP:AF:ID 0.00445507:0.00567773:0.366532:0.763028:rs3892970
1 864938 rs2340587 G A . PASS AF=0.759859 ES:SE:LP:AF:ID 0.00242408:0.00564809:0.173925:0.759859:rs2340587
1 866893 rs2880024 T C . PASS AF=0.611753 ES:SE:LP:AF:ID -0.00196856:0.00494115:0.161151:0.611753:rs2880024
1 868418 rs28546443 C T . PASS AF=0.300782 ES:SE:LP:AF:ID -0.00528979:0.00545555:0.481486:0.300782:rs28546443
1 870645 rs28576697 T C . PASS AF=0.291938 ES:SE:LP:AF:ID -0.00062905:0.00537908:0.0409586:0.291938:rs28576697
1 871334 rs4072383 G T . PASS AF=0.72003 ES:SE:LP:AF:ID -0.00100877:0.00533991:0.0705811:0.72003:rs4072383
1 872352 rs1806780 G C . PASS AF=0.268574 ES:SE:LP:AF:ID 0.00189296:0.00540251:0.136677:0.268574:rs1806780
1 873558 rs1110052 G T . PASS AF=0.71417 ES:SE:LP:AF:ID 0.00100128:0.0052953:0.0705811:0.71417:rs1110052
1 875770 rs4970379 A G . PASS AF=0.601132 ES:SE:LP:AF:ID -0.00608252:0.00499353:0.657577:0.601132:rs4970379
1 877147 rs114982608 G A . PASS AF=0.240741 ES:SE:LP:AF:ID 0.00363266:0.0056537:0.283997:0.240741:rs114982608
1 881627 rs2272757 G A . PASS AF=0.653094 ES:SE:LP:AF:ID -0.003243:0.00502687:0.283997:0.653094:rs2272757
1 882033 rs2272756 G A . PASS AF=0.240468 ES:SE:LP:AF:ID 0.00323259:0.00560825:0.251812:0.240468:rs2272756
1 890104 rs28631199 G A . PASS AF=0.242715 ES:SE:LP:AF:ID 0.00405749:0.00559545:0.327902:0.242715:rs28631199
1 891059 rs13303065 C T . PASS AF=0.65338 ES:SE:LP:AF:ID -0.00323006:0.0050298:0.283997:0.65338:rs13303065