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 | PAL246_S244_L001_R1_001.good.fq | 4,009,977 | 546,246,404 | 100.0% | 136.2 bases | 140 bases | 97.8% |
| errors | PAL246_S244_L001_R2_001.good.fq | 4,009,977 | 546,246,404 | 100.0% | 136.2 bases | 140 bases | 97.5% |
| total | 8,019,954 | 1,092,492,808 | 100.0% | 136.2 bases | 140 bases | 97.7% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | CP009273 | 4,631,469 | 259.7 | 73.5 | 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 | 62843 |
| 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 | 40 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.002 |
| reference sequence | pr(no read start) |
|---|---|
| CP009273 | 0.76148 |
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 | 23:03:06 16 Jun 2022 | 23:05:32 16 Jun 2022 | 2 minutes 26 seconds |
| Read alignment to reference genome | 23:05:32 16 Jun 2022 | 23:23:39 16 Jun 2022 | 18 minutes 7 seconds |
| Preprocessing alignments for candidate junction identification | 23:23:39 16 Jun 2022 | 23:25:24 16 Jun 2022 | 1 minute 45 seconds |
| Preliminary analysis of coverage distribution | 23:25:24 16 Jun 2022 | 23:29:22 16 Jun 2022 | 3 minutes 58 seconds |
| Identifying junction candidates | 23:29:22 16 Jun 2022 | 23:29:49 16 Jun 2022 | 27 seconds |
| Re-alignment to junction candidates | 23:29:49 16 Jun 2022 | 23:34:03 16 Jun 2022 | 4 minutes 14 seconds |
| Resolving best read alignments | 23:34:03 16 Jun 2022 | 23:36:46 16 Jun 2022 | 2 minutes 43 seconds |
| Creating BAM files | 23:36:46 16 Jun 2022 | 23:40:09 16 Jun 2022 | 3 minutes 23 seconds |
| Tabulating error counts | 23:40:09 16 Jun 2022 | 23:41:55 16 Jun 2022 | 1 minute 46 seconds |
| Re-calibrating base error rates | 23:41:55 16 Jun 2022 | 23:41:56 16 Jun 2022 | 1 second |
| Examining read alignment evidence | 23:41:56 16 Jun 2022 | 01:47:19 17 Jun 2022 | 2 hours 5 minutes 23 seconds |
| Polymorphism statistics | 01:47:19 17 Jun 2022 | 01:47:21 17 Jun 2022 | 2 seconds |
| Output | 01:47:21 17 Jun 2022 | 01:47:43 17 Jun 2022 | 22 seconds |
| Total | 2 hours 44 minutes 37 seconds | ||
