mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.35.4
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| read file | reads | bases | passed filters | average | longest | mapped | |
|---|---|---|---|---|---|---|---|
| errors | AA-30R-unknown_S6_L001_R1_001 | 1,209,223 | 269,984,433 | 99.9% | 223.3 bases | 251 bases | 98.6% |
| total | 1,209,223 | 269,984,433 | 99.9% | 223.3 bases | 251 bases | 98.6% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | 1 | 2,120,195 | 134.9 | 7.6 | 100.0% | Aggregatibacter actinomycetemcomitans Aa30S |
| total | 2,120,195 | 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 | 6410 |
| 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 | 97 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.023 |
| reference sequence | pr(no read start) |
|---|---|
| 1 | 0.82539 |
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 | 2.4.1 |
| R | 4.0.0 |
| step | start | end | elapsed |
|---|---|---|---|
| Read and reference sequence file input | 13:14:40 20 Jan 2022 | 13:15:03 20 Jan 2022 | 23 seconds |
| Read alignment to reference genome | 13:15:03 20 Jan 2022 | 13:16:09 20 Jan 2022 | 1 minute 6 seconds |
| Preprocessing alignments for candidate junction identification | 13:16:09 20 Jan 2022 | 13:16:32 20 Jan 2022 | 23 seconds |
| Preliminary analysis of coverage distribution | 13:16:32 20 Jan 2022 | 13:17:30 20 Jan 2022 | 58 seconds |
| Identifying junction candidates | 13:17:30 20 Jan 2022 | 13:17:31 20 Jan 2022 | 1 second |
| Re-alignment to junction candidates | 13:17:31 20 Jan 2022 | 13:17:49 20 Jan 2022 | 18 seconds |
| Resolving best read alignments | 13:17:49 20 Jan 2022 | 13:18:20 20 Jan 2022 | 31 seconds |
| Creating BAM files | 13:18:20 20 Jan 2022 | 13:19:09 20 Jan 2022 | 49 seconds |
| Tabulating error counts | 13:19:09 20 Jan 2022 | 13:19:34 20 Jan 2022 | 25 seconds |
| Re-calibrating base error rates | 13:19:34 20 Jan 2022 | 13:19:36 20 Jan 2022 | 2 seconds |
| Examining read alignment evidence | 13:19:36 20 Jan 2022 | 13:24:28 20 Jan 2022 | 4 minutes 52 seconds |
| Polymorphism statistics | 13:24:28 20 Jan 2022 | 13:24:29 20 Jan 2022 | 1 second |
| Output | 13:24:29 20 Jan 2022 | 13:24:57 20 Jan 2022 | 28 seconds |
| Total | 10 minutes 17 seconds | ||
