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-SUCB-ALE-4-flask-42_S48_L001_R1_001.good.fq | 216,367 | 28,244,186 | 100.0% | 130.5 bases | 149 bases | 95.2% |
| errors | Plate-2-BOP-1000-SUCB-ALE-4-flask-42_S48_L001_R2_001.good.fq | 216,367 | 27,926,157 | 100.0% | 129.1 bases | 149 bases | 98.0% |
| errors | Plate-2-BOP-1000-SUCB-ALE-4-flask-42_S48_L002_R1_001.good.fq | 165,524 | 21,498,481 | 100.0% | 129.9 bases | 149 bases | 94.7% |
| errors | Plate-2-BOP-1000-SUCB-ALE-4-flask-42_S48_L002_R2_001.good.fq | 165,524 | 21,252,434 | 100.0% | 128.4 bases | 149 bases | 97.3% |
| errors | Plate-2-BOP-1000-SUCB-ALE-4-flask-42_S48_L003_R1_001.good.fq | 190,533 | 24,779,719 | 100.0% | 130.1 bases | 149 bases | 95.0% |
| errors | Plate-2-BOP-1000-SUCB-ALE-4-flask-42_S48_L003_R2_001.good.fq | 190,533 | 24,492,301 | 100.0% | 128.5 bases | 149 bases | 97.7% |
| errors | Plate-2-BOP-1000-SUCB-ALE-4-flask-42_S48_L004_R1_001.good.fq | 161,975 | 20,987,377 | 100.0% | 129.6 bases | 149 bases | 94.7% |
| errors | Plate-2-BOP-1000-SUCB-ALE-4-flask-42_S48_L004_R2_001.good.fq | 161,975 | 20,745,626 | 100.0% | 128.1 bases | 149 bases | 97.2% |
| total | 1,468,798 | 189,926,281 | 100.0% | 129.3 bases | 149 bases | 96.3% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_000913 | 4,641,652 | 39.3 | 2.4 | 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 | 19206 |
| 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 | 269 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.018 |
| reference sequence | pr(no read start) |
|---|---|
| NC_000913 | 0.86663 |
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 | 07:18:30 28 Feb 2020 | 07:18:52 28 Feb 2020 | 22 seconds |
| Read alignment to reference genome | 07:18:52 28 Feb 2020 | 07:21:40 28 Feb 2020 | 2 minutes 48 seconds |
| Preprocessing alignments for candidate junction identification | 07:21:40 28 Feb 2020 | 07:22:00 28 Feb 2020 | 20 seconds |
| Preliminary analysis of coverage distribution | 07:22:00 28 Feb 2020 | 07:22:40 28 Feb 2020 | 40 seconds |
| Identifying junction candidates | 07:22:40 28 Feb 2020 | 07:23:21 28 Feb 2020 | 41 seconds |
| Re-alignment to junction candidates | 07:23:21 28 Feb 2020 | 07:24:18 28 Feb 2020 | 57 seconds |
| Resolving best read alignments | 07:24:18 28 Feb 2020 | 07:24:49 28 Feb 2020 | 31 seconds |
| Creating BAM files | 07:24:49 28 Feb 2020 | 07:25:25 28 Feb 2020 | 36 seconds |
| Tabulating error counts | 07:25:25 28 Feb 2020 | 07:25:39 28 Feb 2020 | 14 seconds |
| Re-calibrating base error rates | 07:25:39 28 Feb 2020 | 07:25:42 28 Feb 2020 | 3 seconds |
| Examining read alignment evidence | 07:25:42 28 Feb 2020 | 07:28:29 28 Feb 2020 | 2 minutes 47 seconds |
| Polymorphism statistics | 07:28:29 28 Feb 2020 | 07:28:29 28 Feb 2020 | 0 seconds |
| Output | 07:28:29 28 Feb 2020 | 07:28:43 28 Feb 2020 | 14 seconds |
| Total | 10 minutes 13 seconds | ||
