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:14070,TotalVariants=9851866,VariantsNotRead=0,HarmonisedVariants=9851866,VariantsNotHarmonised=0,SwitchedAlleles=9851866,TotalControls=247792,TotalCases=1918,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_6153_3.vcf.gz --id UKB-b:14070 --data /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/raw-output/data.batch_6153_3.txt.gz --cohort_cases 1918 --cohort_controls 247792 --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": "2019-09-13T01:54:35.180591",
"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-14070/mac_discard.txt -Oz /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-14070/UKB-b-14070_raw.vcf.gz; Date=Thu Oct 17 12:29:56 2019",
"bcftools_viewCommand.1": "view -h /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukb-b-14070/ukb-b-14070.vcf.gz; Date=Sat May 9 15:02:32 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-14070/UKB-b-14070_data.vcf.gz \
--ref-ld-chr ../reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-14070/ldsc.txt \
--w-ld-chr ../reference/eur_w_ld_chr/
Beginning analysis at Thu Oct 17 14:43:10 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-14070/UKB-b-14070_data.vcf.gz ...
Read summary statistics for 3093509 SNPs.
Dropped 424 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, 768014 SNPs remain.
After merging with regression SNP LD, 768014 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0082 (0.0025)
Lambda GC: 1.0419
Mean Chi^2: 1.0486
Intercept: 1.0026 (0.0094)
Ratio: 0.0528 (0.193)
Analysis finished at Thu Oct 17 14:43:51 2019
Total time elapsed: 40.92sQC metrics
Metrics
Metrics
{
"af_correlation": 0.8242,
"inflation_factor": 1.0475,
"mean_EFFECT": 2.1069e-07,
"n": "-Inf",
"n_snps": 9851866,
"n_clumped_hits": 6,
"n_p_sig": 4179,
"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": 24707,
"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": 768014,
"ldsc_nsnp_merge_regression_ld": 768014,
"ldsc_observed_scale_h2_beta": 0.0082,
"ldsc_observed_scale_h2_se": 0.0025,
"ldsc_intercept_beta": 1.0026,
"ldsc_intercept_se": 0.0094,
"ldsc_lambda_gc": 1.0419,
"ldsc_mean_chisq": 1.0486,
"ldsc_ratio": 0.0535
}
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 | 1.0000000 | 3 | 58 | 0 | 3093088 | 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 | 3093509 | 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 | 8.664594e+00 | 5.772550e+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 | 7.856500e+07 | 5.671110e+07 | 828.0000000 | 3.160268e+07 | 6.895969e+07 | 1.148185e+08 | 2.492013e+08 | ▇▆▅▂▁ |
| numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 2.000000e-07 | 2.965000e-04 | -0.0033209 | -1.888000e-04 | -2.400000e-06 | 1.837000e-04 | 7.461400e-03 | ▁▇▁▁▁ |
| numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 2.712000e-04 | 2.200000e-05 | 0.0002381 | 2.520000e-04 | 2.645000e-04 | 2.867000e-04 | 5.646000e-04 | ▇▁▁▁▁ |
| numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.917093e-01 | 2.913531e-01 | 0.0000000 | 2.399999e-01 | 4.899999e-01 | 7.400005e-01 | 1.000000e+00 | ▇▇▇▇▇ |
| numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.917101e-01 | 2.913265e-01 | 0.0000000 | 2.373505e-01 | 4.901127e-01 | 7.440269e-01 | 9.999996e-01 | ▇▇▇▇▇ |
| numeric | AF | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.313450e-01 | 1.791533e-01 | 0.1824820 | 2.740550e-01 | 3.991700e-01 | 5.710050e-01 | 8.175180e-01 | ▇▆▅▃▃ |
| numeric | AF_reference | 24707 | 0.9920133 | NA | NA | NA | NA | NA | NA | NA | 4.157438e-01 | 1.940870e-01 | 0.0000000 | 2.593850e-01 | 3.909740e-01 | 5.583070e-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 | 0.0001523 | 0.0004390 | 0.7300002 | 0.7286539 | 0.623403 | 0.7821490 | NA |
| 1 | 54676 | rs2462492 | C | T | 0.0007793 | 0.0004340 | 0.0729995 | 0.0725529 | 0.400976 | NA | NA |
| 1 | 91536 | rs6702460 | G | T | 0.0004676 | 0.0004276 | 0.2700001 | 0.2740938 | 0.457088 | 0.4207270 | NA |
| 1 | 534192 | rs6680723 | C | T | -0.0000881 | 0.0004887 | 0.8600001 | 0.8570046 | 0.241186 | NA | NA |
| 1 | 706368 | rs55727773 | A | G | 0.0004079 | 0.0003033 | 0.1800002 | 0.1786003 | 0.515134 | 0.2751600 | NA |
| 1 | 763394 | rs369924889 | G | A | -0.0000891 | 0.0003555 | 0.8000000 | 0.8019802 | 0.706352 | 0.6176120 | NA |
| 1 | 768253 | rs2977608 | A | C | 0.0003528 | 0.0002902 | 0.2200002 | 0.2241516 | 0.761050 | 0.4894170 | NA |
| 1 | 776546 | rs12124819 | A | G | 0.0002502 | 0.0003241 | 0.4400003 | 0.4401236 | 0.265521 | 0.0756789 | NA |
| 1 | 798400 | rs10900604 | A | G | -0.0001261 | 0.0003097 | 0.6800001 | 0.6839159 | 0.206639 | 0.4105430 | NA |
| 1 | 798959 | rs11240777 | G | A | -0.0001270 | 0.0003099 | 0.6800001 | 0.6820070 | 0.206462 | 0.4099440 | NA |
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 22 | 51180501 | rs5770999 | T | C | -0.0001082 | 0.0002858 | 0.7099994 | 0.7050905 | 0.714083 | 0.6369810 | NA |
| 22 | 51181919 | rs9616825 | G | C | 0.0000698 | 0.0002842 | 0.8100000 | 0.8059872 | 0.695892 | 0.6194090 | NA |
| 22 | 51182485 | rs6009961 | A | G | -0.0000624 | 0.0002867 | 0.8300000 | 0.8277609 | 0.715964 | 0.6383790 | NA |
| 22 | 51186143 | rs2879914 | T | C | -0.0007188 | 0.0002656 | 0.0068000 | 0.0067987 | 0.381650 | 0.2733630 | NA |
| 22 | 51186228 | rs3865766 | C | T | -0.0006402 | 0.0002588 | 0.0129999 | 0.0133689 | 0.451186 | 0.4532750 | NA |
| 22 | 51197266 | rs61290853 | A | G | -0.0003191 | 0.0002670 | 0.2300001 | 0.2320402 | 0.386391 | 0.4229230 | NA |
| 22 | 51198027 | rs34939255 | A | G | 0.0006819 | 0.0003024 | 0.0239999 | 0.0241519 | 0.254796 | 0.0984425 | NA |
| 22 | 51211106 | rs9628250 | T | C | 0.0006798 | 0.0002996 | 0.0230001 | 0.0232656 | 0.271851 | 0.1671330 | NA |
| 22 | 51212875 | rs2238837 | A | C | -0.0006221 | 0.0002848 | 0.0290001 | 0.0289511 | 0.331269 | 0.3724040 | NA |
| 22 | 51237063 | rs3896457 | T | C | -0.0004785 | 0.0002917 | 0.1000000 | 0.1009226 | 0.297860 | 0.2050720 | NA |
bcf preview
1 49298 rs10399793 T C . PASS AF=0.623403 ES:SE:LP:AF:ID 0.000152286:0.00043897:0.136677:0.623403:rs10399793
1 54676 rs2462492 C T . PASS AF=0.400976 ES:SE:LP:AF:ID 0.000779276:0.000433984:1.13668:0.400976:rs2462492
1 91536 rs6702460 G T . PASS AF=0.457088 ES:SE:LP:AF:ID 0.000467635:0.000427578:0.568636:0.457088:rs6702460
1 534192 rs6680723 C T . PASS AF=0.241186 ES:SE:LP:AF:ID -8.80639e-05:0.000488732:0.0655015:0.241186:rs6680723
1 706368 rs12029736 A G . PASS AF=0.515134 ES:SE:LP:AF:ID 0.000407931:0.000303277:0.744727:0.515134:rs12029736
1 763394 rs3115847 G A . PASS AF=0.706352 ES:SE:LP:AF:ID -8.91446e-05:0.000355462:0.09691:0.706352:rs3115847
1 768253 rs2977608 A C . PASS AF=0.76105 ES:SE:LP:AF:ID 0.000352783:0.000290222:0.657577:0.76105:rs2977608
1 776546 rs12124819 A G . PASS AF=0.265521 ES:SE:LP:AF:ID 0.000250221:0.000324127:0.356547:0.265521:rs12124819
1 798400 rs10900604 A G . PASS AF=0.206639 ES:SE:LP:AF:ID -0.000126103:0.00030974:0.167491:0.206639:rs10900604
1 798959 rs11240777 G A . PASS AF=0.206462 ES:SE:LP:AF:ID -0.000126963:0.000309873:0.167491:0.206462:rs11240777
1 808631 rs11240779 G A . PASS AF=0.772518 ES:SE:LP:AF:ID 0.0001655:0.000294595:0.244125:0.772518:rs11240779
1 808928 rs11240780 C T . PASS AF=0.772745 ES:SE:LP:AF:ID 0.000158282:0.000295075:0.229148:0.772745:rs11240780
1 814495 rs74461805 C A . PASS AF=0.341056 ES:SE:LP:AF:ID -0.000342625:0.000415163:0.387216:0.341056:rs74461805
1 830181 rs28444699 A G . PASS AF=0.697449 ES:SE:LP:AF:ID 0.000239209:0.000278629:0.408935:0.697449:rs28444699
1 831489 rs4970385 C T . PASS AF=0.705372 ES:SE:LP:AF:ID 0.000306077:0.000273555:0.585027:0.705372:rs4970385
1 831909 rs9697642 C T . PASS AF=0.705418 ES:SE:LP:AF:ID 0.00030467:0.000273546:0.568636:0.705418:rs9697642
1 832066 rs9697380 G C . PASS AF=0.70561 ES:SE:LP:AF:ID 0.000298879:0.000273564:0.568636:0.70561:rs9697380
1 832318 rs4500250 C A . PASS AF=0.705638 ES:SE:LP:AF:ID 0.000297586:0.000273591:0.552842:0.705638:rs4500250
1 832398 rs4553118 T C . PASS AF=0.730167 ES:SE:LP:AF:ID 0.000212645:0.000281093:0.346787:0.730167:rs4553118
1 832918 rs28765502 T C . PASS AF=0.294397 ES:SE:LP:AF:ID -0.000298695:0.000273574:0.568636:0.294397:rs28765502
1 833223 rs13303211 C T . PASS AF=0.236366 ES:SE:LP:AF:ID -0.000220373:0.000291321:0.346787:0.236366:rs13303211
1 833302 rs28752186 C T . PASS AF=0.236353 ES:SE:LP:AF:ID -0.000220099:0.000291326:0.346787:0.236353:rs28752186
1 833641 rs28594623 T C . PASS AF=0.239355 ES:SE:LP:AF:ID -0.00021909:0.000290405:0.346787:0.239355:rs28594623
1 833824 rs28484835 T C . PASS AF=0.23636 ES:SE:LP:AF:ID -0.000220617:0.000291329:0.346787:0.23636:rs28484835
1 833927 rs28593608 T C . PASS AF=0.212029 ES:SE:LP:AF:ID -0.000129034:0.000302893:0.173925:0.212029:rs28593608
1 834198 rs28385272 T C . PASS AF=0.211921 ES:SE:LP:AF:ID -0.000123408:0.000302959:0.167491:0.211921:rs28385272
1 834832 rs4411087 G C . PASS AF=0.236851 ES:SE:LP:AF:ID -0.000221878:0.000291091:0.346787:0.236851:rs4411087
1 834928 rs4422949 A G . PASS AF=0.212565 ES:SE:LP:AF:ID -0.000135224:0.0003025:0.187087:0.212565:rs4422949
1 834999 rs28570054 G A . PASS AF=0.212533 ES:SE:LP:AF:ID -0.000133505:0.000302575:0.180456:0.212533:rs28570054
1 835499 rs4422948 A G . PASS AF=0.240871 ES:SE:LP:AF:ID -0.00015731:0.000289032:0.229148:0.240871:rs4422948
1 836529 rs28731045 C G . PASS AF=0.213133 ES:SE:LP:AF:ID -8.44327e-05:0.000302115:0.107905:0.213133:rs28731045
1 836896 rs28705752 T C . PASS AF=0.26932 ES:SE:LP:AF:ID -0.000270399:0.000278866:0.481486:0.26932:rs28705752
1 836924 rs72890788 G A . PASS AF=0.213112 ES:SE:LP:AF:ID -8.34147e-05:0.000302145:0.107905:0.213112:rs72890788
1 838387 rs4970384 T C . PASS AF=0.214162 ES:SE:LP:AF:ID -7.40123e-05:0.000301562:0.091515:0.214162:rs4970384
1 838555 rs4970383 C A . PASS AF=0.245959 ES:SE:LP:AF:ID -0.000170011:0.000287085:0.259637:0.245959:rs4970383
1 839103 rs28562941 A G . PASS AF=0.26983 ES:SE:LP:AF:ID -0.000278709:0.000279038:0.49485:0.26983:rs28562941
1 840753 rs4970382 T C . PASS AF=0.39994 ES:SE:LP:AF:ID -0.000305118:0.000252189:0.638272:0.39994:rs4970382
1 841085 rs1574243 C G . PASS AF=0.236834 ES:SE:LP:AF:ID -0.00020569:0.00029323:0.318759:0.236834:rs1574243
1 842013 rs7419119 T G . PASS AF=0.214883 ES:SE:LP:AF:ID -5.64138e-05:0.000301812:0.0705811:0.214883:rs7419119
1 842362 rs28540380 C T . PASS AF=0.234743 ES:SE:LP:AF:ID -0.000139364:0.000297543:0.19382:0.234743:rs28540380
1 843405 rs11516185 A G . PASS AF=0.363312 ES:SE:LP:AF:ID 3.70663e-05:0.000312811:0.0409586:0.363312:rs11516185
1 845283 rs7366404 G T . PASS AF=0.814416 ES:SE:LP:AF:ID -0.000211903:0.000318857:0.29243:0.814416:rs7366404
1 845635 rs117086422 C T . PASS AF=0.204802 ES:SE:LP:AF:ID -0.000120124:0.000306709:0.154902:0.204802:rs117086422
1 845938 rs57760052 G A . PASS AF=0.210231 ES:SE:LP:AF:ID -7.35475e-05:0.000303745:0.091515:0.210231:rs57760052
1 846078 rs28612348 C T . PASS AF=0.196043 ES:SE:LP:AF:ID 2.59643e-05:0.000311531:0.0315171:0.196043:rs28612348
1 846338 rs4970334 A G . PASS AF=0.813716 ES:SE:LP:AF:ID -0.000209836:0.000318564:0.29243:0.813716:rs4970334
1 846398 rs58781670 G A . PASS AF=0.203864 ES:SE:LP:AF:ID -7.82372e-05:0.000307727:0.09691:0.203864:rs58781670
1 846489 rs4970333 T C . PASS AF=0.813832 ES:SE:LP:AF:ID -0.000205518:0.000318804:0.283997:0.813832:rs4970333
1 846808 rs4475691 C T . PASS AF=0.197641 ES:SE:LP:AF:ID -3.21159e-05:0.000310653:0.0362122:0.197641:rs4475691
1 846864 rs950122 G C . PASS AF=0.197398 ES:SE:LP:AF:ID -2.99628e-05:0.000310438:0.0362122:0.197398:rs950122