mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.26.1
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| read file | reads | bases | passed filters | average | longest | mapped | |
|---|---|---|---|---|---|---|---|
| errors | HRD-KHP-atpIC-pntB-ndh-1_S1_L001_R1_001 | 475,864 | 99,930,833 | 100.0% | 210.0 bases | 210 bases | 88.2% |
| errors | HRD-KHP-atpIC-pntB-ndh-1_S1_L001_R2_001 | 475,832 | 99,924,260 | 100.0% | 210.0 bases | 210 bases | 86.9% |
| total | 951,696 | 199,855,093 | 100.0% | 210.0 bases | 210 bases | 87.6% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_000913 | 4,641,652 | 31.0 | 1.6 | 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 | 3102 |
| 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 | 138 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.013 |
| reference sequence | pr(no read start) |
|---|---|
| NC_000913 | 0.92269 |
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 | ≤ 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 |
| 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 of | OFF |
| Skip base substitutions when they create a homopolymer flanked on each side by | OFF |
| step | start | end | elapsed |
|---|---|---|---|
| Read and reference sequence file input | 19:22:21 11 Nov 2015 | 19:22:39 11 Nov 2015 | 18 seconds |
| Read alignment to reference genome | 19:22:39 11 Nov 2015 | 19:23:40 11 Nov 2015 | 1 minute 1 second |
| Preprocessing alignments for candidate junction identification | 19:23:40 11 Nov 2015 | 19:24:01 11 Nov 2015 | 21 seconds |
| Preliminary analysis of coverage distribution | 19:24:01 11 Nov 2015 | 19:24:52 11 Nov 2015 | 51 seconds |
| Identifying junction candidates | 19:24:52 11 Nov 2015 | 19:24:52 11 Nov 2015 | 0 seconds |
| Re-alignment to junction candidates | 19:24:52 11 Nov 2015 | 19:25:03 11 Nov 2015 | 11 seconds |
| Resolving alignments with junction candidates | 19:25:03 11 Nov 2015 | 19:25:38 11 Nov 2015 | 35 seconds |
| Creating BAM files | 19:25:38 11 Nov 2015 | 19:26:06 11 Nov 2015 | 28 seconds |
| Tabulating error counts | 19:26:06 11 Nov 2015 | 19:27:02 11 Nov 2015 | 56 seconds |
| Re-calibrating base error rates | 19:27:02 11 Nov 2015 | 19:27:03 11 Nov 2015 | 1 second |
| Examining read alignment evidence | 19:27:03 11 Nov 2015 | 19:34:21 11 Nov 2015 | 7 minutes 18 seconds |
| Polymorphism statistics | 19:34:21 11 Nov 2015 | 19:34:21 11 Nov 2015 | 0 seconds |
| Output | 19:34:21 11 Nov 2015 | 19:34:50 11 Nov 2015 | 29 seconds |
| Total | 12 minutes 29 seconds | ||
