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-1-BOP-1000-PFKA-END-3_S27_L001_R1_001.good.fq | 496,256 | 67,971,203 | 100.0% | 137.0 bases | 149 bases | 97.8% |
| errors | Plate-1-BOP-1000-PFKA-END-3_S27_L001_R2_001.good.fq | 496,256 | 67,721,618 | 100.0% | 136.5 bases | 149 bases | 98.2% |
| errors | Plate-1-BOP-1000-PFKA-END-3_S27_L002_R1_001.good.fq | 454,230 | 62,302,067 | 100.0% | 137.2 bases | 149 bases | 97.8% |
| errors | Plate-1-BOP-1000-PFKA-END-3_S27_L002_R2_001.good.fq | 454,230 | 62,095,633 | 100.0% | 136.7 bases | 149 bases | 97.9% |
| errors | Plate-1-BOP-1000-PFKA-END-3_S27_L003_R1_001.good.fq | 483,311 | 66,198,023 | 100.0% | 137.0 bases | 149 bases | 97.6% |
| errors | Plate-1-BOP-1000-PFKA-END-3_S27_L003_R2_001.good.fq | 483,311 | 65,972,915 | 100.0% | 136.5 bases | 149 bases | 97.9% |
| errors | Plate-1-BOP-1000-PFKA-END-3_S27_L004_R1_001.good.fq | 494,103 | 67,628,752 | 100.0% | 136.9 bases | 149 bases | 97.9% |
| errors | Plate-1-BOP-1000-PFKA-END-3_S27_L004_R2_001.good.fq | 494,103 | 67,421,366 | 100.0% | 136.5 bases | 149 bases | 98.0% |
| total | 3,855,800 | 527,311,577 | 100.0% | 136.8 bases | 149 bases | 97.9% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_000913 | 4,641,652 | 112.9 | 3.6 | 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 | 22461 |
| 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 | 18 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.001 |
| reference sequence | pr(no read start) |
|---|---|
| NC_000913 | 0.70210 |
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 | 06:09:36 29 Feb 2020 | 06:10:31 29 Feb 2020 | 55 seconds |
| Read alignment to reference genome | 06:10:32 29 Feb 2020 | 06:18:00 29 Feb 2020 | 7 minutes 28 seconds |
| Preprocessing alignments for candidate junction identification | 06:18:00 29 Feb 2020 | 06:18:54 29 Feb 2020 | 54 seconds |
| Preliminary analysis of coverage distribution | 06:18:54 29 Feb 2020 | 06:21:05 29 Feb 2020 | 2 minutes 11 seconds |
| Identifying junction candidates | 06:21:05 29 Feb 2020 | 06:21:21 29 Feb 2020 | 16 seconds |
| Re-alignment to junction candidates | 06:21:21 29 Feb 2020 | 06:23:38 29 Feb 2020 | 2 minutes 17 seconds |
| Resolving best read alignments | 06:23:38 29 Feb 2020 | 06:25:00 29 Feb 2020 | 1 minute 22 seconds |
| Creating BAM files | 06:25:00 29 Feb 2020 | 06:27:01 29 Feb 2020 | 2 minutes 1 second |
| Tabulating error counts | 06:27:01 29 Feb 2020 | 06:27:42 29 Feb 2020 | 41 seconds |
| Re-calibrating base error rates | 06:27:42 29 Feb 2020 | 06:27:44 29 Feb 2020 | 2 seconds |
| Examining read alignment evidence | 06:27:44 29 Feb 2020 | 06:35:18 29 Feb 2020 | 7 minutes 34 seconds |
| Polymorphism statistics | 06:35:18 29 Feb 2020 | 06:35:18 29 Feb 2020 | 0 seconds |
| Output | 06:35:18 29 Feb 2020 | 06:35:31 29 Feb 2020 | 13 seconds |
| Total | 25 minutes 54 seconds | ||
