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 | SRR3722064_R1.good.fq | 840,596 | 71,027,706 | 100.0% | 84.5 bases | 90 bases | 94.8% |
errors | SRR3722064_R2.good.fq | 840,597 | 71,027,796 | 100.0% | 84.5 bases | 90 bases | 95.4% |
total | 1,681,193 | 142,055,502 | 100.0% | 84.5 bases | 90 bases | 95.1% |
seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
---|---|---|---|---|---|---|---|
coverage | distribution | NZ_CP009273 | 4,631,469 | 28.7 | 3.8 | 100.0% | Escherichia coli BW25113 strain K-12 chromosome, complete genome. |
total | 4,631,469 | 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 | 1248 |
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 | 48 |
Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.002 |
reference sequence | pr(no read start) |
---|---|
NZ_CP009273 | 0.87805 |
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 | 15:13:09 25 Jan 2023 | 15:13:39 25 Jan 2023 | 30 seconds |
Read alignment to reference genome | 15:13:39 25 Jan 2023 | 15:16:09 25 Jan 2023 | 2 minutes 30 seconds |
Preprocessing alignments for candidate junction identification | 15:16:09 25 Jan 2023 | 15:16:27 25 Jan 2023 | 18 seconds |
Preliminary analysis of coverage distribution | 15:16:27 25 Jan 2023 | 15:17:07 25 Jan 2023 | 40 seconds |
Identifying junction candidates | 15:17:07 25 Jan 2023 | 15:17:07 25 Jan 2023 | 0 seconds |
Re-alignment to junction candidates | 15:17:07 25 Jan 2023 | 15:17:37 25 Jan 2023 | 30 seconds |
Resolving best read alignments | 15:17:37 25 Jan 2023 | 15:18:00 25 Jan 2023 | 23 seconds |
Creating BAM files | 15:18:00 25 Jan 2023 | 15:18:35 25 Jan 2023 | 35 seconds |
Tabulating error counts | 15:18:35 25 Jan 2023 | 15:18:47 25 Jan 2023 | 12 seconds |
Re-calibrating base error rates | 15:18:47 25 Jan 2023 | 15:18:48 25 Jan 2023 | 1 second |
Examining read alignment evidence | 15:18:48 25 Jan 2023 | 15:21:26 25 Jan 2023 | 2 minutes 38 seconds |
Polymorphism statistics | 15:21:26 25 Jan 2023 | 15:21:26 25 Jan 2023 | 0 seconds |
Output | 15:21:26 25 Jan 2023 | 15:21:34 25 Jan 2023 | 8 seconds |
Total | 8 minutes 25 seconds |