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-1-flask-11_S65_L001_R1_001.good.fq | 244,982 | 30,265,696 | 100.0% | 123.5 bases | 149 bases | 94.3% |
| errors | Plate-2-BOP-27-PFKA-ALE-1-flask-11_S65_L001_R2_001.good.fq | 244,982 | 29,809,293 | 100.0% | 121.7 bases | 149 bases | 97.6% |
| errors | Plate-2-BOP-27-PFKA-ALE-1-flask-11_S65_L002_R1_001.good.fq | 198,464 | 24,437,630 | 100.0% | 123.1 bases | 149 bases | 94.0% |
| errors | Plate-2-BOP-27-PFKA-ALE-1-flask-11_S65_L002_R2_001.good.fq | 198,464 | 24,074,069 | 100.0% | 121.3 bases | 149 bases | 97.1% |
| errors | Plate-2-BOP-27-PFKA-ALE-1-flask-11_S65_L003_R1_001.good.fq | 225,602 | 27,785,372 | 100.0% | 123.2 bases | 149 bases | 94.2% |
| errors | Plate-2-BOP-27-PFKA-ALE-1-flask-11_S65_L003_R2_001.good.fq | 225,602 | 27,360,911 | 100.0% | 121.3 bases | 149 bases | 97.6% |
| errors | Plate-2-BOP-27-PFKA-ALE-1-flask-11_S65_L004_R1_001.good.fq | 197,054 | 24,206,598 | 100.0% | 122.8 bases | 149 bases | 94.0% |
| errors | Plate-2-BOP-27-PFKA-ALE-1-flask-11_S65_L004_R2_001.good.fq | 197,054 | 23,856,367 | 100.0% | 121.1 bases | 149 bases | 96.9% |
| total | 1,732,204 | 211,795,936 | 100.0% | 122.3 bases | 149 bases | 95.7% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_000913 | 4,641,652 | 43.3 | 2.9 | 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 | 26730 |
| 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 | 284 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.019 |
| reference sequence | pr(no read start) |
|---|---|
| NC_000913 | 0.84611 |
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 | 17:20:58 24 Feb 2020 | 17:21:22 24 Feb 2020 | 24 seconds |
| Read alignment to reference genome | 17:21:23 24 Feb 2020 | 17:24:29 24 Feb 2020 | 3 minutes 6 seconds |
| Preprocessing alignments for candidate junction identification | 17:24:29 24 Feb 2020 | 17:24:53 24 Feb 2020 | 24 seconds |
| Preliminary analysis of coverage distribution | 17:24:53 24 Feb 2020 | 17:25:37 24 Feb 2020 | 44 seconds |
| Identifying junction candidates | 17:25:37 24 Feb 2020 | 17:26:44 24 Feb 2020 | 1 minute 7 seconds |
| Re-alignment to junction candidates | 17:26:44 24 Feb 2020 | 17:27:47 24 Feb 2020 | 1 minute 3 seconds |
| Resolving best read alignments | 17:27:47 24 Feb 2020 | 17:28:23 24 Feb 2020 | 36 seconds |
| Creating BAM files | 17:28:23 24 Feb 2020 | 17:29:03 24 Feb 2020 | 40 seconds |
| Tabulating error counts | 17:29:03 24 Feb 2020 | 17:29:18 24 Feb 2020 | 15 seconds |
| Re-calibrating base error rates | 17:29:18 24 Feb 2020 | 17:29:21 24 Feb 2020 | 3 seconds |
| Examining read alignment evidence | 17:29:21 24 Feb 2020 | 17:32:21 24 Feb 2020 | 3 minutes 0 seconds |
| Polymorphism statistics | 17:32:21 24 Feb 2020 | 17:32:22 24 Feb 2020 | 1 second |
| Output | 17:32:22 24 Feb 2020 | 17:32:39 24 Feb 2020 | 17 seconds |
| Total | 11 minutes 40 seconds | ||
