mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
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 | c13-Redo-6-23_S12_L001_R1_001.good.fq | 1,092,357 | 295,722,134 | 100.0% | 270.7 bases | 289 bases | 99.1% |
| errors | c13-Redo-6-23_S12_L001_R2_001.good.fq | 1,092,357 | 296,399,714 | 100.0% | 271.3 bases | 289 bases | 87.1% |
| total | 2,184,714 | 592,121,848 | 100.0% | 271.0 bases | 289 bases | 93.1% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_000913 | 4,641,652 | 120.0 | 6.0 | 100.0% | Escherichia coli str. K-12 substr. MG1655, complete genome. |
| total | 4,641,652 | 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 | 2695 |
| 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 | 250 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.032 |
| reference sequence | pr(no read start) |
|---|---|
| NC_000913 | 0.86316 |
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 | 09:31:06 09 Jul 2022 | 09:32:00 09 Jul 2022 | 54 seconds |
| Read alignment to reference genome | 09:32:00 09 Jul 2022 | 09:43:49 09 Jul 2022 | 11 minutes 49 seconds |
| Preprocessing alignments for candidate junction identification | 09:43:49 09 Jul 2022 | 09:44:26 09 Jul 2022 | 37 seconds |
| Preliminary analysis of coverage distribution | 09:44:26 09 Jul 2022 | 09:46:24 09 Jul 2022 | 1 minute 58 seconds |
| Identifying junction candidates | 09:46:24 09 Jul 2022 | 09:46:26 09 Jul 2022 | 2 seconds |
| Re-alignment to junction candidates | 09:46:26 09 Jul 2022 | 09:48:29 09 Jul 2022 | 2 minutes 3 seconds |
| Resolving best read alignments | 09:48:29 09 Jul 2022 | 09:49:23 09 Jul 2022 | 54 seconds |
| Creating BAM files | 09:49:23 09 Jul 2022 | 09:51:02 09 Jul 2022 | 1 minute 39 seconds |
| Tabulating error counts | 09:51:02 09 Jul 2022 | 09:51:58 09 Jul 2022 | 56 seconds |
| Re-calibrating base error rates | 09:51:58 09 Jul 2022 | 09:51:59 09 Jul 2022 | 1 second |
| Examining read alignment evidence | 09:51:59 09 Jul 2022 | 10:03:33 09 Jul 2022 | 11 minutes 34 seconds |
| Polymorphism statistics | 10:03:33 09 Jul 2022 | 10:03:33 09 Jul 2022 | 0 seconds |
| Output | 10:03:33 09 Jul 2022 | 10:03:45 09 Jul 2022 | 12 seconds |
| Total | 32 minutes 39 seconds | ||
