mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.26.0
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| read file | reads | bases | passed filters | average | longest | mapped | |
|---|---|---|---|---|---|---|---|
| errors | 2-Gly-Redo_S17_L001_R1_001 | 976,451 | 272,501,485 | 100.0% | 279.1 bases | 301 bases | 99.4% |
| errors | 2-Gly-Redo_S17_L001_R2_001 | 976,397 | 274,067,681 | 100.0% | 280.7 bases | 301 bases | 93.3% |
| total | 1,952,848 | 546,569,166 | 100.0% | 279.9 bases | 301 bases | 96.3% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_000913 | 4,641,652 | 123.6 | 5.2 | 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 | 3289 |
| 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 | 193 |
| Total length of all junction candidates (factor times the reference genome length) | ≥ 0.1 | 0.025 |
| reference sequence | pr(no read start) |
|---|---|
| NC_000913 | 0.87517 |
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 |
| 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 |
| Polymorphism E-value cutoff | 2 |
| Polymorphism frequency cutoff | 0.05 |
| Polymorphism minimum coverage each strand | 2 |
| Polymorphism bias cutoff | 0.001 |
| 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 | ≥2 bases |
| step | start | end | elapsed |
|---|---|---|---|
| Read and reference sequence file input | 18:27:12 07 Jul 2015 | 18:28:00 07 Jul 2015 | 48 seconds |
| Read alignment to reference genome | 18:28:00 07 Jul 2015 | 18:32:32 07 Jul 2015 | 4 minutes 32 seconds |
| Preprocessing alignments for candidate junction identification | 18:32:32 07 Jul 2015 | 18:33:33 07 Jul 2015 | 1 minute 1 second |
| Preliminary analysis of coverage distribution | 18:33:33 07 Jul 2015 | 18:36:35 07 Jul 2015 | 3 minutes 2 seconds |
| Identifying junction candidates | 18:36:35 07 Jul 2015 | 18:36:36 07 Jul 2015 | 1 second |
| Re-alignment to junction candidates | 18:36:36 07 Jul 2015 | 18:37:08 07 Jul 2015 | 32 seconds |
| Resolving alignments with junction candidates | 18:37:08 07 Jul 2015 | 18:38:42 07 Jul 2015 | 1 minute 34 seconds |
| Creating BAM files | 18:38:42 07 Jul 2015 | 18:40:31 07 Jul 2015 | 1 minute 49 seconds |
| Tabulating error counts | 18:40:31 07 Jul 2015 | 18:43:30 07 Jul 2015 | 2 minutes 59 seconds |
| Re-calibrating base error rates | 18:43:30 07 Jul 2015 | 18:43:31 07 Jul 2015 | 1 second |
| Examining read alignment evidence | 18:43:31 07 Jul 2015 | 20:37:46 07 Jul 2015 | 1 hour 54 minutes 15 seconds |
| Polymorphism statistics | 20:37:46 07 Jul 2015 | 20:37:48 07 Jul 2015 | 2 seconds |
| Output | 20:37:48 07 Jul 2015 | 20:39:39 07 Jul 2015 | 1 minute 51 seconds |
| Total | 2 hours 12 minutes 27 seconds | ||
