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:15932,TotalVariants=9851866,VariantsNotRead=0,HarmonisedVariants=9851866,VariantsNotHarmonised=0,SwitchedAlleles=9851866,TotalControls=460904,TotalCases=2106,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_41200_T521.vcf.gz --id UKB-b:15932 --data /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/raw-output/data.batch_41200_T521.txt.gz --cohort_cases 2106 --cohort_controls 460904 --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": "2019-09-13T06:43:47.653170",
"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-15932/mac_discard.txt -Oz /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-15932/UKB-b-15932_raw.vcf.gz; Date=Thu Oct 17 12:32:45 2019",
"bcftools_viewCommand.1": "view -h /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukb-b-15932/ukb-b-15932.vcf.gz; Date=Sun May 10 14:46:45 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-15932/UKB-b-15932_data.vcf.gz \
--ref-ld-chr ../reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-15932/ldsc.txt \
--w-ld-chr ../reference/eur_w_ld_chr/
Beginning analysis at Thu Oct 17 14:44:37 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-15932/UKB-b-15932_data.vcf.gz ...
Read summary statistics for 3303739 SNPs.
Dropped 476 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, 813439 SNPs remain.
After merging with regression SNP LD, 813439 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0113 (0.0021)
Lambda GC: 1.0836
Mean Chi^2: 1.1309
Intercept: 1.0134 (0.0111)
Ratio: 0.1023 (0.0848)
Analysis finished at Thu Oct 17 14:45:19 2019
Total time elapsed: 42.5sQC metrics
Metrics
Metrics
{
"af_correlation": 0.8391,
"inflation_factor": 1.0966,
"mean_EFFECT": 4.153e-07,
"n": "-Inf",
"n_snps": 9851866,
"n_clumped_hits": 19,
"n_p_sig": 1349,
"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": 26486,
"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": 813439,
"ldsc_nsnp_merge_regression_ld": 813439,
"ldsc_observed_scale_h2_beta": 0.0113,
"ldsc_observed_scale_h2_se": 0.0021,
"ldsc_intercept_beta": 1.0134,
"ldsc_intercept_se": 0.0111,
"ldsc_lambda_gc": 1.0836,
"ldsc_mean_chisq": 1.1309,
"ldsc_ratio": 0.1024
}
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 | 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 | logical.mean | logical.count | numeric.mean | numeric.sd | numeric.p0 | numeric.p25 | numeric.p50 | numeric.p75 | numeric.p100 | numeric.hist |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| character | ID | 0 | 1.000000 | 3 | 58 | 0 | 3303266 | 0 | NA | NA | 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 | NA | NA |
| character | ALT | 0 | 1.000000 | 1 | 1 | 0 | 4 | 0 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| logical | N | 3303739 | 0.000000 | NA | NA | NA | NA | NA | NaN | : | NA | NA | NA | NA | NA | NA | NA | NA |
| numeric | CHROM | 0 | 1.000000 | NA | NA | NA | NA | NA | NA | NA | 8.662211e+00 | 5.772737e+00 | 1.0000000 | 4.000000e+00 | 8.000000e+00 | 1.300000e+01 | 2.200000e+01 | ▇▅▃▂▂ |
| numeric | POS | 0 | 1.000000 | NA | NA | NA | NA | NA | NA | NA | 7.853882e+07 | 5.671684e+07 | 828.0000000 | 3.157986e+07 | 6.891639e+07 | 1.147716e+08 | 2.492385e+08 | ▇▆▅▂▁ |
| numeric | EFFECT | 0 | 1.000000 | NA | NA | NA | NA | NA | NA | NA | 4.000000e-07 | 1.666000e-04 | -0.0049807 | -1.081000e-04 | 1.000000e-06 | 1.089000e-04 | 5.947900e-03 | ▁▁▇▁▁ |
| numeric | SE | 0 | 1.000000 | NA | NA | NA | NA | NA | NA | NA | 1.553000e-04 | 1.430000e-05 | 0.0001348 | 1.428000e-04 | 1.509000e-04 | 1.655000e-04 | 3.334000e-04 | ▇▁▁▁▁ |
| numeric | PVAL | 0 | 1.000000 | NA | NA | NA | NA | NA | NA | NA | 4.864482e-01 | 2.925958e-01 | 0.0000000 | 2.300001e-01 | 4.799997e-01 | 7.400005e-01 | 1.000000e+00 | ▇▇▇▇▇ |
| numeric | PVAL_ztest | 0 | 1.000000 | NA | NA | NA | NA | NA | NA | NA | 4.864474e-01 | 2.925715e-01 | 0.0000000 | 2.301583e-01 | 4.819181e-01 | 7.398125e-01 | 9.999997e-01 | ▇▇▇▇▇ |
| numeric | AF | 0 | 1.000000 | NA | NA | NA | NA | NA | NA | NA | 4.231576e-01 | 1.879146e-01 | 0.1661920 | 2.584070e-01 | 3.877080e-01 | 5.679325e-01 | 8.338080e-01 | ▇▆▅▃▂ |
| numeric | AF_reference | 26486 | 0.991983 | NA | NA | NA | NA | NA | NA | NA | 4.085852e-01 | 1.999037e-01 | 0.0000000 | 2.464060e-01 | 3.801920e-01 | 5.551120e-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 | 0.0000433 | 0.0002481 | 0.8600001 | 0.8613204 | 0.623765 | 0.7821490 | NA |
| 1 | 54676 | rs2462492 | C | T | 0.0000465 | 0.0002458 | 0.8499999 | 0.8500005 | 0.400401 | NA | NA |
| 1 | 91536 | rs6702460 | G | T | -0.0001232 | 0.0002420 | 0.6100002 | 0.6105911 | 0.456846 | 0.4207270 | NA |
| 1 | 534192 | rs6680723 | C | T | 0.0003897 | 0.0002764 | 0.1600000 | 0.1585843 | 0.240959 | NA | NA |
| 1 | 706368 | rs55727773 | A | G | 0.0002621 | 0.0001716 | 0.1299999 | 0.1265770 | 0.515645 | 0.2751600 | NA |
| 1 | 763394 | rs369924889 | G | A | -0.0001357 | 0.0002012 | 0.5000000 | 0.4999699 | 0.706753 | 0.6176120 | NA |
| 1 | 768253 | rs2977608 | A | C | 0.0000572 | 0.0001642 | 0.7300002 | 0.7275635 | 0.761297 | 0.4894170 | NA |
| 1 | 776546 | rs12124819 | A | G | 0.0002652 | 0.0001834 | 0.1499999 | 0.1481333 | 0.265385 | 0.0756789 | NA |
| 1 | 798400 | rs10900604 | A | G | -0.0000021 | 0.0001752 | 0.9900000 | 0.9904233 | 0.206591 | 0.4105430 | NA |
| 1 | 798959 | rs11240777 | G | A | -0.0000077 | 0.0001752 | 0.9599999 | 0.9647827 | 0.206420 | 0.4099440 | NA |
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 22 | 51182485 | rs6009961 | A | G | 0.0000965 | 0.0001620 | 0.5500004 | 0.5512713 | 0.715502 | 0.6383790 | NA |
| 22 | 51186143 | rs2879914 | T | C | 0.0000398 | 0.0001502 | 0.7899998 | 0.7909014 | 0.381825 | 0.2733630 | NA |
| 22 | 51186228 | rs3865766 | C | T | 0.0000916 | 0.0001464 | 0.5300002 | 0.5314749 | 0.451061 | 0.4532750 | NA |
| 22 | 51192586 | rs5771006 | G | A | -0.0000259 | 0.0001973 | 0.9000000 | 0.8954390 | 0.167627 | 0.0848642 | NA |
| 22 | 51193227 | rs34608236 | T | G | -0.0001005 | 0.0002017 | 0.6200004 | 0.6182261 | 0.168490 | 0.0692891 | NA |
| 22 | 51197266 | rs61290853 | A | G | 0.0000342 | 0.0001512 | 0.8200001 | 0.8211409 | 0.386333 | 0.4229230 | NA |
| 22 | 51198027 | rs34939255 | A | G | -0.0000059 | 0.0001711 | 0.9699999 | 0.9726750 | 0.254562 | 0.0984425 | NA |
| 22 | 51211106 | rs9628250 | T | C | -0.0000316 | 0.0001697 | 0.8499999 | 0.8522951 | 0.271547 | 0.1671330 | NA |
| 22 | 51212875 | rs2238837 | A | C | -0.0001167 | 0.0001612 | 0.4700002 | 0.4690788 | 0.331457 | 0.3724040 | NA |
| 22 | 51237063 | rs3896457 | T | C | -0.0000310 | 0.0001650 | 0.8499999 | 0.8511860 | 0.297974 | 0.2050720 | NA |
bcf preview
1 49298 rs10399793 T C . PASS AF=0.623765 ES:SE:LP:AF:ID 4.33373e-05:0.000248076:0.0655015:0.623765:rs10399793
1 54676 rs2462492 C T . PASS AF=0.400401 ES:SE:LP:AF:ID 4.64789e-05:0.000245767:0.0705811:0.400401:rs2462492
1 91536 rs6702460 G T . PASS AF=0.456846 ES:SE:LP:AF:ID -0.000123227:0.000241987:0.21467:0.456846:rs6702460
1 534192 rs6680723 C T . PASS AF=0.240959 ES:SE:LP:AF:ID 0.000389702:0.000276414:0.79588:0.240959:rs6680723
1 706368 rs12029736 A G . PASS AF=0.515645 ES:SE:LP:AF:ID 0.000262148:0.000171592:0.886057:0.515645:rs12029736
1 763394 rs3115847 G A . PASS AF=0.706753 ES:SE:LP:AF:ID -0.0001357:0.000201175:0.30103:0.706753:rs3115847
1 768253 rs2977608 A C . PASS AF=0.761297 ES:SE:LP:AF:ID 5.72e-05:0.000164194:0.136677:0.761297:rs2977608
1 776546 rs12124819 A G . PASS AF=0.265385 ES:SE:LP:AF:ID 0.000265241:0.000183411:0.823909:0.265385:rs12124819
1 798400 rs10900604 A G . PASS AF=0.206591 ES:SE:LP:AF:ID -2.10244e-06:0.000175161:0.00436481:0.206591:rs10900604
1 798959 rs11240777 G A . PASS AF=0.20642 ES:SE:LP:AF:ID -7.73718e-06:0.000175237:0.0177288:0.20642:rs11240777
1 808631 rs11240779 G A . PASS AF=0.772619 ES:SE:LP:AF:ID 8.76013e-05:0.000166699:0.221849:0.772619:rs11240779
1 808928 rs11240780 C T . PASS AF=0.772847 ES:SE:LP:AF:ID 7.62943e-05:0.000166979:0.187087:0.772847:rs11240780
1 814495 rs74461805 C A . PASS AF=0.340396 ES:SE:LP:AF:ID -0.000100181:0.000235282:0.173925:0.340396:rs74461805
1 830181 rs28444699 A G . PASS AF=0.697255 ES:SE:LP:AF:ID 0.000235988:0.000157416:0.886057:0.697255:rs28444699
1 831489 rs4970385 C T . PASS AF=0.705397 ES:SE:LP:AF:ID 0.00032533:0.000154567:1.45593:0.705397:rs4970385
1 831909 rs9697642 C T . PASS AF=0.705442 ES:SE:LP:AF:ID 0.00033322:0.000154562:1.50864:0.705442:rs9697642
1 832066 rs9697380 G C . PASS AF=0.705627 ES:SE:LP:AF:ID 0.000332711:0.000154569:1.50864:0.705627:rs9697380
1 832318 rs4500250 C A . PASS AF=0.705655 ES:SE:LP:AF:ID 0.000332373:0.000154585:1.49485:0.705655:rs4500250
1 832398 rs4553118 T C . PASS AF=0.730129 ES:SE:LP:AF:ID 0.00027427:0.000158797:1.07572:0.730129:rs4553118
1 832918 rs28765502 T C . PASS AF=0.294377 ES:SE:LP:AF:ID -0.000331579:0.000154578:1.49485:0.294377:rs28765502
1 833223 rs13303211 C T . PASS AF=0.236703 ES:SE:LP:AF:ID -0.000416191:0.000164572:1.95861:0.236703:rs13303211
1 833302 rs28752186 C T . PASS AF=0.236691 ES:SE:LP:AF:ID -0.000415863:0.000164574:1.92082:0.236691:rs28752186
1 833641 rs28594623 T C . PASS AF=0.23975 ES:SE:LP:AF:ID -0.000399325:0.000164046:1.82391:0.23975:rs28594623
1 833824 rs28484835 T C . PASS AF=0.236693 ES:SE:LP:AF:ID -0.000415859:0.000164573:1.92082:0.236693:rs28484835
1 833927 rs28593608 T C . PASS AF=0.212421 ES:SE:LP:AF:ID -0.000361631:0.000171051:1.45593:0.212421:rs28593608
1 834198 rs28385272 T C . PASS AF=0.212316 ES:SE:LP:AF:ID -0.000360445:0.000171081:1.45593:0.212316:rs28385272
1 834832 rs4411087 G C . PASS AF=0.237178 ES:SE:LP:AF:ID -0.000419269:0.000164447:1.95861:0.237178:rs4411087
1 834928 rs4422949 A G . PASS AF=0.212962 ES:SE:LP:AF:ID -0.000365738:0.000170838:1.49485:0.212962:rs4422949
1 834999 rs28570054 G A . PASS AF=0.212924 ES:SE:LP:AF:ID -0.000360031:0.000170873:1.45593:0.212924:rs28570054
1 835499 rs4422948 A G . PASS AF=0.241162 ES:SE:LP:AF:ID -0.000392314:0.000163299:1.79588:0.241162:rs4422948
1 836529 rs28731045 C G . PASS AF=0.213543 ES:SE:LP:AF:ID -0.000344869:0.000170621:1.36653:0.213543:rs28731045
1 836896 rs28705752 T C . PASS AF=0.269511 ES:SE:LP:AF:ID -0.000355144:0.000157571:1.61979:0.269511:rs28705752
1 836924 rs72890788 G A . PASS AF=0.213513 ES:SE:LP:AF:ID -0.00034532:0.000170642:1.36653:0.213513:rs72890788
1 838387 rs4970384 T C . PASS AF=0.214587 ES:SE:LP:AF:ID -0.000342518:0.000170313:1.35655:0.214587:rs4970384
1 838555 rs4970383 C A . PASS AF=0.246204 ES:SE:LP:AF:ID -0.000285223:0.000162176:1.10237:0.246204:rs4970383
1 839103 rs28562941 A G . PASS AF=0.270019 ES:SE:LP:AF:ID -0.000340859:0.000157682:1.50864:0.270019:rs28562941
1 840753 rs4970382 T C . PASS AF=0.400124 ES:SE:LP:AF:ID -0.000215936:0.000142575:0.886057:0.400124:rs4970382
1 841085 rs1574243 C G . PASS AF=0.237102 ES:SE:LP:AF:ID -0.000227763:0.000165606:0.769551:0.237102:rs1574243
1 842013 rs7419119 T G . PASS AF=0.215391 ES:SE:LP:AF:ID -0.000338842:0.000170427:1.3279:0.215391:rs7419119
1 842362 rs28540380 C T . PASS AF=0.235323 ES:SE:LP:AF:ID -0.000279125:0.000168087:1.01323:0.235323:rs28540380
1 843405 rs11516185 A G . PASS AF=0.362606 ES:SE:LP:AF:ID 7.77313e-05:0.000176987:0.180456:0.362606:rs11516185
1 844300 rs61769713 C G . PASS AF=0.818811 ES:SE:LP:AF:ID 0.000117096:0.000181899:0.283997:0.818811:rs61769713
1 845283 rs7366404 G T . PASS AF=0.814497 ES:SE:LP:AF:ID 0.000140913:0.000180296:0.366532:0.814497:rs7366404
1 845635 rs117086422 C T . PASS AF=0.205429 ES:SE:LP:AF:ID -0.000394205:0.000173325:1.63827:0.205429:rs117086422
1 845938 rs57760052 G A . PASS AF=0.210864 ES:SE:LP:AF:ID -0.000451933:0.000171657:2.07058:0.210864:rs57760052
1 846078 rs28612348 C T . PASS AF=0.196785 ES:SE:LP:AF:ID -0.000477956:0.000175981:2.18046:0.196785:rs28612348
1 846338 rs4970334 A G . PASS AF=0.813828 ES:SE:LP:AF:ID 0.000133097:0.000180142:0.337242:0.813828:rs4970334
1 846398 rs58781670 G A . PASS AF=0.204447 ES:SE:LP:AF:ID -0.000467965:0.000173917:2.14874:0.204447:rs58781670
1 846489 rs4970333 T C . PASS AF=0.81392 ES:SE:LP:AF:ID 0.00013131:0.000180267:0.327902:0.81392:rs4970333
1 846808 rs4475691 C T . PASS AF=0.198378 ES:SE:LP:AF:ID -0.000494235:0.000175481:2.3098:0.198378:rs4475691