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-PFKA-ALE-1-flask-13_S49_L001_R1_001.good.fq | 201,658 | 27,008,072 | 100.0% | 133.9 bases | 149 bases | 95.8% |
| errors | Plate-2-BOP-1000-PFKA-ALE-1-flask-13_S49_L001_R2_001.good.fq | 201,658 | 26,766,509 | 100.0% | 132.7 bases | 149 bases | 98.0% |
| errors | Plate-2-BOP-1000-PFKA-ALE-1-flask-13_S49_L002_R1_001.good.fq | 158,133 | 21,105,143 | 100.0% | 133.5 bases | 149 bases | 95.6% |
| errors | Plate-2-BOP-1000-PFKA-ALE-1-flask-13_S49_L002_R2_001.good.fq | 158,133 | 20,922,445 | 100.0% | 132.3 bases | 149 bases | 97.5% |
| errors | Plate-2-BOP-1000-PFKA-ALE-1-flask-13_S49_L003_R1_001.good.fq | 180,614 | 24,079,665 | 100.0% | 133.3 bases | 149 bases | 95.7% |
| errors | Plate-2-BOP-1000-PFKA-ALE-1-flask-13_S49_L003_R2_001.good.fq | 180,614 | 23,859,139 | 100.0% | 132.1 bases | 149 bases | 97.8% |
| errors | Plate-2-BOP-1000-PFKA-ALE-1-flask-13_S49_L004_R1_001.good.fq | 155,180 | 20,660,801 | 100.0% | 133.1 bases | 149 bases | 95.4% |
| errors | Plate-2-BOP-1000-PFKA-ALE-1-flask-13_S49_L004_R2_001.good.fq | 155,180 | 20,481,159 | 100.0% | 132.0 bases | 149 bases | 97.3% |
| total | 1,391,170 | 184,882,933 | 100.0% | 132.9 bases | 149 bases | 96.7% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_000913 | 4,641,652 | 38.6 | 2.2 | 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 | 12300 |
| 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 | 73 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.005 |
| reference sequence | pr(no read start) |
|---|---|
| NC_000913 | 0.87248 |
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 | 03:30:30 29 Feb 2020 | 03:30:50 29 Feb 2020 | 20 seconds |
| Read alignment to reference genome | 03:30:51 29 Feb 2020 | 03:33:32 29 Feb 2020 | 2 minutes 41 seconds |
| Preprocessing alignments for candidate junction identification | 03:33:32 29 Feb 2020 | 03:33:52 29 Feb 2020 | 20 seconds |
| Preliminary analysis of coverage distribution | 03:33:52 29 Feb 2020 | 03:34:31 29 Feb 2020 | 39 seconds |
| Identifying junction candidates | 03:34:31 29 Feb 2020 | 03:34:56 29 Feb 2020 | 25 seconds |
| Re-alignment to junction candidates | 03:34:56 29 Feb 2020 | 03:35:46 29 Feb 2020 | 50 seconds |
| Resolving best read alignments | 03:35:46 29 Feb 2020 | 03:36:16 29 Feb 2020 | 30 seconds |
| Creating BAM files | 03:36:16 29 Feb 2020 | 03:36:52 29 Feb 2020 | 36 seconds |
| Tabulating error counts | 03:36:52 29 Feb 2020 | 03:37:05 29 Feb 2020 | 13 seconds |
| Re-calibrating base error rates | 03:37:05 29 Feb 2020 | 03:37:08 29 Feb 2020 | 3 seconds |
| Examining read alignment evidence | 03:37:08 29 Feb 2020 | 03:39:52 29 Feb 2020 | 2 minutes 44 seconds |
| Polymorphism statistics | 03:39:52 29 Feb 2020 | 03:39:53 29 Feb 2020 | 1 second |
| Output | 03:39:53 29 Feb 2020 | 03:40:03 29 Feb 2020 | 10 seconds |
| Total | 9 minutes 32 seconds | ||
