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 | PAL245_S243_L001_R1_001.good.fq | 880,314 | 119,232,282 | 100.0% | 135.4 bases | 140 bases | 94.9% |
| errors | PAL245_S243_L001_R2_001.good.fq | 880,314 | 119,232,282 | 100.0% | 135.4 bases | 140 bases | 95.7% |
| total | 1,760,628 | 238,464,564 | 100.0% | 135.4 bases | 140 bases | 95.3% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | CP009273 | 4,631,469 | 46.5 | 6.6 | 100.0% | Escherichia coli BW25113, 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 | 43596 |
| Coverage evenness (position-hash) score of junction candidates | ≥ 2 | ≥ 3 |
| Test this many junction candidates (n). May be smaller if not enough passed the coverage evenness threshold | 100 ≤ n ≤ 5000 | 23 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.001 |
| reference sequence | pr(no read start) |
|---|---|
| CP009273 | 0.91676 |
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 | ≤ 0 |
| Number of bases that at least one read must overlap each uniquely aligned side of a predicted junction | ≥ 6 |
| option | value |
|---|---|
| Mode | Full Polymorphism |
| 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 | 2 |
| Polymorphism frequency cutoff | 0.05 |
| Polymorphism minimum variant coverage each strand | 2 |
| 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 | ≥3 bases |
| Skip base substitutions when they create a homopolymer flanked on each side by | ≥5 bases |
| program | version |
|---|---|
| bowtie2 | 2.2.6 |
| R | 3.4.4 |
| step | start | end | elapsed |
|---|---|---|---|
| Read and reference sequence file input | 22:45:09 16 Jun 2022 | 22:45:52 16 Jun 2022 | 43 seconds |
| Read alignment to reference genome | 22:45:52 16 Jun 2022 | 22:52:36 16 Jun 2022 | 6 minutes 44 seconds |
| Preprocessing alignments for candidate junction identification | 22:52:36 16 Jun 2022 | 22:53:09 16 Jun 2022 | 33 seconds |
| Preliminary analysis of coverage distribution | 22:53:09 16 Jun 2022 | 22:54:02 16 Jun 2022 | 53 seconds |
| Identifying junction candidates | 22:54:02 16 Jun 2022 | 22:54:18 16 Jun 2022 | 16 seconds |
| Re-alignment to junction candidates | 22:54:18 16 Jun 2022 | 22:55:12 16 Jun 2022 | 54 seconds |
| Resolving best read alignments | 22:55:12 16 Jun 2022 | 22:55:44 16 Jun 2022 | 32 seconds |
| Creating BAM files | 22:55:44 16 Jun 2022 | 22:56:26 16 Jun 2022 | 42 seconds |
| Tabulating error counts | 22:56:26 16 Jun 2022 | 22:56:47 16 Jun 2022 | 21 seconds |
| Re-calibrating base error rates | 22:56:47 16 Jun 2022 | 22:56:48 16 Jun 2022 | 1 second |
| Examining read alignment evidence | 22:56:48 16 Jun 2022 | 23:08:01 16 Jun 2022 | 11 minutes 13 seconds |
| Polymorphism statistics | 23:08:01 16 Jun 2022 | 23:08:02 16 Jun 2022 | 1 second |
| Output | 23:08:02 16 Jun 2022 | 23:08:21 16 Jun 2022 | 19 seconds |
| Total | 23 minutes 12 seconds | ||
