mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.24rc7
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| read file | reads | bases | passed filters | average | longest | mapped | |
|---|---|---|---|---|---|---|---|
| errors | BOP27Reseq_S1_L001_R1 | 5,978,523 | 980,052,088 | 100.0% | 163.9 bases | 251 bases | 99.0% |
| errors | BOP27Reseq_S1_L001_R2 | 5,977,520 | 980,235,110 | 100.0% | 164.0 bases | 251 bases | 98.7% |
| total | 11,956,043 | 1,960,287,198 | 100.0% | 164.0 bases | 251 bases | 98.9% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_000913 | 4,641,652 | 422.4 | 11.9 | 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.
| reference sequence | pr(no read start) |
|---|---|
| NC_000913 | 0.62484 |
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 |
|---|---|
| Mode | Consensus/Mixed Base |
| Ploidy | 1 (haploid) |
| Consensus mutation E-value cutoff | 10 |
| Polymorphism E-value cutoff | 10 |
| Polymorphism frequency cutoff | 0.1 |
| Polymorphism minimum coverage each strand | 2 |
| Polymorphism bias cutoff | 0.05 |
| Predict indel polymorphisms | YES |
| Skip indel polymorphisms in homopolymers runs | ≥3 bases |
| step | start | end | elapsed |
|---|---|---|---|
| Read and reference sequence file input | 17:12:10 12 Mar 2015 | 17:13:52 12 Mar 2015 | 1 minute 42 seconds |
| Read alignment to reference genome | 17:13:52 12 Mar 2015 | 17:50:05 12 Mar 2015 | 36 minutes 13 seconds |
| Preprocessing alignments for candidate junction identification | 17:50:05 12 Mar 2015 | 17:53:01 12 Mar 2015 | 2 minutes 56 seconds |
| Preliminary analysis of coverage distribution | 17:53:01 12 Mar 2015 | 18:01:42 12 Mar 2015 | 8 minutes 41 seconds |
| Identifying junction candidates | 18:01:42 12 Mar 2015 | 18:01:42 12 Mar 2015 | 0 seconds |
| Re-alignment to junction candidates | 18:01:42 12 Mar 2015 | 18:12:38 12 Mar 2015 | 10 minutes 56 seconds |
| Resolving alignments with junction candidates | 18:12:38 12 Mar 2015 | 18:18:43 12 Mar 2015 | 6 minutes 5 seconds |
| Creating BAM files | 18:18:43 12 Mar 2015 | 18:26:26 12 Mar 2015 | 7 minutes 43 seconds |
| Tabulating error counts | 18:26:26 12 Mar 2015 | 18:29:08 12 Mar 2015 | 2 minutes 42 seconds |
| Re-calibrating base error rates | 18:29:08 12 Mar 2015 | 18:29:10 12 Mar 2015 | 2 seconds |
| Examining read alignment evidence | 18:29:10 12 Mar 2015 | 19:10:07 12 Mar 2015 | 40 minutes 57 seconds |
| Polymorphism statistics | 19:10:07 12 Mar 2015 | 19:10:48 12 Mar 2015 | 41 seconds |
| Output | 19:10:48 12 Mar 2015 | 19:11:45 12 Mar 2015 | 57 seconds |
| Total | 1 hour 59 minutes 35 seconds | ||
