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:11189,TotalVariants=9851866,VariantsNotRead=0,HarmonisedVariants=9851866,VariantsNotHarmonised=0,SwitchedAlleles=9851866,TotalControls=63573,TotalCases=1376,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_20086_8.vcf.gz --id UKB-b:11189 --data /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/raw-output/data.batch_20086_8.txt.gz --cohort_cases 1376 --cohort_controls 63573 --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": "2019-09-13T13:37:05.220634",
"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-11189/mac_discard.txt -Oz /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-11189/UKB-b-11189_raw.vcf.gz; Date=Thu Oct 17 12:25:05 2019",
"bcftools_viewCommand.1": "view -h /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukb-b-11189/ukb-b-11189.vcf.gz; Date=Sun May 10 11:22:24 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-11189/UKB-b-11189_data.vcf.gz \
--ref-ld-chr ../reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-11189/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-11189/UKB-b-11189_data.vcf.gz ...
Read summary statistics for 2273867 SNPs.
Dropped 247 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, 578933 SNPs remain.
After merging with regression SNP LD, 578933 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0122 (0.0085)
Lambda GC: 1.017
Mean Chi^2: 1.0145
Intercept: 0.9955 (0.0095)
Ratio < 0 (usually indicates GC correction).
Analysis finished at Thu Oct 17 14:40:51 2019
Total time elapsed: 32.79sQC metrics
Metrics
Metrics
{
"af_correlation": 0.7392,
"inflation_factor": 1.0475,
"mean_EFFECT": -1.7564e-06,
"n": "-Inf",
"n_snps": 9851866,
"n_clumped_hits": 3,
"n_p_sig": 1505,
"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": 17997,
"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": 578933,
"ldsc_nsnp_merge_regression_ld": 578933,
"ldsc_observed_scale_h2_beta": 0.0122,
"ldsc_observed_scale_h2_se": 0.0085,
"ldsc_intercept_beta": 0.9955,
"ldsc_intercept_se": 0.0095,
"ldsc_lambda_gc": 1.017,
"ldsc_mean_chisq": 1.0145,
"ldsc_ratio": -0.3103
}
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 | 4 | 58 | 0 | 2273622 | 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 | 2273867 | 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 | 8.650877e+00 | 5.767783e+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 | 7.862013e+07 | 5.664016e+07 | 5687.0000000 | 3.175002e+07 | 6.909904e+07 | 1.147360e+08 | 2.491722e+08 | ▇▆▅▂▁ |
| numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | -1.800000e-06 | 8.737000e-04 | -0.0072723 | -5.774000e-04 | -5.200000e-06 | 5.722000e-04 | 1.048430e-02 | ▁▆▇▁▁ |
| numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 8.397000e-04 | 3.870000e-05 | 0.0007703 | 8.076000e-04 | 8.289000e-04 | 8.656000e-04 | 1.666500e-03 | ▇▁▁▁▁ |
| numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.946306e-01 | 2.901840e-01 | 0.0000000 | 2.399999e-01 | 4.899999e-01 | 7.499995e-01 | 1.000000e+00 | ▇▇▇▇▇ |
| numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.946279e-01 | 2.901608e-01 | 0.0000000 | 2.423893e-01 | 4.927251e-01 | 7.456814e-01 | 9.999991e-01 | ▇▇▇▇▇ |
| numeric | AF | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.608365e-01 | 1.400151e-01 | 0.2543610 | 3.377245e-01 | 4.419870e-01 | 5.743365e-01 | 7.456390e-01 | ▇▆▅▅▃ |
| numeric | AF_reference | 17997 | 0.9920853 | NA | NA | NA | NA | NA | NA | NA | 4.416152e-01 | 1.692640e-01 | 0.0001997 | 3.095050e-01 | 4.291130e-01 | 5.648960e-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 | -0.0008073 | 0.0014196 | 0.5700002 | 0.5695622 | 0.623812 | 0.7821490 | NA |
| 1 | 54676 | rs2462492 | C | T | -0.0005104 | 0.0014155 | 0.7199992 | 0.7184102 | 0.399144 | NA | NA |
| 1 | 91536 | rs6702460 | G | T | 0.0014980 | 0.0013922 | 0.2800000 | 0.2819236 | 0.455916 | 0.4207270 | NA |
| 1 | 706368 | rs55727773 | A | G | 0.0010394 | 0.0009814 | 0.2900000 | 0.2895661 | 0.513304 | 0.2751600 | NA |
| 1 | 763394 | rs369924889 | G | A | 0.0016040 | 0.0011498 | 0.1600000 | 0.1630035 | 0.705804 | 0.6176120 | NA |
| 1 | 776546 | rs12124819 | A | G | 0.0003206 | 0.0010530 | 0.7600007 | 0.7607452 | 0.263729 | 0.0756789 | NA |
| 1 | 814495 | rs74461805 | C | A | 0.0006990 | 0.0013439 | 0.5999997 | 0.6030101 | 0.340108 | NA | NA |
| 1 | 830181 | rs28444699 | A | G | -0.0015012 | 0.0008991 | 0.0949992 | 0.0949921 | 0.696612 | 0.6912940 | NA |
| 1 | 831489 | rs4970385 | C | T | -0.0010863 | 0.0008828 | 0.2200002 | 0.2185097 | 0.705031 | 0.6491610 | NA |
| 1 | 831909 | rs9697642 | C | T | -0.0010703 | 0.0008828 | 0.2300001 | 0.2253675 | 0.705083 | 0.6485620 | NA |
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 22 | 51180501 | rs5770999 | T | C | 0.0009351 | 0.0009197 | 0.3100002 | 0.3092715 | 0.712571 | 0.6369810 | NA |
| 22 | 51181919 | rs9616825 | G | C | 0.0006033 | 0.0009159 | 0.5099998 | 0.5100878 | 0.695031 | 0.6194090 | NA |
| 22 | 51182485 | rs6009961 | A | G | 0.0010532 | 0.0009227 | 0.2500000 | 0.2537186 | 0.714237 | 0.6383790 | NA |
| 22 | 51186143 | rs2879914 | T | C | 0.0007562 | 0.0008593 | 0.3800004 | 0.3788474 | 0.380077 | 0.2733630 | NA |
| 22 | 51186228 | rs3865766 | C | T | 0.0011972 | 0.0008370 | 0.1499999 | 0.1526259 | 0.449547 | 0.4532750 | NA |
| 22 | 51197266 | rs61290853 | A | G | 0.0012130 | 0.0008626 | 0.1600000 | 0.1596226 | 0.386693 | 0.4229230 | NA |
| 22 | 51198027 | rs34939255 | A | G | -0.0004758 | 0.0009783 | 0.6300007 | 0.6267108 | 0.254586 | 0.0984425 | NA |
| 22 | 51211106 | rs9628250 | T | C | -0.0004509 | 0.0009704 | 0.6400000 | 0.6421925 | 0.271468 | 0.1671330 | NA |
| 22 | 51212875 | rs2238837 | A | C | 0.0013616 | 0.0009224 | 0.1400000 | 0.1399360 | 0.331351 | 0.3724040 | NA |
| 22 | 51237063 | rs3896457 | T | C | 0.0002124 | 0.0009424 | 0.8200001 | 0.8216742 | 0.298393 | 0.2050720 | NA |
bcf preview
1 49298 rs10399793 T C . PASS AF=0.623812 ES:SE:LP:AF:ID -0.000807327:0.00141961:0.244125:0.623812:rs10399793
1 54676 rs2462492 C T . PASS AF=0.399144 ES:SE:LP:AF:ID -0.0005104:0.00141548:0.142668:0.399144:rs2462492
1 91536 rs6702460 G T . PASS AF=0.455916 ES:SE:LP:AF:ID 0.00149804:0.00139222:0.552842:0.455916:rs6702460
1 706368 rs12029736 A G . PASS AF=0.513304 ES:SE:LP:AF:ID 0.00103939:0.000981414:0.537602:0.513304:rs12029736
1 763394 rs3115847 G A . PASS AF=0.705804 ES:SE:LP:AF:ID 0.00160399:0.00114978:0.79588:0.705804:rs3115847
1 776546 rs12124819 A G . PASS AF=0.263729 ES:SE:LP:AF:ID 0.000320644:0.00105301:0.119186:0.263729:rs12124819
1 814495 rs74461805 C A . PASS AF=0.340108 ES:SE:LP:AF:ID 0.000698952:0.00134394:0.221849:0.340108:rs74461805
1 830181 rs28444699 A G . PASS AF=0.696612 ES:SE:LP:AF:ID -0.00150122:0.000899132:1.02228:0.696612:rs28444699
1 831489 rs4970385 C T . PASS AF=0.705031 ES:SE:LP:AF:ID -0.00108634:0.000882844:0.657577:0.705031:rs4970385
1 831909 rs9697642 C T . PASS AF=0.705083 ES:SE:LP:AF:ID -0.00107034:0.000882843:0.638272:0.705083:rs9697642
1 832066 rs9697380 G C . PASS AF=0.705261 ES:SE:LP:AF:ID -0.00107535:0.000882802:0.657577:0.705261:rs9697380
1 832318 rs4500250 C A . PASS AF=0.705286 ES:SE:LP:AF:ID -0.00108428:0.000882925:0.657577:0.705286:rs4500250
1 832398 rs4553118 T C . PASS AF=0.730154 ES:SE:LP:AF:ID -0.00101465:0.000907281:0.585027:0.730154:rs4553118
1 832918 rs28765502 T C . PASS AF=0.294729 ES:SE:LP:AF:ID 0.00107555:0.000882897:0.657577:0.294729:rs28765502
1 836896 rs28705752 T C . PASS AF=0.269687 ES:SE:LP:AF:ID 0.000796975:0.000900826:0.420216:0.269687:rs28705752
1 839103 rs28562941 A G . PASS AF=0.270067 ES:SE:LP:AF:ID 0.000752739:0.000901565:0.39794:0.270067:rs28562941
1 840753 rs4970382 T C . PASS AF=0.400406 ES:SE:LP:AF:ID 0.000417142:0.000815002:0.21467:0.400406:rs4970382
1 843405 rs11516185 A G . PASS AF=0.362367 ES:SE:LP:AF:ID -0.00121037:0.001014:0.638272:0.362367:rs11516185
1 850218 rs6664536 T A . PASS AF=0.589315 ES:SE:LP:AF:ID 0.000168442:0.000810583:0.0757207:0.589315:rs6664536
1 850371 rs6679046 G T . PASS AF=0.603035 ES:SE:LP:AF:ID -0.000133994:0.000814461:0.0604807:0.603035:rs6679046
1 850780 rs6657440 C T . PASS AF=0.603381 ES:SE:LP:AF:ID -0.000149582:0.000814475:0.0705811:0.603381:rs6657440
1 852037 rs4970463 G A . PASS AF=0.588673 ES:SE:LP:AF:ID 0.000174858:0.00081174:0.0809219:0.588673:rs4970463
1 852063 rs28436996 G A . PASS AF=0.588649 ES:SE:LP:AF:ID 0.000203829:0.000811374:0.09691:0.588649:rs28436996
1 852875 rs13303369 C T . PASS AF=0.606715 ES:SE:LP:AF:ID -0.000114022:0.000815815:0.05061:0.606715:rs13303369
1 853954 rs1806509 C A . PASS AF=0.60688 ES:SE:LP:AF:ID -0.000132033:0.0008159:0.0604807:0.60688:rs1806509
1 854777 rs13303019 A G . PASS AF=0.609504 ES:SE:LP:AF:ID -6.23117e-05:0.000816716:0.0268721:0.609504:rs13303019
1 854978 rs13303057 A C . PASS AF=0.602505 ES:SE:LP:AF:ID -0.000124801:0.000814603:0.0555173:0.602505:rs13303057
1 855075 rs6673914 C G . PASS AF=0.609473 ES:SE:LP:AF:ID -4.41143e-05:0.000816608:0.0177288:0.609473:rs6673914
1 856099 rs28534711 T G . PASS AF=0.390835 ES:SE:LP:AF:ID 5.56984e-05:0.00081694:0.0222764:0.390835:rs28534711
1 856108 rs28742275 A G . PASS AF=0.390777 ES:SE:LP:AF:ID 5.94923e-05:0.000817024:0.0268721:0.390777:rs28742275
1 856476 rs4040605 A G . PASS AF=0.352504 ES:SE:LP:AF:ID -0.000285729:0.000838651:0.136677:0.352504:rs4040605
1 866893 rs2880024 T C . PASS AF=0.608083 ES:SE:LP:AF:ID -0.000214284:0.000824165:0.102373:0.608083:rs2880024
1 868418 rs28546443 C T . PASS AF=0.301063 ES:SE:LP:AF:ID 0.00149276:0.000902658:1.00877:0.301063:rs28546443
1 870645 rs28576697 T C . PASS AF=0.293389 ES:SE:LP:AF:ID 0.000587494:0.000892791:0.29243:0.293389:rs28576697
1 871334 rs4072383 G T . PASS AF=0.717959 ES:SE:LP:AF:ID -0.000583777:0.000888157:0.29243:0.717959:rs4072383
1 872352 rs1806780 G C . PASS AF=0.269716 ES:SE:LP:AF:ID 0.000968756:0.000899184:0.552842:0.269716:rs1806780
1 873558 rs1110052 G T . PASS AF=0.71249 ES:SE:LP:AF:ID -0.000785389:0.000881508:0.431798:0.71249:rs1110052
1 875770 rs4970379 A G . PASS AF=0.598464 ES:SE:LP:AF:ID -0.000454027:0.000830329:0.236572:0.598464:rs4970379
1 881627 rs2272757 G A . PASS AF=0.65048 ES:SE:LP:AF:ID -0.000436406:0.000838783:0.221849:0.65048:rs2272757
1 891059 rs13303065 C T . PASS AF=0.650626 ES:SE:LP:AF:ID -0.000445328:0.000838702:0.221849:0.650626:rs13303065
1 891945 rs13303106 A G . PASS AF=0.650689 ES:SE:LP:AF:ID -0.00045557:0.000839661:0.229148:0.650689:rs13303106
1 900505 rs28705211 G C . PASS AF=0.273272 ES:SE:LP:AF:ID 0.00117238:0.000905179:0.69897:0.273272:rs28705211
1 903245 rs28690976 A G . PASS AF=0.565133 ES:SE:LP:AF:ID -0.000677946:0.000833773:0.376751:0.565133:rs28690976
1 909073 rs3892467 C T . PASS AF=0.386217 ES:SE:LP:AF:ID 0.000340624:0.000832031:0.167491:0.386217:rs3892467
1 909238 rs3829740 G C . PASS AF=0.572164 ES:SE:LP:AF:ID 0.00084245:0.000804945:0.522879:0.572164:rs3829740
1 910394 rs28477686 C T . PASS AF=0.322663 ES:SE:LP:AF:ID -0.000347085:0.00087433:0.161151:0.322663:rs28477686
1 912049 rs7367995 T C . PASS AF=0.585242 ES:SE:LP:AF:ID -0.000483807:0.000812749:0.259637:0.585242:rs7367995
1 913889 rs2340596 G A . PASS AF=0.600025 ES:SE:LP:AF:ID -0.000347015:0.000814365:0.173925:0.600025:rs2340596
1 914333 rs13302979 C G . PASS AF=0.60338 ES:SE:LP:AF:ID -0.000432837:0.000817128:0.221849:0.60338:rs13302979
1 914852 rs13303368 G C . PASS AF=0.60101 ES:SE:LP:AF:ID -0.000290982:0.000815624:0.142668:0.60101:rs13303368