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-4-flask-9_S71_L001_R1_001.good.fq | 197,436 | 25,794,973 | 100.0% | 130.6 bases | 149 bases | 94.4% |
| errors | Plate-2-BOP-27-PFKA-ALE-4-flask-9_S71_L001_R2_001.good.fq | 197,436 | 25,510,051 | 100.0% | 129.2 bases | 149 bases | 97.2% |
| errors | Plate-2-BOP-27-PFKA-ALE-4-flask-9_S71_L002_R1_001.good.fq | 158,730 | 20,673,323 | 100.0% | 130.2 bases | 149 bases | 94.0% |
| errors | Plate-2-BOP-27-PFKA-ALE-4-flask-9_S71_L002_R2_001.good.fq | 158,730 | 20,428,227 | 100.0% | 128.7 bases | 149 bases | 96.8% |
| errors | Plate-2-BOP-27-PFKA-ALE-4-flask-9_S71_L003_R1_001.good.fq | 180,118 | 23,472,021 | 100.0% | 130.3 bases | 149 bases | 94.2% |
| errors | Plate-2-BOP-27-PFKA-ALE-4-flask-9_S71_L003_R2_001.good.fq | 180,118 | 23,198,863 | 100.0% | 128.8 bases | 149 bases | 97.1% |
| errors | Plate-2-BOP-27-PFKA-ALE-4-flask-9_S71_L004_R1_001.good.fq | 156,249 | 20,339,098 | 100.0% | 130.2 bases | 149 bases | 93.7% |
| errors | Plate-2-BOP-27-PFKA-ALE-4-flask-9_S71_L004_R2_001.good.fq | 156,249 | 20,089,316 | 100.0% | 128.6 bases | 149 bases | 96.6% |
| total | 1,385,066 | 179,505,872 | 100.0% | 129.6 bases | 149 bases | 95.5% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_000913 | 4,641,652 | 36.8 | 2.7 | 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 | 17572 |
| 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 | 107 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.007 |
| reference sequence | pr(no read start) |
|---|---|
| NC_000913 | 0.87479 |
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 | 10:11:36 29 Feb 2020 | 10:11:57 29 Feb 2020 | 21 seconds |
| Read alignment to reference genome | 10:11:57 29 Feb 2020 | 10:14:37 29 Feb 2020 | 2 minutes 40 seconds |
| Preprocessing alignments for candidate junction identification | 10:14:37 29 Feb 2020 | 10:14:56 29 Feb 2020 | 19 seconds |
| Preliminary analysis of coverage distribution | 10:14:56 29 Feb 2020 | 10:15:34 29 Feb 2020 | 38 seconds |
| Identifying junction candidates | 10:15:34 29 Feb 2020 | 10:16:19 29 Feb 2020 | 45 seconds |
| Re-alignment to junction candidates | 10:16:19 29 Feb 2020 | 10:17:09 29 Feb 2020 | 50 seconds |
| Resolving best read alignments | 10:17:09 29 Feb 2020 | 10:17:38 29 Feb 2020 | 29 seconds |
| Creating BAM files | 10:17:38 29 Feb 2020 | 10:18:12 29 Feb 2020 | 34 seconds |
| Tabulating error counts | 10:18:12 29 Feb 2020 | 10:18:25 29 Feb 2020 | 13 seconds |
| Re-calibrating base error rates | 10:18:25 29 Feb 2020 | 10:18:28 29 Feb 2020 | 3 seconds |
| Examining read alignment evidence | 10:18:28 29 Feb 2020 | 10:21:06 29 Feb 2020 | 2 minutes 38 seconds |
| Polymorphism statistics | 10:21:06 29 Feb 2020 | 10:21:06 29 Feb 2020 | 0 seconds |
| Output | 10:21:06 29 Feb 2020 | 10:21:20 29 Feb 2020 | 14 seconds |
| Total | 9 minutes 44 seconds | ||
