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_4_S84_L002_R1_001.good.fq | 19,513,867 | 2,658,528,256 | 100.0% | 136.2 bases | 137 bases | 99.7% |
| errors | HL2KG8_4_S84_L002_R2_001.good.fq | 19,513,867 | 2,658,528,256 | 100.0% | 136.2 bases | 137 bases | 99.0% |
| total | 39,027,734 | 5,317,056,512 | 100.0% | 136.2 bases | 137 bases | 99.3% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | AE015451_phaM1 | 6,179,149 | 908.3 | 18.6 | 98.0% | Pseudomonas putida KT2440, complete sequence , pha::M1. |
| coverage | distribution | pS4413_qbsFH | 5,211 | 20293.7 | 166.0 | 2.0% | 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 | 89491 |
| 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 | 1388 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.063 |
| reference sequence | pr(no read start) |
|---|---|
| AE015451_phaM1 | 0.54641 |
| pS4413_qbsFH | 0.08431 |
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 | 20:44:59 04 Feb 2026 | 20:50:10 04 Feb 2026 | 5 minutes 11 seconds |
| Read alignment to reference genome | 20:50:11 04 Feb 2026 | 21:23:56 04 Feb 2026 | 33 minutes 45 seconds |
| Preprocessing alignments for candidate junction identification | 21:23:56 04 Feb 2026 | 21:29:54 04 Feb 2026 | 5 minutes 58 seconds |
| Preliminary analysis of coverage distribution | 21:29:54 04 Feb 2026 | 21:41:16 04 Feb 2026 | 11 minutes 22 seconds |
| Identifying junction candidates | 21:41:16 04 Feb 2026 | 21:42:17 04 Feb 2026 | 1 minute 1 second |
| Re-alignment to junction candidates | 21:42:17 04 Feb 2026 | 21:54:36 04 Feb 2026 | 12 minutes 19 seconds |
| Resolving best read alignments | 21:54:36 04 Feb 2026 | 22:04:24 04 Feb 2026 | 9 minutes 48 seconds |
| Creating BAM files | 22:04:24 04 Feb 2026 | 22:13:47 04 Feb 2026 | 9 minutes 23 seconds |
| Tabulating error counts | 22:13:47 04 Feb 2026 | 22:19:45 04 Feb 2026 | 5 minutes 58 seconds |
| Re-calibrating base error rates | 22:19:45 04 Feb 2026 | 22:19:47 04 Feb 2026 | 2 seconds |
| Examining read alignment evidence | 22:19:47 04 Feb 2026 | 23:39:31 04 Feb 2026 | 1 hour 19 minutes 44 seconds |
| Polymorphism statistics | 23:39:31 04 Feb 2026 | 23:39:33 04 Feb 2026 | 2 seconds |
| Output | 23:39:33 04 Feb 2026 | 23:41:07 04 Feb 2026 | 1 minute 34 seconds |
| Total | 2 hours 56 minutes 7 seconds | ||
