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 | JADR40_end_pooled_R1.good.fq | 5,023,032 | 753,396,429 | 100.0% | 150.0 bases | 150 bases | 99.6% |
| errors | JADR40_end_pooled_R2.good.fq | 5,023,032 | 753,396,429 | 100.0% | 150.0 bases | 150 bases | 99.5% |
| total | 10,046,064 | 1,506,792,858 | 100.0% | 150.0 bases | 150 bases | 99.6% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | BS168_reference_genome | 4,215,606 | 326.5 | 6.4 | 90.6% | Bacillus subtilis subsp. subtilis str. 168 complete genome. |
| coverage | distribution | Exported | 6,538 | 24270.6 | 486.1 | 9.4% | natural circular DNA |
| total | 4,222,144 | 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 | 46181 |
| 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 | 124 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.009 |
| reference sequence | pr(no read start) |
|---|---|
| BS168_reference_genome | 0.38229 |
| Exported | 0.02853 |
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 | 11:45:35 20 Jan 2021 | 11:48:32 20 Jan 2021 | 2 minutes 57 seconds |
| Read alignment to reference genome | 11:48:32 20 Jan 2021 | 12:09:20 20 Jan 2021 | 20 minutes 48 seconds |
| Preprocessing alignments for candidate junction identification | 12:09:20 20 Jan 2021 | 12:11:35 20 Jan 2021 | 2 minutes 15 seconds |
| Preliminary analysis of coverage distribution | 12:11:35 20 Jan 2021 | 12:19:38 20 Jan 2021 | 8 minutes 3 seconds |
| Identifying junction candidates | 12:19:38 20 Jan 2021 | 12:19:41 20 Jan 2021 | 3 seconds |
| Re-alignment to junction candidates | 12:19:41 20 Jan 2021 | 12:26:41 20 Jan 2021 | 7 minutes 0 seconds |
| Resolving best read alignments | 12:26:41 20 Jan 2021 | 12:30:18 20 Jan 2021 | 3 minutes 37 seconds |
| Creating BAM files | 12:30:18 20 Jan 2021 | 12:37:51 20 Jan 2021 | 7 minutes 33 seconds |
| Tabulating error counts | 12:37:51 20 Jan 2021 | 12:40:19 20 Jan 2021 | 2 minutes 28 seconds |
| Re-calibrating base error rates | 12:40:19 20 Jan 2021 | 12:40:21 20 Jan 2021 | 2 seconds |
| Examining read alignment evidence | 12:40:21 20 Jan 2021 | 15:36:17 20 Jan 2021 | 2 hours 55 minutes 56 seconds |
| Polymorphism statistics | 15:36:17 20 Jan 2021 | 15:36:19 20 Jan 2021 | 2 seconds |
| Output | 15:36:19 20 Jan 2021 | 15:38:18 20 Jan 2021 | 1 minute 59 seconds |
| Total | 3 hours 52 minutes 43 seconds | ||
