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-27-PFKA-ALE-3-flask-34_S70_L001_R1_001.good.fq | 202,439 | 25,792,034 | 100.0% | 127.4 bases | 149 bases | 93.9% |
| errors | Plate-2-BOP-27-PFKA-ALE-3-flask-34_S70_L001_R2_001.good.fq | 202,439 | 25,413,724 | 100.0% | 125.5 bases | 149 bases | 97.4% |
| errors | Plate-2-BOP-27-PFKA-ALE-3-flask-34_S70_L002_R1_001.good.fq | 163,547 | 20,767,232 | 100.0% | 127.0 bases | 149 bases | 93.4% |
| errors | Plate-2-BOP-27-PFKA-ALE-3-flask-34_S70_L002_R2_001.good.fq | 163,547 | 20,445,762 | 100.0% | 125.0 bases | 149 bases | 96.9% |
| errors | Plate-2-BOP-27-PFKA-ALE-3-flask-34_S70_L003_R1_001.good.fq | 184,957 | 23,489,018 | 100.0% | 127.0 bases | 149 bases | 93.8% |
| errors | Plate-2-BOP-27-PFKA-ALE-3-flask-34_S70_L003_R2_001.good.fq | 184,957 | 23,139,032 | 100.0% | 125.1 bases | 149 bases | 97.3% |
| errors | Plate-2-BOP-27-PFKA-ALE-3-flask-34_S70_L004_R1_001.good.fq | 161,373 | 20,448,055 | 100.0% | 126.7 bases | 149 bases | 93.4% |
| errors | Plate-2-BOP-27-PFKA-ALE-3-flask-34_S70_L004_R2_001.good.fq | 161,373 | 20,133,927 | 100.0% | 124.8 bases | 149 bases | 96.9% |
| total | 1,424,632 | 179,628,784 | 100.0% | 126.1 bases | 149 bases | 95.4% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_000913 | 4,641,652 | 36.8 | 2.5 | 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 | 18788 |
| 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 | 121 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.008 |
| reference sequence | pr(no read start) |
|---|---|
| NC_000913 | 0.87155 |
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 | 01:20:07 25 Feb 2020 | 01:20:28 25 Feb 2020 | 21 seconds |
| Read alignment to reference genome | 01:20:28 25 Feb 2020 | 01:23:14 25 Feb 2020 | 2 minutes 46 seconds |
| Preprocessing alignments for candidate junction identification | 01:23:14 25 Feb 2020 | 01:23:34 25 Feb 2020 | 20 seconds |
| Preliminary analysis of coverage distribution | 01:23:34 25 Feb 2020 | 01:24:13 25 Feb 2020 | 39 seconds |
| Identifying junction candidates | 01:24:13 25 Feb 2020 | 01:24:57 25 Feb 2020 | 44 seconds |
| Re-alignment to junction candidates | 01:24:57 25 Feb 2020 | 01:25:50 25 Feb 2020 | 53 seconds |
| Resolving best read alignments | 01:25:50 25 Feb 2020 | 01:26:19 25 Feb 2020 | 29 seconds |
| Creating BAM files | 01:26:19 25 Feb 2020 | 01:26:54 25 Feb 2020 | 35 seconds |
| Tabulating error counts | 01:26:54 25 Feb 2020 | 01:27:07 25 Feb 2020 | 13 seconds |
| Re-calibrating base error rates | 01:27:07 25 Feb 2020 | 01:27:10 25 Feb 2020 | 3 seconds |
| Examining read alignment evidence | 01:27:10 25 Feb 2020 | 01:29:49 25 Feb 2020 | 2 minutes 39 seconds |
| Polymorphism statistics | 01:29:49 25 Feb 2020 | 01:29:49 25 Feb 2020 | 0 seconds |
| Output | 01:29:49 25 Feb 2020 | 01:30:04 25 Feb 2020 | 15 seconds |
| Total | 9 minutes 57 seconds | ||
