mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.35.7 revision b7a44cd89118
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| read file | reads | bases | passed filters | average | longest | mapped | |
|---|---|---|---|---|---|---|---|
| errors | SRR2584534_1 | 1,720,420 | 173,762,420 | 100.0% | 101.0 bases | 101 bases | 81.2% |
| errors | SRR2584534_2 | 1,720,414 | 173,761,814 | 100.0% | 101.0 bases | 101 bases | 80.5% |
| total | 3,440,834 | 347,524,234 | 100.0% | 101.0 bases | 101 bases | 80.8% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_000913 | 4,641,652 | 63.1 | 2.7 | 100.0% | Escherichia coli str. K-12 substr. MG1655, complete genome. |
| total | 4,641,652 | 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 | 48130 |
| Coverage evenness (position-hash) score of junction candidates | ≥ 2 | ≥ 4 |
| Test this many junction candidates (n). May be smaller if not enough passed the coverage evenness threshold | 100 ≤ n ≤ 5000 | 1967 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.091 |
| reference sequence | pr(no read start) |
|---|---|
| NC_000913 | 0.77273 |
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 | ≤ 3 |
| Number of bases that at least one read must overlap each uniquely aligned side of a predicted junction | ≥ 1 |
| option | value |
|---|---|
| Mode | Consensus/Mixed Base |
| Ploidy | 1 (haploid) |
| Consensus mutation E-value cutoff | 10 |
| Consensus frequency cutoff | 0.8 |
| 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 | 10 |
| Polymorphism frequency cutoff | 0.2 |
| Polymorphism minimum variant coverage each strand | OFF |
| 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 | OFF |
| Skip base substitutions when they create a homopolymer flanked on each side by | OFF |
| program | version |
|---|---|
| bowtie2 | 2.3.4.1 |
| R | 4.0.0 |
| step | start | end | elapsed |
|---|---|---|---|
| Read and reference sequence file input | 07:24:52 20 Jul 2021 | 07:26:26 20 Jul 2021 | 1 minute 34 seconds |
| Read alignment to reference genome | 07:26:27 20 Jul 2021 | 07:27:57 20 Jul 2021 | 1 minute 30 seconds |
| Preprocessing alignments for candidate junction identification | 07:27:57 20 Jul 2021 | 07:28:55 20 Jul 2021 | 58 seconds |
| Preliminary analysis of coverage distribution | 07:28:55 20 Jul 2021 | 07:29:51 20 Jul 2021 | 56 seconds |
| Identifying junction candidates | 07:29:51 20 Jul 2021 | 07:41:02 20 Jul 2021 | 11 minutes 11 seconds |
| Re-alignment to junction candidates | 07:41:02 20 Jul 2021 | 07:41:30 20 Jul 2021 | 28 seconds |
| Resolving best read alignments | 07:41:30 20 Jul 2021 | 07:43:03 20 Jul 2021 | 1 minute 33 seconds |
| Creating BAM files | 07:43:03 20 Jul 2021 | 07:43:54 20 Jul 2021 | 51 seconds |
| Tabulating error counts | 07:43:54 20 Jul 2021 | 07:44:18 20 Jul 2021 | 24 seconds |
| Re-calibrating base error rates | 07:44:18 20 Jul 2021 | 07:44:19 20 Jul 2021 | 1 second |
| Examining read alignment evidence | 07:44:19 20 Jul 2021 | 07:49:05 20 Jul 2021 | 4 minutes 46 seconds |
| Polymorphism statistics | 07:49:05 20 Jul 2021 | 07:49:09 20 Jul 2021 | 4 seconds |
| Output | 07:49:09 20 Jul 2021 | 10:05:00 20 Jul 2021 | 2 hours 15 minutes 51 seconds |
| Output :: Mutation Prediction | 07:49:09 20 Jul 2021 | 08:04:38 20 Jul 2021 | 15 minutes 29 seconds |
| Output :: Mutation Annotation | 08:04:38 20 Jul 2021 | 08:04:51 20 Jul 2021 | 13 seconds |
| Total | 2 hours 55 minutes 49 seconds | ||
