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-RPE-ALE-1-flask-16_S57_L001_R1_001.good.fq | 277,540 | 36,126,000 | 100.0% | 130.2 bases | 149 bases | 95.2% |
| errors | Plate-2-BOP-1000-RPE-ALE-1-flask-16_S57_L001_R2_001.good.fq | 277,540 | 35,696,552 | 100.0% | 128.6 bases | 149 bases | 98.0% |
| errors | Plate-2-BOP-1000-RPE-ALE-1-flask-16_S57_L002_R1_001.good.fq | 218,918 | 28,372,104 | 100.0% | 129.6 bases | 149 bases | 94.7% |
| errors | Plate-2-BOP-1000-RPE-ALE-1-flask-16_S57_L002_R2_001.good.fq | 218,918 | 28,010,763 | 100.0% | 128.0 bases | 149 bases | 97.4% |
| errors | Plate-2-BOP-1000-RPE-ALE-1-flask-16_S57_L003_R1_001.good.fq | 247,429 | 32,078,821 | 100.0% | 129.6 bases | 149 bases | 94.9% |
| errors | Plate-2-BOP-1000-RPE-ALE-1-flask-16_S57_L003_R2_001.good.fq | 247,429 | 31,661,686 | 100.0% | 128.0 bases | 149 bases | 97.8% |
| errors | Plate-2-BOP-1000-RPE-ALE-1-flask-16_S57_L004_R1_001.good.fq | 213,794 | 27,613,005 | 100.0% | 129.2 bases | 149 bases | 94.7% |
| errors | Plate-2-BOP-1000-RPE-ALE-1-flask-16_S57_L004_R2_001.good.fq | 213,794 | 27,271,176 | 100.0% | 127.6 bases | 149 bases | 97.3% |
| total | 1,915,362 | 246,830,107 | 100.0% | 128.9 bases | 149 bases | 96.3% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_000913 | 4,641,652 | 47.8 | 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 | 21015 |
| 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 | 267 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.017 |
| reference sequence | pr(no read start) |
|---|---|
| NC_000913 | 0.83361 |
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 | 09:21:37 26 Feb 2020 | 09:22:04 26 Feb 2020 | 27 seconds |
| Read alignment to reference genome | 09:22:05 26 Feb 2020 | 09:25:39 26 Feb 2020 | 3 minutes 34 seconds |
| Preprocessing alignments for candidate junction identification | 09:25:39 26 Feb 2020 | 09:26:05 26 Feb 2020 | 26 seconds |
| Preliminary analysis of coverage distribution | 09:26:05 26 Feb 2020 | 09:26:57 26 Feb 2020 | 52 seconds |
| Identifying junction candidates | 09:26:57 26 Feb 2020 | 09:27:45 26 Feb 2020 | 48 seconds |
| Re-alignment to junction candidates | 09:27:45 26 Feb 2020 | 09:28:57 26 Feb 2020 | 1 minute 12 seconds |
| Resolving best read alignments | 09:28:57 26 Feb 2020 | 09:29:37 26 Feb 2020 | 40 seconds |
| Creating BAM files | 09:29:37 26 Feb 2020 | 09:30:25 26 Feb 2020 | 48 seconds |
| Tabulating error counts | 09:30:25 26 Feb 2020 | 09:30:43 26 Feb 2020 | 18 seconds |
| Re-calibrating base error rates | 09:30:43 26 Feb 2020 | 09:30:46 26 Feb 2020 | 3 seconds |
| Examining read alignment evidence | 09:30:46 26 Feb 2020 | 09:34:15 26 Feb 2020 | 3 minutes 29 seconds |
| Polymorphism statistics | 09:34:15 26 Feb 2020 | 09:34:16 26 Feb 2020 | 1 second |
| Output | 09:34:16 26 Feb 2020 | 09:34:32 26 Feb 2020 | 16 seconds |
| Total | 12 minutes 54 seconds | ||
