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 | HL2KG8_3_S83_L002_R1_001.good.fq | 18,645,334 | 2,541,326,932 | 100.0% | 136.3 bases | 137 bases | 99.7% |
| errors | HL2KG8_3_S83_L002_R2_001.good.fq | 18,645,334 | 2,541,326,932 | 100.0% | 136.3 bases | 137 bases | 99.0% |
| total | 37,290,668 | 5,082,653,864 | 100.0% | 136.3 bases | 137 bases | 99.4% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | AE015451_phaM1 | 6,179,149 | 833.2 | 15.9 | 98.2% | Pseudomonas putida KT2440, complete sequence , pha::M1. |
| coverage | distribution | pS4413_qbsFH | 5,211 | 18059.6 | 151.0 | 1.8% | Plasmid. |
| total | 6,184,360 | 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 | 85592 |
| 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 | 1257 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.057 |
| reference sequence | pr(no read start) |
|---|---|
| AE015451_phaM1 | 0.54660 |
| pS4413_qbsFH | 0.09592 |
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 | 21:37:40 04 Feb 2026 | 21:42:51 04 Feb 2026 | 5 minutes 11 seconds |
| Read alignment to reference genome | 21:42:51 04 Feb 2026 | 22:16:37 04 Feb 2026 | 33 minutes 46 seconds |
| Preprocessing alignments for candidate junction identification | 22:16:37 04 Feb 2026 | 22:22:32 04 Feb 2026 | 5 minutes 55 seconds |
| Preliminary analysis of coverage distribution | 22:22:32 04 Feb 2026 | 22:33:31 04 Feb 2026 | 10 minutes 59 seconds |
| Identifying junction candidates | 22:33:31 04 Feb 2026 | 22:34:20 04 Feb 2026 | 49 seconds |
| Re-alignment to junction candidates | 22:34:20 04 Feb 2026 | 22:46:14 04 Feb 2026 | 11 minutes 54 seconds |
| Resolving best read alignments | 22:46:14 04 Feb 2026 | 22:55:33 04 Feb 2026 | 9 minutes 19 seconds |
| Creating BAM files | 22:55:33 04 Feb 2026 | 23:04:21 04 Feb 2026 | 8 minutes 48 seconds |
| Tabulating error counts | 23:04:21 04 Feb 2026 | 23:10:04 04 Feb 2026 | 5 minutes 43 seconds |
| Re-calibrating base error rates | 23:10:04 04 Feb 2026 | 23:10:06 04 Feb 2026 | 2 seconds |
| Examining read alignment evidence | 23:10:06 04 Feb 2026 | 00:25:28 05 Feb 2026 | 1 hour 15 minutes 22 seconds |
| Polymorphism statistics | 00:25:28 05 Feb 2026 | 00:25:30 05 Feb 2026 | 2 seconds |
| Output | 00:25:30 05 Feb 2026 | 00:26:52 05 Feb 2026 | 1 minute 22 seconds |
| Total | 2 hours 49 minutes 12 seconds | ||
