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-27-PFKA-ALE-3-flask-12_S69_L001_R1_001.good.fq | 195,086 | 24,679,059 | 100.0% | 126.5 bases | 149 bases | 93.6% |
| errors | Plate-2-BOP-27-PFKA-ALE-3-flask-12_S69_L001_R2_001.good.fq | 195,086 | 24,269,026 | 100.0% | 124.4 bases | 149 bases | 97.6% |
| errors | Plate-2-BOP-27-PFKA-ALE-3-flask-12_S69_L002_R1_001.good.fq | 155,593 | 19,633,132 | 100.0% | 126.2 bases | 149 bases | 93.2% |
| errors | Plate-2-BOP-27-PFKA-ALE-3-flask-12_S69_L002_R2_001.good.fq | 155,593 | 19,289,860 | 100.0% | 124.0 bases | 149 bases | 97.2% |
| errors | Plate-2-BOP-27-PFKA-ALE-3-flask-12_S69_L003_R1_001.good.fq | 178,496 | 22,520,325 | 100.0% | 126.2 bases | 149 bases | 93.4% |
| errors | Plate-2-BOP-27-PFKA-ALE-3-flask-12_S69_L003_R2_001.good.fq | 178,496 | 22,128,117 | 100.0% | 124.0 bases | 149 bases | 97.5% |
| errors | Plate-2-BOP-27-PFKA-ALE-3-flask-12_S69_L004_R1_001.good.fq | 153,324 | 19,283,757 | 100.0% | 125.8 bases | 149 bases | 93.1% |
| errors | Plate-2-BOP-27-PFKA-ALE-3-flask-12_S69_L004_R2_001.good.fq | 153,324 | 18,949,053 | 100.0% | 123.6 bases | 149 bases | 97.0% |
| total | 1,364,998 | 170,752,329 | 100.0% | 125.1 bases | 149 bases | 95.3% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_000913 | 4,641,652 | 34.7 | 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 | 15349 |
| 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 | 49 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.003 |
| reference sequence | pr(no read start) |
|---|---|
| NC_000913 | 0.87628 |
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 | 2.3.4.1 |
| R | 3.4.4 |
| step | start | end | elapsed |
|---|---|---|---|
| Read and reference sequence file input | 08:09:15 25 Feb 2020 | 08:09:35 25 Feb 2020 | 20 seconds |
| Read alignment to reference genome | 08:09:36 25 Feb 2020 | 08:12:14 25 Feb 2020 | 2 minutes 38 seconds |
| Preprocessing alignments for candidate junction identification | 08:12:14 25 Feb 2020 | 08:12:32 25 Feb 2020 | 18 seconds |
| Preliminary analysis of coverage distribution | 08:12:32 25 Feb 2020 | 08:13:08 25 Feb 2020 | 36 seconds |
| Identifying junction candidates | 08:13:08 25 Feb 2020 | 08:13:41 25 Feb 2020 | 33 seconds |
| Re-alignment to junction candidates | 08:13:41 25 Feb 2020 | 08:14:30 25 Feb 2020 | 49 seconds |
| Resolving best read alignments | 08:14:30 25 Feb 2020 | 08:14:58 25 Feb 2020 | 28 seconds |
| Creating BAM files | 08:14:58 25 Feb 2020 | 08:15:31 25 Feb 2020 | 33 seconds |
| Tabulating error counts | 08:15:31 25 Feb 2020 | 08:15:43 25 Feb 2020 | 12 seconds |
| Re-calibrating base error rates | 08:15:43 25 Feb 2020 | 08:15:46 25 Feb 2020 | 3 seconds |
| Examining read alignment evidence | 08:15:46 25 Feb 2020 | 08:18:19 25 Feb 2020 | 2 minutes 33 seconds |
| Polymorphism statistics | 08:18:19 25 Feb 2020 | 08:18:19 25 Feb 2020 | 0 seconds |
| Output | 08:18:19 25 Feb 2020 | 08:18:32 25 Feb 2020 | 13 seconds |
| Total | 9 minutes 16 seconds | ||
