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_16_36_1_S2382_L007_R1_001.good.fq | 1,309,120 | 170,910,238 | 100.0% | 130.6 bases | 150 bases | 95.1% |
| errors | SvNSRound4_16_36_1_S2382_L007_R2_001.good.fq | 1,309,120 | 170,910,238 | 100.0% | 130.6 bases | 150 bases | 94.3% |
| errors | SvNSRound4_16_36_1_S2382_L008_R1_001.good.fq | 808,192 | 106,241,266 | 100.0% | 131.5 bases | 150 bases | 94.6% |
| errors | SvNSRound4_16_36_1_S2382_L008_R2_001.good.fq | 808,192 | 106,241,266 | 100.0% | 131.5 bases | 150 bases | 93.5% |
| total | 4,234,624 | 554,303,008 | 100.0% | 130.9 bases | 150 bases | 94.5% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_000913_3_pae_tpiA | 4,641,568 | 110.2 | 2.2 | 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 | 100000 |
| 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 | 671 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.045 |
| reference sequence | pr(no read start) |
|---|---|
| NC_000913_3_pae_tpiA | 0.68006 |
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 | 18:35:05 19 Dec 2020 | 18:38:45 19 Dec 2020 | 3 minutes 40 seconds |
| Read alignment to reference genome | 18:38:46 19 Dec 2020 | 19:09:58 19 Dec 2020 | 31 minutes 12 seconds |
| Preprocessing alignments for candidate junction identification | 19:09:58 19 Dec 2020 | 19:13:27 19 Dec 2020 | 3 minutes 29 seconds |
| Preliminary analysis of coverage distribution | 19:13:27 19 Dec 2020 | 19:20:15 19 Dec 2020 | 6 minutes 48 seconds |
| Identifying junction candidates | 19:20:15 19 Dec 2020 | 19:50:46 19 Dec 2020 | 30 minutes 31 seconds |
| Re-alignment to junction candidates | 19:50:46 19 Dec 2020 | 19:59:57 19 Dec 2020 | 9 minutes 11 seconds |
| Resolving best read alignments | 19:59:57 19 Dec 2020 | 20:04:10 19 Dec 2020 | 4 minutes 13 seconds |
| Creating BAM files | 20:04:10 19 Dec 2020 | 20:10:21 19 Dec 2020 | 6 minutes 11 seconds |
| Tabulating error counts | 20:10:21 19 Dec 2020 | 20:12:52 19 Dec 2020 | 2 minutes 31 seconds |
| Re-calibrating base error rates | 20:12:52 19 Dec 2020 | 20:12:57 19 Dec 2020 | 5 seconds |
| Examining read alignment evidence | 20:12:57 19 Dec 2020 | 20:44:12 19 Dec 2020 | 31 minutes 15 seconds |
| Polymorphism statistics | 20:44:12 19 Dec 2020 | 20:44:15 19 Dec 2020 | 3 seconds |
| Output | 20:44:15 19 Dec 2020 | 20:45:13 19 Dec 2020 | 58 seconds |
| Total | 2 hours 10 minutes 7 seconds | ||
