mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.33.1 revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| read file | reads | bases | passed filters | average | longest | mapped | |
|---|---|---|---|---|---|---|---|
| errors | Plate-2-BOP-1000-ACNB-ALE-1-flask-18_S18_L001_R1_001.good.fq | 215,361 | 26,002,618 | 100.0% | 120.7 bases | 149 bases | 94.0% |
| errors | Plate-2-BOP-1000-ACNB-ALE-1-flask-18_S18_L001_R2_001.good.fq | 215,361 | 25,548,887 | 100.0% | 118.6 bases | 149 bases | 97.9% |
| errors | Plate-2-BOP-1000-ACNB-ALE-1-flask-18_S18_L002_R1_001.good.fq | 177,787 | 21,359,147 | 100.0% | 120.1 bases | 149 bases | 93.7% |
| errors | Plate-2-BOP-1000-ACNB-ALE-1-flask-18_S18_L002_R2_001.good.fq | 177,787 | 20,983,435 | 100.0% | 118.0 bases | 149 bases | 97.5% |
| errors | Plate-2-BOP-1000-ACNB-ALE-1-flask-18_S18_L003_R1_001.good.fq | 198,017 | 23,820,294 | 100.0% | 120.3 bases | 149 bases | 93.8% |
| errors | Plate-2-BOP-1000-ACNB-ALE-1-flask-18_S18_L003_R2_001.good.fq | 198,017 | 23,393,580 | 100.0% | 118.1 bases | 149 bases | 97.8% |
| errors | Plate-2-BOP-1000-ACNB-ALE-1-flask-18_S18_L004_R1_001.good.fq | 175,230 | 20,991,881 | 100.0% | 119.8 bases | 149 bases | 93.6% |
| errors | Plate-2-BOP-1000-ACNB-ALE-1-flask-18_S18_L004_R2_001.good.fq | 175,230 | 20,629,049 | 100.0% | 117.7 bases | 149 bases | 97.3% |
| total | 1,532,790 | 182,728,891 | 100.0% | 119.2 bases | 149 bases | 95.7% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_000913 | 4,641,652 | 34.3 | 2.5 | 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 | 23331 |
| Coverage evenness (position-hash) score of junction candidates | ≥ 2 | ≥ 3 |
| Test this many junction candidates (n). May be smaller if not enough passed the coverage evenness threshold | 100 ≤ n ≤ 5000 | 211 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.014 |
| reference sequence | pr(no read start) |
|---|---|
| NC_000913 | 0.86323 |
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 | 0.75 |
| Consensus minimum variant coverage each strand | OFF |
| Consensus minimum total coverage each strand | OFF |
| Consensus minimum variant coverage | OFF |
| Consensus minimum total coverage | OFF |
| Polymorphism E-value cutoff | 10 |
| Polymorphism frequency cutoff | 0.2 |
| Polymorphism minimum variant coverage each strand | OFF |
| Polymorphism minimum total coverage each strand | OFF |
| Polymorphism minimum variant coverage | OFF |
| Polymorphism minimum total coverage | 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 |
| program | version |
|---|---|
| bowtie2 | 2.2.6 |
| R | 3.4.4 |
| step | start | end | elapsed |
|---|---|---|---|
| Read and reference sequence file input | 10:20:17 12 Sep 2020 | 10:20:40 12 Sep 2020 | 23 seconds |
| Read alignment to reference genome | 10:20:40 12 Sep 2020 | 10:23:18 12 Sep 2020 | 2 minutes 38 seconds |
| Preprocessing alignments for candidate junction identification | 10:23:18 12 Sep 2020 | 10:23:41 12 Sep 2020 | 23 seconds |
| Preliminary analysis of coverage distribution | 10:23:41 12 Sep 2020 | 10:24:19 12 Sep 2020 | 38 seconds |
| Identifying junction candidates | 10:24:19 12 Sep 2020 | 10:26:08 12 Sep 2020 | 1 minute 49 seconds |
| Re-alignment to junction candidates | 10:26:08 12 Sep 2020 | 10:26:58 12 Sep 2020 | 50 seconds |
| Resolving best read alignments | 10:26:58 12 Sep 2020 | 10:27:31 12 Sep 2020 | 33 seconds |
| Creating BAM files | 10:27:31 12 Sep 2020 | 10:28:06 12 Sep 2020 | 35 seconds |
| Tabulating error counts | 10:28:06 12 Sep 2020 | 10:28:19 12 Sep 2020 | 13 seconds |
| Re-calibrating base error rates | 10:28:19 12 Sep 2020 | 10:28:22 12 Sep 2020 | 3 seconds |
| Examining read alignment evidence | 10:28:22 12 Sep 2020 | 10:31:14 12 Sep 2020 | 2 minutes 52 seconds |
| Polymorphism statistics | 10:31:14 12 Sep 2020 | 10:31:14 12 Sep 2020 | 0 seconds |
| Output | 10:31:14 12 Sep 2020 | 10:31:33 12 Sep 2020 | 19 seconds |
| Total | 11 minutes 16 seconds | ||
