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 | 2Xyl_S4_L001_R2_001 | 1,251,945 | 361,221,127 | 100.0% | 288.5 bases | 301 bases | 80.1% |
| errors | 2Xyl_S4_L001_R1_001 | 1,251,985 | 357,974,071 | 100.0% | 285.9 bases | 301 bases | 96.9% |
| total | 2,503,930 | 719,195,198 | 100.0% | 287.2 bases | 301 bases | 88.5% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_000913 | 4,641,652 | 141.2 | 3.9 | 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.
| option | limit | actual |
|---|---|---|
| Number of alignment pairs examined for constructing junction candidates | ≤ 100000 | 3691 |
| 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 | 165 |
| Total length of all junction candidates (factor times the reference genome length) | ≥ 0.1 | 0.022 |
| reference sequence | pr(no read start) |
|---|---|
| NC_000913 | 0.87270 |
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 | 03:07:44 17 Apr 2015 | 03:08:45 17 Apr 2015 | 1 minute 1 second |
| Read alignment to reference genome | 03:08:45 17 Apr 2015 | 03:16:02 17 Apr 2015 | 7 minutes 17 seconds |
| Preprocessing alignments for candidate junction identification | 03:16:02 17 Apr 2015 | 03:17:17 17 Apr 2015 | 1 minute 15 seconds |
| Preliminary analysis of coverage distribution | 03:17:17 17 Apr 2015 | 03:20:56 17 Apr 2015 | 3 minutes 39 seconds |
| Identifying junction candidates | 03:20:56 17 Apr 2015 | 03:20:57 17 Apr 2015 | 1 second |
| Re-alignment to junction candidates | 03:20:57 17 Apr 2015 | 03:21:34 17 Apr 2015 | 37 seconds |
| Resolving alignments with junction candidates | 03:21:34 17 Apr 2015 | 03:23:28 17 Apr 2015 | 1 minute 54 seconds |
| Creating BAM files | 03:23:28 17 Apr 2015 | 03:25:43 17 Apr 2015 | 2 minutes 15 seconds |
| Tabulating error counts | 03:25:43 17 Apr 2015 | 03:29:12 17 Apr 2015 | 3 minutes 29 seconds |
| Re-calibrating base error rates | 03:29:12 17 Apr 2015 | 03:29:13 17 Apr 2015 | 1 second |
| Examining read alignment evidence | 03:29:13 17 Apr 2015 | 06:21:07 17 Apr 2015 | 2 hours 51 minutes 54 seconds |
| Polymorphism statistics | 06:21:07 17 Apr 2015 | 06:21:08 17 Apr 2015 | 1 second |
| Output | 06:21:08 17 Apr 2015 | 06:21:56 17 Apr 2015 | 48 seconds |
| Total | 3 hours 14 minutes 12 seconds | ||
