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 | 7-Glu_S20_L001_R2_001 | 1,148,933 | 329,414,673 | 100.0% | 286.7 bases | 301 bases | 95.8% |
| errors | 7-Glu_S20_L001_R1_001 | 1,148,986 | 328,815,017 | 100.0% | 286.2 bases | 301 bases | 99.6% |
| total | 2,297,919 | 658,229,690 | 100.0% | 286.4 bases | 301 bases | 97.7% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_000913 | 4,641,652 | 146.9 | 4.0 | 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 | 3389 |
| 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 | 180 |
| Total length of all junction candidates (factor times the reference genome length) | ≥ 0.1 | 0.024 |
| reference sequence | pr(no read start) |
|---|---|
| NC_000913 | 0.85850 |
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 | 17:15:28 06 Jul 2015 | 17:16:21 06 Jul 2015 | 53 seconds |
| Read alignment to reference genome | 17:16:21 06 Jul 2015 | 17:21:20 06 Jul 2015 | 4 minutes 59 seconds |
| Preprocessing alignments for candidate junction identification | 17:21:20 06 Jul 2015 | 17:22:30 06 Jul 2015 | 1 minute 10 seconds |
| Preliminary analysis of coverage distribution | 17:22:30 06 Jul 2015 | 17:26:03 06 Jul 2015 | 3 minutes 33 seconds |
| Identifying junction candidates | 17:26:03 06 Jul 2015 | 17:26:04 06 Jul 2015 | 1 second |
| Re-alignment to junction candidates | 17:26:04 06 Jul 2015 | 17:26:38 06 Jul 2015 | 34 seconds |
| Resolving alignments with junction candidates | 17:26:38 06 Jul 2015 | 17:28:27 06 Jul 2015 | 1 minute 49 seconds |
| Creating BAM files | 17:28:27 06 Jul 2015 | 17:30:32 06 Jul 2015 | 2 minutes 5 seconds |
| Tabulating error counts | 17:30:32 06 Jul 2015 | 17:34:01 06 Jul 2015 | 3 minutes 29 seconds |
| Re-calibrating base error rates | 17:34:01 06 Jul 2015 | 17:34:02 06 Jul 2015 | 1 second |
| Examining read alignment evidence | 17:34:02 06 Jul 2015 | 19:56:12 06 Jul 2015 | 2 hours 22 minutes 10 seconds |
| Polymorphism statistics | 19:56:12 06 Jul 2015 | 19:56:14 06 Jul 2015 | 2 seconds |
| Output | 19:56:14 06 Jul 2015 | 19:57:14 06 Jul 2015 | 1 minute 0 seconds |
| Total | 2 hours 41 minutes 46 seconds | ||
