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 | SSW-KHP-3-164-11_S21_L001_R1_001 | 684,658 | 205,766,609 | 100.0% | 300.5 bases | 301 bases | 84.9% |
| errors | SSW-KHP-3-164-11_S21_L001_R2_001 | 684,646 | 205,796,760 | 100.0% | 300.6 bases | 301 bases | 82.3% |
| total | 1,369,304 | 411,563,369 | 100.0% | 300.6 bases | 301 bases | 83.6% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_000913 | 4,641,652 | 71.3 | 2.7 | 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 | 6666 |
| 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 | 737 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.096 |
| reference sequence | pr(no read start) |
|---|---|
| NC_000913 | 0.90221 |
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 | 23:23:37 16 Apr 2016 | 23:24:20 16 Apr 2016 | 43 seconds |
| Read alignment to reference genome | 23:24:20 16 Apr 2016 | 23:27:16 16 Apr 2016 | 2 minutes 56 seconds |
| Preprocessing alignments for candidate junction identification | 23:27:16 16 Apr 2016 | 23:27:57 16 Apr 2016 | 41 seconds |
| Preliminary analysis of coverage distribution | 23:27:57 16 Apr 2016 | 23:29:48 16 Apr 2016 | 1 minute 51 seconds |
| Identifying junction candidates | 23:29:48 16 Apr 2016 | 23:29:49 16 Apr 2016 | 1 second |
| Re-alignment to junction candidates | 23:29:49 16 Apr 2016 | 23:30:18 16 Apr 2016 | 29 seconds |
| Resolving alignments with junction candidates | 23:30:18 16 Apr 2016 | 23:31:59 16 Apr 2016 | 1 minute 41 seconds |
| Creating BAM files | 23:31:59 16 Apr 2016 | 23:33:05 16 Apr 2016 | 1 minute 6 seconds |
| Tabulating error counts | 23:33:05 16 Apr 2016 | 23:34:56 16 Apr 2016 | 1 minute 51 seconds |
| Re-calibrating base error rates | 23:34:56 16 Apr 2016 | 23:34:57 16 Apr 2016 | 1 second |
| Examining read alignment evidence | 23:34:57 16 Apr 2016 | 23:48:51 16 Apr 2016 | 13 minutes 54 seconds |
| Polymorphism statistics | 23:48:51 16 Apr 2016 | 23:48:52 16 Apr 2016 | 1 second |
| Output | 23:48:52 16 Apr 2016 | 23:49:20 16 Apr 2016 | 28 seconds |
| Total | 25 minutes 43 seconds | ||
