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-ACEF-ALE-3-flask-51_S14_L001_R1_001.good.fq | 158,084 | 20,292,308 | 100.0% | 128.4 bases | 149 bases | 95.5% |
| errors | Plate-2-BOP-1000-ACEF-ALE-3-flask-51_S14_L001_R2_001.good.fq | 158,084 | 20,083,815 | 100.0% | 127.0 bases | 149 bases | 97.9% |
| errors | Plate-2-BOP-1000-ACEF-ALE-3-flask-51_S14_L002_R1_001.good.fq | 126,773 | 16,186,765 | 100.0% | 127.7 bases | 149 bases | 95.5% |
| errors | Plate-2-BOP-1000-ACEF-ALE-3-flask-51_S14_L002_R2_001.good.fq | 126,773 | 16,029,380 | 100.0% | 126.4 bases | 149 bases | 97.5% |
| errors | Plate-2-BOP-1000-ACEF-ALE-3-flask-51_S14_L003_R1_001.good.fq | 144,141 | 18,441,121 | 100.0% | 127.9 bases | 149 bases | 95.4% |
| errors | Plate-2-BOP-1000-ACEF-ALE-3-flask-51_S14_L003_R2_001.good.fq | 144,141 | 18,248,424 | 100.0% | 126.6 bases | 149 bases | 97.8% |
| errors | Plate-2-BOP-1000-ACEF-ALE-3-flask-51_S14_L004_R1_001.good.fq | 124,266 | 15,825,633 | 100.0% | 127.4 bases | 149 bases | 95.1% |
| errors | Plate-2-BOP-1000-ACEF-ALE-3-flask-51_S14_L004_R2_001.good.fq | 124,266 | 15,665,157 | 100.0% | 126.1 bases | 149 bases | 97.2% |
| total | 1,106,528 | 140,772,603 | 100.0% | 127.2 bases | 149 bases | 96.5% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_000913 | 4,641,652 | 29.3 | 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 | 12606 |
| 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 | 96 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.006 |
| reference sequence | pr(no read start) |
|---|---|
| NC_000913 | 0.89679 |
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 | 20:09:32 28 Feb 2020 | 20:09:48 28 Feb 2020 | 16 seconds |
| Read alignment to reference genome | 20:09:49 28 Feb 2020 | 20:11:53 28 Feb 2020 | 2 minutes 4 seconds |
| Preprocessing alignments for candidate junction identification | 20:11:53 28 Feb 2020 | 20:12:08 28 Feb 2020 | 15 seconds |
| Preliminary analysis of coverage distribution | 20:12:08 28 Feb 2020 | 20:12:39 28 Feb 2020 | 31 seconds |
| Identifying junction candidates | 20:12:39 28 Feb 2020 | 20:13:20 28 Feb 2020 | 41 seconds |
| Re-alignment to junction candidates | 20:13:20 28 Feb 2020 | 20:13:59 28 Feb 2020 | 39 seconds |
| Resolving best read alignments | 20:13:59 28 Feb 2020 | 20:14:22 28 Feb 2020 | 23 seconds |
| Creating BAM files | 20:14:22 28 Feb 2020 | 20:14:50 28 Feb 2020 | 28 seconds |
| Tabulating error counts | 20:14:50 28 Feb 2020 | 20:15:00 28 Feb 2020 | 10 seconds |
| Re-calibrating base error rates | 20:15:00 28 Feb 2020 | 20:15:03 28 Feb 2020 | 3 seconds |
| Examining read alignment evidence | 20:15:03 28 Feb 2020 | 20:17:14 28 Feb 2020 | 2 minutes 11 seconds |
| Polymorphism statistics | 20:17:14 28 Feb 2020 | 20:17:14 28 Feb 2020 | 0 seconds |
| Output | 20:17:14 28 Feb 2020 | 20:17:30 28 Feb 2020 | 16 seconds |
| Total | 7 minutes 57 seconds | ||
