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_1_S2376_L007_R1_001.good.fq | 1,467,494 | 193,688,517 | 100.0% | 132.0 bases | 150 bases | 94.1% |
| errors | SvNSRound4_15_36_1_S2376_L007_R2_001.good.fq | 1,467,494 | 193,688,517 | 100.0% | 132.0 bases | 150 bases | 93.1% |
| errors | SvNSRound4_15_36_1_S2376_L008_R1_001.good.fq | 911,128 | 120,991,596 | 100.0% | 132.8 bases | 150 bases | 93.6% |
| errors | SvNSRound4_15_36_1_S2376_L008_R2_001.good.fq | 911,128 | 120,991,596 | 100.0% | 132.8 bases | 150 bases | 92.2% |
| total | 4,757,244 | 629,360,226 | 100.0% | 132.3 bases | 150 bases | 93.3% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_000913_3_pae_tpiA | 4,641,568 | 125.4 | 2.3 | 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 | 619 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.041 |
| reference sequence | pr(no read start) |
|---|---|
| NC_000913_3_pae_tpiA | 0.65360 |
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 | 18:39:02 19 Dec 2020 | 18:43:35 19 Dec 2020 | 4 minutes 33 seconds |
| Read alignment to reference genome | 18:43:36 19 Dec 2020 | 19:21:50 19 Dec 2020 | 38 minutes 14 seconds |
| Preprocessing alignments for candidate junction identification | 19:21:50 19 Dec 2020 | 19:25:48 19 Dec 2020 | 3 minutes 58 seconds |
| Preliminary analysis of coverage distribution | 19:25:48 19 Dec 2020 | 19:33:46 19 Dec 2020 | 7 minutes 58 seconds |
| Identifying junction candidates | 19:33:46 19 Dec 2020 | 19:55:16 19 Dec 2020 | 21 minutes 30 seconds |
| Re-alignment to junction candidates | 19:55:16 19 Dec 2020 | 20:05:42 19 Dec 2020 | 10 minutes 26 seconds |
| Resolving best read alignments | 20:05:42 19 Dec 2020 | 20:10:57 19 Dec 2020 | 5 minutes 15 seconds |
| Creating BAM files | 20:10:57 19 Dec 2020 | 20:18:04 19 Dec 2020 | 7 minutes 7 seconds |
| Tabulating error counts | 20:18:04 19 Dec 2020 | 20:21:08 19 Dec 2020 | 3 minutes 4 seconds |
| Re-calibrating base error rates | 20:21:08 19 Dec 2020 | 20:21:14 19 Dec 2020 | 6 seconds |
| Examining read alignment evidence | 20:21:14 19 Dec 2020 | 21:00:27 19 Dec 2020 | 39 minutes 13 seconds |
| Polymorphism statistics | 21:00:27 19 Dec 2020 | 21:00:29 19 Dec 2020 | 2 seconds |
| Output | 21:00:29 19 Dec 2020 | 21:01:34 19 Dec 2020 | 1 minute 5 seconds |
| Total | 2 hours 22 minutes 31 seconds | ||
