mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.29.0 revision 8f9c342918e4
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| read file | reads | bases | passed filters | average | longest | mapped | |
|---|---|---|---|---|---|---|---|
| errors | qtrim-HMDA3-6_S6_L001_R1_001 | 1,282,680 | 192,951,941 | 100.0% | 150.4 bases | 151 bases | 99.5% |
| errors | qtrim-HMDA3-6_S6_L001_R2_001 | 1,282,613 | 192,752,673 | 100.0% | 150.3 bases | 151 bases | 98.4% |
| total | 2,565,293 | 385,704,614 | 100.0% | 150.4 bases | 151 bases | 99.0% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_000913 | 4,641,652 | 82.5 | 1.4 | 98.3% | 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 | 1920 |
| 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 | 28 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.002 |
| reference sequence | pr(no read start) |
|---|---|
| NC_000913 | 0.77239 |
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 | 15:00:42 03 Jan 2017 | 15:01:38 03 Jan 2017 | 56 seconds |
| Read alignment to reference genome | 15:01:39 03 Jan 2017 | 15:09:54 03 Jan 2017 | 8 minutes 15 seconds |
| Preprocessing alignments for candidate junction identification | 15:09:54 03 Jan 2017 | 15:11:20 03 Jan 2017 | 1 minute 26 seconds |
| Preliminary analysis of coverage distribution | 15:11:20 03 Jan 2017 | 15:14:04 03 Jan 2017 | 2 minutes 44 seconds |
| Identifying junction candidates | 15:14:04 03 Jan 2017 | 15:14:04 03 Jan 2017 | 0 seconds |
| Re-alignment to junction candidates | 15:14:04 03 Jan 2017 | 15:15:45 03 Jan 2017 | 1 minute 41 seconds |
| Resolving alignments with junction candidates | 15:15:45 03 Jan 2017 | 15:18:36 03 Jan 2017 | 2 minutes 51 seconds |
| Creating BAM files | 15:18:36 03 Jan 2017 | 15:20:30 03 Jan 2017 | 1 minute 54 seconds |
| Tabulating error counts | 15:20:30 03 Jan 2017 | 15:22:50 03 Jan 2017 | 2 minutes 20 seconds |
| Re-calibrating base error rates | 15:22:50 03 Jan 2017 | 15:22:51 03 Jan 2017 | 1 second |
| Examining read alignment evidence | 15:22:51 03 Jan 2017 | 15:41:06 03 Jan 2017 | 18 minutes 15 seconds |
| Polymorphism statistics | 15:41:06 03 Jan 2017 | 15:41:07 03 Jan 2017 | 1 second |
| Output | 15:41:07 03 Jan 2017 | 15:41:27 03 Jan 2017 | 20 seconds |
| Total | 40 minutes 44 seconds | ||
