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 | 59_S59_L001_R1_001.good.fq | 316,595 | 46,587,510 | 100.0% | 147.2 bases | 149 bases | 99.1% |
| errors | 59_S59_L001_R2_001.good.fq | 316,595 | 46,586,714 | 100.0% | 147.1 bases | 149 bases | 97.9% |
| errors | 59_S59_L002_R1_001.good.fq | 311,104 | 45,770,569 | 100.0% | 147.1 bases | 149 bases | 99.0% |
| errors | 59_S59_L002_R2_001.good.fq | 311,104 | 45,773,669 | 100.0% | 147.1 bases | 149 bases | 97.5% |
| errors | 59_S59_L003_R1_001.good.fq | 316,866 | 46,617,127 | 100.0% | 147.1 bases | 149 bases | 99.2% |
| errors | 59_S59_L003_R2_001.good.fq | 316,866 | 46,614,208 | 100.0% | 147.1 bases | 149 bases | 98.2% |
| errors | 59_S59_L004_R1_001.good.fq | 325,504 | 47,540,735 | 100.0% | 146.1 bases | 148 bases | 99.3% |
| errors | 59_S59_L004_R2_001.good.fq | 325,504 | 47,536,766 | 100.0% | 146.0 bases | 148 bases | 98.6% |
| total | 2,540,138 | 373,027,298 | 100.0% | 146.9 bases | 149 bases | 98.6% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_002947_CJ-RC | 6,184,688 | 60.3 | 1.8 | 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 | 7787 |
| 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 | 362 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.018 |
| reference sequence | pr(no read start) |
|---|---|
| NC_002947_CJ-RC | 0.83089 |
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 | 14:41:51 25 Oct 2024 | 14:42:36 25 Oct 2024 | 45 seconds |
| Read alignment to reference genome | 14:42:37 25 Oct 2024 | 14:47:46 25 Oct 2024 | 5 minutes 9 seconds |
| Preprocessing alignments for candidate junction identification | 14:47:46 25 Oct 2024 | 14:48:20 25 Oct 2024 | 34 seconds |
| Preliminary analysis of coverage distribution | 14:48:20 25 Oct 2024 | 14:49:45 25 Oct 2024 | 1 minute 25 seconds |
| Identifying junction candidates | 14:49:45 25 Oct 2024 | 14:49:47 25 Oct 2024 | 2 seconds |
| Re-alignment to junction candidates | 14:49:47 25 Oct 2024 | 14:51:09 25 Oct 2024 | 1 minute 22 seconds |
| Resolving best read alignments | 14:51:09 25 Oct 2024 | 14:51:55 25 Oct 2024 | 46 seconds |
| Creating BAM files | 14:51:55 25 Oct 2024 | 14:53:11 25 Oct 2024 | 1 minute 16 seconds |
| Tabulating error counts | 14:53:11 25 Oct 2024 | 14:53:46 25 Oct 2024 | 35 seconds |
| Re-calibrating base error rates | 14:53:46 25 Oct 2024 | 14:53:49 25 Oct 2024 | 3 seconds |
| Examining read alignment evidence | 14:53:49 25 Oct 2024 | 15:00:44 25 Oct 2024 | 6 minutes 55 seconds |
| Polymorphism statistics | 15:00:44 25 Oct 2024 | 15:00:44 25 Oct 2024 | 0 seconds |
| Output | 15:00:44 25 Oct 2024 | 15:00:59 25 Oct 2024 | 15 seconds |
| Total | 19 minutes 7 seconds | ||
