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 | SvNSRound4_15_36_2_S2377_L007_R1_001.good.fq | 1,124,970 | 152,422,625 | 100.0% | 135.5 bases | 150 bases | 94.6% |
| errors | SvNSRound4_15_36_2_S2377_L007_R2_001.good.fq | 1,124,970 | 152,422,625 | 100.0% | 135.5 bases | 150 bases | 93.5% |
| errors | SvNSRound4_15_36_2_S2377_L008_R1_001.good.fq | 696,987 | 94,948,953 | 100.0% | 136.2 bases | 150 bases | 94.4% |
| errors | SvNSRound4_15_36_2_S2377_L008_R2_001.good.fq | 696,987 | 94,948,953 | 100.0% | 136.2 bases | 150 bases | 92.9% |
| total | 3,643,914 | 494,743,156 | 100.0% | 135.8 bases | 150 bases | 93.9% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_000913_3_pae_tpiA | 4,641,568 | 99.4 | 2.1 | 100.0% | Escherichia coli str. K-12 substr. MG1655, P. aerophilum tpiA gene, complete genome. |
| total | 4,641,568 | 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 | 100153 |
| 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 | 583 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.039 |
| reference sequence | pr(no read start) |
|---|---|
| NC_000913_3_pae_tpiA | 0.71740 |
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 | 18:30:57 19 Dec 2020 | 18:34:23 19 Dec 2020 | 3 minutes 26 seconds |
| Read alignment to reference genome | 18:34:23 19 Dec 2020 | 19:04:35 19 Dec 2020 | 30 minutes 12 seconds |
| Preprocessing alignments for candidate junction identification | 19:04:35 19 Dec 2020 | 19:07:49 19 Dec 2020 | 3 minutes 14 seconds |
| Preliminary analysis of coverage distribution | 19:07:49 19 Dec 2020 | 19:14:14 19 Dec 2020 | 6 minutes 25 seconds |
| Identifying junction candidates | 19:14:14 19 Dec 2020 | 19:31:54 19 Dec 2020 | 17 minutes 40 seconds |
| Re-alignment to junction candidates | 19:31:54 19 Dec 2020 | 19:40:09 19 Dec 2020 | 8 minutes 15 seconds |
| Resolving best read alignments | 19:40:09 19 Dec 2020 | 19:44:10 19 Dec 2020 | 4 minutes 1 second |
| Creating BAM files | 19:44:10 19 Dec 2020 | 19:49:56 19 Dec 2020 | 5 minutes 46 seconds |
| Tabulating error counts | 19:49:56 19 Dec 2020 | 19:52:22 19 Dec 2020 | 2 minutes 26 seconds |
| Re-calibrating base error rates | 19:52:22 19 Dec 2020 | 19:52:27 19 Dec 2020 | 5 seconds |
| Examining read alignment evidence | 19:52:27 19 Dec 2020 | 20:23:21 19 Dec 2020 | 30 minutes 54 seconds |
| Polymorphism statistics | 20:23:21 19 Dec 2020 | 20:23:23 19 Dec 2020 | 2 seconds |
| Output | 20:23:23 19 Dec 2020 | 20:24:14 19 Dec 2020 | 51 seconds |
| Total | 1 hour 53 minutes 17 seconds | ||
