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 | PAL213_S211_L001_R1_001.good.fq | 8,614,804 | 1,161,914,882 | 100.0% | 134.9 bases | 138 bases | 98.9% |
| errors | PAL213_S211_L001_R2_001.good.fq | 8,614,804 | 1,161,914,882 | 100.0% | 134.9 bases | 138 bases | 98.1% |
| total | 17,229,608 | 2,323,829,764 | 100.0% | 134.9 bases | 138 bases | 98.5% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | CP009273 | 4,631,469 | 488.0 | 28.5 | 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 | 24984 |
| 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 | 657 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.040 |
| reference sequence | pr(no read start) |
|---|---|
| CP009273 | 0.65579 |
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 | 23:21:11 16 Jun 2022 | 23:25:59 16 Jun 2022 | 4 minutes 48 seconds |
| Read alignment to reference genome | 23:25:59 16 Jun 2022 | 00:00:43 17 Jun 2022 | 34 minutes 44 seconds |
| Preprocessing alignments for candidate junction identification | 00:00:43 17 Jun 2022 | 00:04:59 17 Jun 2022 | 4 minutes 16 seconds |
| Preliminary analysis of coverage distribution | 00:04:59 17 Jun 2022 | 00:13:03 17 Jun 2022 | 8 minutes 4 seconds |
| Identifying junction candidates | 00:13:03 17 Jun 2022 | 00:13:08 17 Jun 2022 | 5 seconds |
| Re-alignment to junction candidates | 00:13:08 17 Jun 2022 | 00:23:39 17 Jun 2022 | 10 minutes 31 seconds |
| Resolving best read alignments | 00:23:39 17 Jun 2022 | 00:29:14 17 Jun 2022 | 5 minutes 35 seconds |
| Creating BAM files | 00:29:14 17 Jun 2022 | 00:36:26 17 Jun 2022 | 7 minutes 12 seconds |
| Tabulating error counts | 00:36:26 17 Jun 2022 | 00:39:46 17 Jun 2022 | 3 minutes 20 seconds |
| Re-calibrating base error rates | 00:39:46 17 Jun 2022 | 00:39:47 17 Jun 2022 | 1 second |
| Examining read alignment evidence | 00:39:47 17 Jun 2022 | 06:22:36 17 Jun 2022 | 5 hours 42 minutes 49 seconds |
| Polymorphism statistics | 06:22:36 17 Jun 2022 | 06:22:38 17 Jun 2022 | 2 seconds |
| Output | 06:22:38 17 Jun 2022 | 06:23:19 17 Jun 2022 | 41 seconds |
| Total | 7 hours 2 minutes 8 seconds | ||
