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 | G2_CCGTCC_L007_R1_001 | 503,257 | 63,410,382 | 100.0% | 126.0 bases | 126 bases | 98.1% |
| errors | G2_CCGTCC_L007_R2_001 | 502,544 | 63,320,544 | 99.9% | 126.0 bases | 126 bases | 97.9% |
| total | 1,005,801 | 126,730,926 | 99.9% | 126.0 bases | 126 bases | 98.0% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | ADP1-WT | 3,600,835 | 35.1 | 1.7 | 100.0% | Acinetobacter sp. ADP1 chromosome, complete genome. |
| coverage | distribution | pYTK001_with_tdk_kan | 3,341 | 34.1 | 2.5 | 0.0% | . |
| total | 3,604,176 | 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 | 336 |
| 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 | 14 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.001 |
| reference sequence | pr(no read start) |
|---|---|
| ADP1-WT | 0.88368 |
| pYTK001_with_tdk_kan | 0.95001 |
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 | 10:36:15 20 Jul 2021 | 10:37:17 20 Jul 2021 | 1 minute 2 seconds |
| Read alignment to reference genome | 10:37:17 20 Jul 2021 | 10:38:15 20 Jul 2021 | 58 seconds |
| Preprocessing alignments for candidate junction identification | 10:38:15 20 Jul 2021 | 10:38:38 20 Jul 2021 | 23 seconds |
| Preliminary analysis of coverage distribution | 10:38:38 20 Jul 2021 | 10:38:57 20 Jul 2021 | 19 seconds |
| Identifying junction candidates | 10:38:57 20 Jul 2021 | 10:38:57 20 Jul 2021 | 0 seconds |
| Re-alignment to junction candidates | 10:38:57 20 Jul 2021 | 10:39:04 20 Jul 2021 | 7 seconds |
| Resolving best read alignments | 10:39:04 20 Jul 2021 | 10:39:54 20 Jul 2021 | 50 seconds |
| Creating BAM files | 10:39:54 20 Jul 2021 | 10:40:10 20 Jul 2021 | 16 seconds |
| Tabulating error counts | 10:40:10 20 Jul 2021 | 10:40:21 20 Jul 2021 | 11 seconds |
| Re-calibrating base error rates | 10:40:21 20 Jul 2021 | 10:40:23 20 Jul 2021 | 2 seconds |
| Examining read alignment evidence | 10:40:23 20 Jul 2021 | 10:42:12 20 Jul 2021 | 1 minute 49 seconds |
| Polymorphism statistics | 10:42:12 20 Jul 2021 | 10:42:13 20 Jul 2021 | 1 second |
| Output | 10:42:13 20 Jul 2021 | 10:42:16 20 Jul 2021 | 3 seconds |
| Output :: Mutation Prediction | 10:42:13 20 Jul 2021 | 10:42:13 20 Jul 2021 | 0 seconds |
| Output :: Mutation Annotation | 10:42:13 20 Jul 2021 | 10:42:13 20 Jul 2021 | 0 seconds |
| Total | 6 minutes 1 second | ||
