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_19POP_S572_L003_R1_001.good.fq | 1,425,722 | 210,909,896 | 100.0% | 147.9 bases | 149 bases | 98.2% |
| errors | SvNSRound4_16_19POP_S572_L003_R2_001.good.fq | 1,425,722 | 210,909,896 | 100.0% | 147.9 bases | 149 bases | 91.8% |
| total | 2,851,444 | 421,819,792 | 100.0% | 147.9 bases | 149 bases | 95.0% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_000913_3_pae_tpiA | 4,641,568 | 84.8 | 4.4 | 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 | 6904 |
| Coverage evenness (position-hash) score of junction candidates | ≥ 2 | ≥ 2 |
| Test this many junction candidates (n). May be smaller if not enough passed the coverage evenness threshold | 100 ≤ n ≤ 5000 | 225 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.015 |
| reference sequence | pr(no read start) |
|---|---|
| NC_000913_3_pae_tpiA | 0.78813 |
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 | ≤ 0 |
| Number of bases that at least one read must overlap each uniquely aligned side of a predicted junction | ≥ 6 |
| option | value |
|---|---|
| Mode | Full Polymorphism |
| 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 | 2 |
| Polymorphism frequency cutoff | 0.05 |
| Polymorphism minimum variant coverage each strand | 2 |
| 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 | ≥3 bases |
| Skip base substitutions when they create a homopolymer flanked on each side by | ≥5 bases |
| program | version |
|---|---|
| bowtie2 | 2.2.6 |
| R | 3.4.4 |
| step | start | end | elapsed |
|---|---|---|---|
| Read and reference sequence file input | 18:13:48 19 Dec 2020 | 18:16:18 19 Dec 2020 | 2 minutes 30 seconds |
| Read alignment to reference genome | 18:16:19 19 Dec 2020 | 18:40:44 19 Dec 2020 | 24 minutes 25 seconds |
| Preprocessing alignments for candidate junction identification | 18:40:44 19 Dec 2020 | 18:42:47 19 Dec 2020 | 2 minutes 3 seconds |
| Preliminary analysis of coverage distribution | 18:42:47 19 Dec 2020 | 18:48:43 19 Dec 2020 | 5 minutes 56 seconds |
| Identifying junction candidates | 18:48:43 19 Dec 2020 | 18:48:46 19 Dec 2020 | 3 seconds |
| Re-alignment to junction candidates | 18:48:46 19 Dec 2020 | 18:53:56 19 Dec 2020 | 5 minutes 10 seconds |
| Resolving best read alignments | 18:53:56 19 Dec 2020 | 18:56:50 19 Dec 2020 | 2 minutes 54 seconds |
| Creating BAM files | 18:56:50 19 Dec 2020 | 19:02:21 19 Dec 2020 | 5 minutes 31 seconds |
| Tabulating error counts | 19:02:21 19 Dec 2020 | 19:04:12 19 Dec 2020 | 1 minute 51 seconds |
| Re-calibrating base error rates | 19:04:12 19 Dec 2020 | 19:04:15 19 Dec 2020 | 3 seconds |
| Examining read alignment evidence | 19:04:15 19 Dec 2020 | 21:40:57 19 Dec 2020 | 2 hours 36 minutes 42 seconds |
| Polymorphism statistics | 21:40:57 19 Dec 2020 | 21:40:58 19 Dec 2020 | 1 second |
| Output | 21:40:58 19 Dec 2020 | 21:41:32 19 Dec 2020 | 34 seconds |
| Total | 3 hours 27 minutes 43 seconds | ||
