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-27-SUCB-ALE-4-flask-16_S40_L001_R1_001.good.fq | 177,506 | 24,389,615 | 100.0% | 137.4 bases | 149 bases | 93.5% |
| errors | Plate-2-BOP-27-SUCB-ALE-4-flask-16_S40_L001_R2_001.good.fq | 177,506 | 24,014,047 | 100.0% | 135.3 bases | 149 bases | 97.7% |
| errors | Plate-2-BOP-27-SUCB-ALE-4-flask-16_S40_L002_R1_001.good.fq | 147,135 | 20,168,109 | 100.0% | 137.1 bases | 149 bases | 93.5% |
| errors | Plate-2-BOP-27-SUCB-ALE-4-flask-16_S40_L002_R2_001.good.fq | 147,135 | 19,868,529 | 100.0% | 135.0 bases | 149 bases | 97.2% |
| errors | Plate-2-BOP-27-SUCB-ALE-4-flask-16_S40_L003_R1_001.good.fq | 160,549 | 22,014,970 | 100.0% | 137.1 bases | 149 bases | 93.2% |
| errors | Plate-2-BOP-27-SUCB-ALE-4-flask-16_S40_L003_R2_001.good.fq | 160,549 | 21,665,753 | 100.0% | 134.9 bases | 149 bases | 97.5% |
| errors | Plate-2-BOP-27-SUCB-ALE-4-flask-16_S40_L004_R1_001.good.fq | 142,946 | 19,533,168 | 100.0% | 136.6 bases | 149 bases | 93.2% |
| errors | Plate-2-BOP-27-SUCB-ALE-4-flask-16_S40_L004_R2_001.good.fq | 142,946 | 19,232,640 | 100.0% | 134.5 bases | 149 bases | 97.1% |
| total | 1,256,272 | 170,886,831 | 100.0% | 136.0 bases | 149 bases | 95.4% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_000913 | 4,641,652 | 35.0 | 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 | 15225 |
| 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 | 0.88614 |
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 | 10:27:34 06 Apr 2022 | 10:27:57 06 Apr 2022 | 23 seconds |
| Read alignment to reference genome | 10:27:57 06 Apr 2022 | 10:30:24 06 Apr 2022 | 2 minutes 27 seconds |
| Preprocessing alignments for candidate junction identification | 10:30:24 06 Apr 2022 | 10:30:40 06 Apr 2022 | 16 seconds |
| Preliminary analysis of coverage distribution | 10:30:40 06 Apr 2022 | 10:31:21 06 Apr 2022 | 41 seconds |
| Identifying junction candidates | 10:31:21 06 Apr 2022 | 10:31:35 06 Apr 2022 | 14 seconds |
| Re-alignment to junction candidates | 10:31:35 06 Apr 2022 | 10:32:09 06 Apr 2022 | 34 seconds |
| Resolving best read alignments | 10:32:09 06 Apr 2022 | 10:32:31 06 Apr 2022 | 22 seconds |
| Creating BAM files | 10:32:31 06 Apr 2022 | 10:33:07 06 Apr 2022 | 36 seconds |
| Tabulating error counts | 10:33:07 06 Apr 2022 | 10:33:22 06 Apr 2022 | 15 seconds |
| Re-calibrating base error rates | 10:33:22 06 Apr 2022 | 10:33:24 06 Apr 2022 | 2 seconds |
| Examining read alignment evidence | 10:33:24 06 Apr 2022 | 10:36:37 06 Apr 2022 | 3 minutes 13 seconds |
| Polymorphism statistics | 10:36:37 06 Apr 2022 | 10:36:38 06 Apr 2022 | 1 second |
| Output | 10:36:38 06 Apr 2022 | 10:36:44 06 Apr 2022 | 6 seconds |
| Total | 9 minutes 10 seconds | ||
