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 | XYL_S10_L001_R2_001 | 643,401 | 193,663,701 | 99.9% | 301.0 bases | 301 bases | 70.7% |
| errors | XYL_S10_L001_R1_001 | 644,278 | 193,927,678 | 100.0% | 301.0 bases | 301 bases | 74.2% |
| total | 1,287,679 | 387,591,379 | 99.9% | 301.0 bases | 301 bases | 72.4% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_000913 | 4,641,652 | 60.1 | 2.2 | 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 | 5249 |
| 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 | 465 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.061 |
| reference sequence | pr(no read start) |
|---|---|
| NC_000913 | 0.93067 |
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 |
| Consensus frequency cutoff | 0.95 |
| Consensus minimum coverage each strand | OFF |
| Polymorphism E-value cutoff | 2 |
| Polymorphism frequency cutoff | OFF |
| Polymorphism minimum coverage each strand | 2 |
| Polymorphism bias cutoff | OFF |
| 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 | 16:22:35 25 May 2016 | 16:23:15 25 May 2016 | 40 seconds |
| Read alignment to reference genome | 16:23:16 25 May 2016 | 16:26:44 25 May 2016 | 3 minutes 28 seconds |
| Preprocessing alignments for candidate junction identification | 16:26:44 25 May 2016 | 16:27:20 25 May 2016 | 36 seconds |
| Preliminary analysis of coverage distribution | 16:27:20 25 May 2016 | 16:28:47 25 May 2016 | 1 minute 27 seconds |
| Identifying junction candidates | 16:28:47 25 May 2016 | 16:28:48 25 May 2016 | 1 second |
| Re-alignment to junction candidates | 16:28:48 25 May 2016 | 16:29:13 25 May 2016 | 25 seconds |
| Resolving alignments with junction candidates | 16:29:13 25 May 2016 | 16:30:25 25 May 2016 | 1 minute 12 seconds |
| Creating BAM files | 16:30:25 25 May 2016 | 16:31:15 25 May 2016 | 50 seconds |
| Tabulating error counts | 16:31:15 25 May 2016 | 16:32:48 25 May 2016 | 1 minute 33 seconds |
| Re-calibrating base error rates | 16:32:48 25 May 2016 | 16:32:49 25 May 2016 | 1 second |
| Examining read alignment evidence | 16:32:49 25 May 2016 | 17:16:03 25 May 2016 | 43 minutes 14 seconds |
| Polymorphism statistics | 17:16:03 25 May 2016 | 17:16:04 25 May 2016 | 1 second |
| Output | 17:16:04 25 May 2016 | 17:18:50 25 May 2016 | 2 minutes 46 seconds |
| Total | 56 minutes 14 seconds | ||
