mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.27.1 revision 87c22d663cc3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| read file | reads | bases | passed filters | average | longest | mapped | |
|---|---|---|---|---|---|---|---|
| errors | gctrim-C13-Redo-4-59_S4_L001_R1_001 | 1,807,227 | 421,340,537 | 100.0% | 233.1 bases | 251 bases | 97.8% |
| errors | gctrim-C13-Redo-4-59_S4_L001_R2_001 | 1,807,578 | 423,385,842 | 100.0% | 234.2 bases | 251 bases | 92.4% |
| total | 3,614,805 | 844,726,379 | 100.0% | 233.7 bases | 251 bases | 95.1% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_000913 | 4,641,652 | 174.3 | 5.0 | 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 | 3755 |
| 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 | 377 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.041 |
| reference sequence | pr(no read start) |
|---|---|
| NC_000913 | 0.80158 |
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 |
| Consensus frequency cutoff | 0.8 |
| Consensus minimum coverage each strand | OFF |
| Polymorphism E-value cutoff | 10 |
| Polymorphism frequency cutoff | 0.2 |
| Polymorphism minimum coverage each strand | OFF |
| Polymorphism bias cutoff | OFF |
| 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 | 23:30:19 25 Jun 2016 | 23:31:35 25 Jun 2016 | 1 minute 16 seconds |
| Read alignment to reference genome | 23:31:36 25 Jun 2016 | 23:36:09 25 Jun 2016 | 4 minutes 33 seconds |
| Preprocessing alignments for candidate junction identification | 23:36:09 25 Jun 2016 | 23:37:42 25 Jun 2016 | 1 minute 33 seconds |
| Preliminary analysis of coverage distribution | 23:37:42 25 Jun 2016 | 23:42:19 25 Jun 2016 | 4 minutes 37 seconds |
| Identifying junction candidates | 23:42:19 25 Jun 2016 | 23:42:21 25 Jun 2016 | 2 seconds |
| Re-alignment to junction candidates | 23:42:21 25 Jun 2016 | 23:43:14 25 Jun 2016 | 53 seconds |
| Resolving alignments with junction candidates | 23:43:14 25 Jun 2016 | 23:46:47 25 Jun 2016 | 3 minutes 33 seconds |
| Creating BAM files | 23:46:47 25 Jun 2016 | 23:49:40 25 Jun 2016 | 2 minutes 53 seconds |
| Tabulating error counts | 23:49:40 25 Jun 2016 | 23:53:57 25 Jun 2016 | 4 minutes 17 seconds |
| Re-calibrating base error rates | 23:53:57 25 Jun 2016 | 23:53:58 25 Jun 2016 | 1 second |
| Examining read alignment evidence | 23:53:58 25 Jun 2016 | 00:25:39 26 Jun 2016 | 31 minutes 41 seconds |
| Polymorphism statistics | 00:25:39 26 Jun 2016 | 00:25:40 26 Jun 2016 | 1 second |
| Output | 00:25:40 26 Jun 2016 | 00:26:21 26 Jun 2016 | 41 seconds |
| Total | 56 minutes 1 second | ||
