mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.35.4 revision f352f80f4bc9
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-4-flask-14_S56_L001_R1_001.good.fq | 193,094 | 26,091,638 | 100.0% | 135.1 bases | 149 bases | 95.2% |
| errors | Plate-2-BOP-1000-PFKA-ALE-4-flask-14_S56_L001_R2_001.good.fq | 193,094 | 25,807,267 | 100.0% | 133.7 bases | 149 bases | 98.0% |
| errors | Plate-2-BOP-1000-PFKA-ALE-4-flask-14_S56_L002_R1_001.good.fq | 150,782 | 20,299,933 | 100.0% | 134.6 bases | 149 bases | 94.8% |
| errors | Plate-2-BOP-1000-PFKA-ALE-4-flask-14_S56_L002_R2_001.good.fq | 150,782 | 20,070,469 | 100.0% | 133.1 bases | 149 bases | 97.4% |
| errors | Plate-2-BOP-1000-PFKA-ALE-4-flask-14_S56_L003_R1_001.good.fq | 172,943 | 23,295,541 | 100.0% | 134.7 bases | 149 bases | 95.0% |
| errors | Plate-2-BOP-1000-PFKA-ALE-4-flask-14_S56_L003_R2_001.good.fq | 172,943 | 23,030,774 | 100.0% | 133.2 bases | 149 bases | 97.7% |
| errors | Plate-2-BOP-1000-PFKA-ALE-4-flask-14_S56_L004_R1_001.good.fq | 147,577 | 19,837,223 | 100.0% | 134.4 bases | 149 bases | 94.7% |
| errors | Plate-2-BOP-1000-PFKA-ALE-4-flask-14_S56_L004_R2_001.good.fq | 147,577 | 19,615,666 | 100.0% | 132.9 bases | 149 bases | 97.2% |
| total | 1,328,792 | 178,048,511 | 100.0% | 134.0 bases | 149 bases | 96.3% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_000913 | 4,641,652 | 36.6 | 2.3 | 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 | 13272 |
| 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 | 74 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.005 |
| reference sequence | pr(no read start) |
|---|---|
| NC_000913 | 0.87838 |
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 |
| Minimum probablilty assigned that no mapped read will start at a given position and strand for junction prediction | 0.1 |
| Junction allow suboptimal matches | FALSE |
| 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 | 2.2.6 |
| R | 3.4.4 |
| step | start | end | elapsed |
|---|---|---|---|
| Read and reference sequence file input | 10:28:29 06 Apr 2022 | 10:28:53 06 Apr 2022 | 24 seconds |
| Read alignment to reference genome | 10:28:53 06 Apr 2022 | 10:31:31 06 Apr 2022 | 2 minutes 38 seconds |
| Preprocessing alignments for candidate junction identification | 10:31:31 06 Apr 2022 | 10:31:47 06 Apr 2022 | 16 seconds |
| Preliminary analysis of coverage distribution | 10:31:47 06 Apr 2022 | 10:32:30 06 Apr 2022 | 43 seconds |
| Identifying junction candidates | 10:32:30 06 Apr 2022 | 10:32:45 06 Apr 2022 | 15 seconds |
| Re-alignment to junction candidates | 10:32:45 06 Apr 2022 | 10:33:22 06 Apr 2022 | 37 seconds |
| Resolving best read alignments | 10:33:22 06 Apr 2022 | 10:33:45 06 Apr 2022 | 23 seconds |
| Creating BAM files | 10:33:45 06 Apr 2022 | 10:34:24 06 Apr 2022 | 39 seconds |
| Tabulating error counts | 10:34:24 06 Apr 2022 | 10:34:40 06 Apr 2022 | 16 seconds |
| Re-calibrating base error rates | 10:34:40 06 Apr 2022 | 10:34:42 06 Apr 2022 | 2 seconds |
| Examining read alignment evidence | 10:34:42 06 Apr 2022 | 10:38:06 06 Apr 2022 | 3 minutes 24 seconds |
| Polymorphism statistics | 10:38:06 06 Apr 2022 | 10:38:07 06 Apr 2022 | 1 second |
| Output | 10:38:07 06 Apr 2022 | 10:38:15 06 Apr 2022 | 8 seconds |
| Total | 9 minutes 46 seconds | ||
