breseq version 0.35.4 revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
read file | reads | bases | passed filters | average | longest | mapped | |
---|---|---|---|---|---|---|---|
errors | 29_S29_L001_R1_001.good.fq | 355,546 | 52,169,244 | 100.0% | 146.7 bases | 149 bases | 98.9% |
errors | 29_S29_L001_R2_001.good.fq | 355,546 | 52,169,308 | 100.0% | 146.7 bases | 149 bases | 97.5% |
errors | 29_S29_L002_R1_001.good.fq | 349,023 | 51,227,188 | 100.0% | 146.8 bases | 149 bases | 98.8% |
errors | 29_S29_L002_R2_001.good.fq | 349,023 | 51,233,329 | 100.0% | 146.8 bases | 149 bases | 97.1% |
errors | 29_S29_L003_R1_001.good.fq | 356,631 | 51,979,641 | 100.0% | 145.8 bases | 148 bases | 99.0% |
errors | 29_S29_L003_R2_001.good.fq | 356,631 | 51,979,093 | 100.0% | 145.8 bases | 148 bases | 97.9% |
errors | 29_S29_L004_R1_001.good.fq | 367,807 | 53,953,910 | 100.0% | 146.7 bases | 149 bases | 99.0% |
errors | 29_S29_L004_R2_001.good.fq | 367,807 | 53,953,685 | 100.0% | 146.7 bases | 149 bases | 98.1% |
total | 2,858,014 | 418,665,398 | 100.0% | 146.5 bases | 149 bases | 98.3% |
seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
---|---|---|---|---|---|---|---|
coverage | distribution | NC_002947_CJ-RC | 6,184,688 | 67.4 | 1.7 | 100.0% | Pseudomonas putida KT2440 chromosome, complete genome. |
total | 6,184,688 | 100.0% |
fit dispersion is the ratio of the variance to the mean for the negative binomial fit. It is =1 for Poisson and >1 for over-dispersed data.
option | limit | actual |
---|---|---|
Number of alignment pairs examined for constructing junction candidates | ≤ 100000 | 13975 |
Coverage evenness (position-hash) score of junction candidates | ≥ 2 | ≥ 2 |
Test this many junction candidates (n). May be smaller if not enough passed the coverage evenness threshold | 100 ≤ n ≤ 5000 | 714 |
Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.035 |
reference sequence | pr(no read start) |
---|---|
NC_002947_CJ-RC | 0.81188 |
pr(no read start) is the probability that there will not be an aligned read whose first base matches a given position on a given strand.
option | value |
---|---|
Coverage evenness (position-hash) score of predicted junctions must be | ≥ 3 |
Minimum probablilty assigned that no mapped read will start at a given position and strand for junction prediction | 0.1 |
Junction allow suboptimal matches | FALSE |
Skew score of predicted junction (−log10 probability of unusual coverage evenness) must be | ≤ 3 |
Number of bases that at least one read must overlap each uniquely aligned side of a predicted junction | ≥ 1 |
option | value |
---|---|
Mode | Consensus/Mixed Base |
Ploidy | 1 (haploid) |
Consensus mutation E-value cutoff | 10 |
Consensus frequency cutoff | 0.75 |
Consensus minimum variant coverage each strand | OFF |
Consensus minimum total coverage each strand | OFF |
Consensus minimum variant coverage | OFF |
Consensus minimum total coverage | OFF |
Polymorphism E-value cutoff | 10 |
Polymorphism frequency cutoff | 0.2 |
Polymorphism minimum variant coverage each strand | OFF |
Polymorphism minimum total coverage each strand | OFF |
Polymorphism minimum variant coverage | OFF |
Polymorphism minimum total coverage | OFF |
Polymorphism bias cutoff | OFF |
Predict indel polymorphisms | YES |
Skip indel polymorphisms in homopolymers runs of | OFF |
Skip base substitutions when they create a homopolymer flanked on each side by | OFF |
program | version |
---|---|
bowtie2 | 2.2.6 |
R | 3.4.4 |
step | start | end | elapsed |
---|---|---|---|
Read and reference sequence file input | 14:43:36 25 Oct 2024 | 14:44:27 25 Oct 2024 | 51 seconds |
Read alignment to reference genome | 14:44:27 25 Oct 2024 | 14:50:29 25 Oct 2024 | 6 minutes 2 seconds |
Preprocessing alignments for candidate junction identification | 14:50:29 25 Oct 2024 | 14:51:07 25 Oct 2024 | 38 seconds |
Preliminary analysis of coverage distribution | 14:51:07 25 Oct 2024 | 14:52:43 25 Oct 2024 | 1 minute 36 seconds |
Identifying junction candidates | 14:52:43 25 Oct 2024 | 14:52:47 25 Oct 2024 | 4 seconds |
Re-alignment to junction candidates | 14:52:47 25 Oct 2024 | 14:54:30 25 Oct 2024 | 1 minute 43 seconds |
Resolving best read alignments | 14:54:30 25 Oct 2024 | 14:55:22 25 Oct 2024 | 52 seconds |
Creating BAM files | 14:55:22 25 Oct 2024 | 14:56:48 25 Oct 2024 | 1 minute 26 seconds |
Tabulating error counts | 14:56:48 25 Oct 2024 | 14:57:27 25 Oct 2024 | 39 seconds |
Re-calibrating base error rates | 14:57:27 25 Oct 2024 | 14:57:30 25 Oct 2024 | 3 seconds |
Examining read alignment evidence | 14:57:30 25 Oct 2024 | 15:05:15 25 Oct 2024 | 7 minutes 45 seconds |
Polymorphism statistics | 15:05:15 25 Oct 2024 | 15:05:16 25 Oct 2024 | 1 second |
Output | 15:05:16 25 Oct 2024 | 15:05:33 25 Oct 2024 | 17 seconds |
Total | 21 minutes 57 seconds |