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-SUCB-ALE-3-flask-37_S46_L001_R1_001.good.fq | 184,506 | 24,433,080 | 100.0% | 132.4 bases | 149 bases | 95.5% |
| errors | Plate-2-BOP-1000-SUCB-ALE-3-flask-37_S46_L001_R2_001.good.fq | 184,506 | 24,182,108 | 100.0% | 131.1 bases | 149 bases | 98.0% |
| errors | Plate-2-BOP-1000-SUCB-ALE-3-flask-37_S46_L002_R1_001.good.fq | 143,331 | 18,904,261 | 100.0% | 131.9 bases | 149 bases | 95.0% |
| errors | Plate-2-BOP-1000-SUCB-ALE-3-flask-37_S46_L002_R2_001.good.fq | 143,331 | 18,701,075 | 100.0% | 130.5 bases | 149 bases | 97.3% |
| errors | Plate-2-BOP-1000-SUCB-ALE-3-flask-37_S46_L003_R1_001.good.fq | 164,565 | 21,704,874 | 100.0% | 131.9 bases | 149 bases | 95.1% |
| errors | Plate-2-BOP-1000-SUCB-ALE-3-flask-37_S46_L003_R2_001.good.fq | 164,565 | 21,466,221 | 100.0% | 130.4 bases | 149 bases | 97.7% |
| errors | Plate-2-BOP-1000-SUCB-ALE-3-flask-37_S46_L004_R1_001.good.fq | 139,796 | 18,394,193 | 100.0% | 131.6 bases | 149 bases | 94.9% |
| errors | Plate-2-BOP-1000-SUCB-ALE-3-flask-37_S46_L004_R2_001.good.fq | 139,796 | 18,199,528 | 100.0% | 130.2 bases | 149 bases | 97.1% |
| total | 1,264,396 | 165,985,340 | 100.0% | 131.3 bases | 149 bases | 96.3% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_000913 | 4,641,652 | 34.0 | 3.1 | 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 | 13194 |
| 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 | 56 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.004 |
| reference sequence | pr(no read start) |
|---|---|
| NC_000913 | 0.88446 |
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 | 10:28:39 06 Apr 2022 | 10:29:02 06 Apr 2022 | 23 seconds |
| Read alignment to reference genome | 10:29:03 06 Apr 2022 | 10:31:37 06 Apr 2022 | 2 minutes 34 seconds |
| Preprocessing alignments for candidate junction identification | 10:31:37 06 Apr 2022 | 10:31:53 06 Apr 2022 | 16 seconds |
| Preliminary analysis of coverage distribution | 10:31:53 06 Apr 2022 | 10:32:34 06 Apr 2022 | 41 seconds |
| Identifying junction candidates | 10:32:34 06 Apr 2022 | 10:32:53 06 Apr 2022 | 19 seconds |
| Re-alignment to junction candidates | 10:32:53 06 Apr 2022 | 10:33:28 06 Apr 2022 | 35 seconds |
| Resolving best read alignments | 10:33:28 06 Apr 2022 | 10:33:51 06 Apr 2022 | 23 seconds |
| Creating BAM files | 10:33:51 06 Apr 2022 | 10:34:27 06 Apr 2022 | 36 seconds |
| Tabulating error counts | 10:34:27 06 Apr 2022 | 10:34:41 06 Apr 2022 | 14 seconds |
| Re-calibrating base error rates | 10:34:41 06 Apr 2022 | 10:34:44 06 Apr 2022 | 3 seconds |
| Examining read alignment evidence | 10:34:44 06 Apr 2022 | 10:37:59 06 Apr 2022 | 3 minutes 15 seconds |
| Polymorphism statistics | 10:37:59 06 Apr 2022 | 10:38:00 06 Apr 2022 | 1 second |
| Output | 10:38:00 06 Apr 2022 | 10:38:07 06 Apr 2022 | 7 seconds |
| Total | 9 minutes 27 seconds | ||
