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 | JADR46_end_pooled_R1.good.fq | 5,850,485 | 877,508,415 | 100.0% | 150.0 bases | 150 bases | 99.6% |
| errors | JADR46_end_pooled_R2.good.fq | 5,850,485 | 877,508,415 | 100.0% | 150.0 bases | 150 bases | 99.6% |
| total | 11,700,970 | 1,755,016,830 | 100.0% | 150.0 bases | 150 bases | 99.6% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | CP006881 | 4,033,459 | 414.6 | 7.5 | 93.9% | Bacillus subtilis PY79, complete genome. |
| coverage | distribution | Exported | 6,538 | 17063.9 | 142.0 | 6.1% | natural circular DNA |
| total | 4,039,997 | 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 | 35757 |
| 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 | 149 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.011 |
| reference sequence | pr(no read start) |
|---|---|
| CP006881 | 0.30354 |
| Exported | 0.02875 |
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 | 11:50:34 20 Jan 2021 | 11:54:04 20 Jan 2021 | 3 minutes 30 seconds |
| Read alignment to reference genome | 11:54:04 20 Jan 2021 | 12:20:17 20 Jan 2021 | 26 minutes 13 seconds |
| Preprocessing alignments for candidate junction identification | 12:20:18 20 Jan 2021 | 12:23:02 20 Jan 2021 | 2 minutes 44 seconds |
| Preliminary analysis of coverage distribution | 12:23:02 20 Jan 2021 | 12:32:35 20 Jan 2021 | 9 minutes 33 seconds |
| Identifying junction candidates | 12:32:35 20 Jan 2021 | 12:32:37 20 Jan 2021 | 2 seconds |
| Re-alignment to junction candidates | 12:32:37 20 Jan 2021 | 12:40:28 20 Jan 2021 | 7 minutes 51 seconds |
| Resolving best read alignments | 12:40:28 20 Jan 2021 | 12:44:34 20 Jan 2021 | 4 minutes 6 seconds |
| Creating BAM files | 12:44:34 20 Jan 2021 | 12:53:30 20 Jan 2021 | 8 minutes 56 seconds |
| Tabulating error counts | 12:53:30 20 Jan 2021 | 12:56:18 20 Jan 2021 | 2 minutes 48 seconds |
| Re-calibrating base error rates | 12:56:18 20 Jan 2021 | 12:56:20 20 Jan 2021 | 2 seconds |
| Examining read alignment evidence | 12:56:20 20 Jan 2021 | 16:32:54 20 Jan 2021 | 3 hours 36 minutes 34 seconds |
| Polymorphism statistics | 16:32:54 20 Jan 2021 | 16:32:56 20 Jan 2021 | 2 seconds |
| Output | 16:32:56 20 Jan 2021 | 16:34:29 20 Jan 2021 | 1 minute 33 seconds |
| Total | 4 hours 43 minutes 54 seconds | ||
