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 | HAT0_R1.good.fq | 1,082,941 | 117,010,550 | 100.0% | 108.0 bases | 134 bases | 89.8% |
| errors | HAT0_R2.good.fq | 1,082,941 | 116,998,426 | 100.0% | 108.0 bases | 134 bases | 89.7% |
| total | 2,165,882 | 234,008,976 | 100.0% | 108.0 bases | 134 bases | 89.8% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | AM260479 | 4,052,032 | 27.1 | 4.0 | 53.3% | Ralstonia eutropha H16 chromosome 1. |
| coverage | distribution | AM260480 | 2,912,490 | 29.8 | 4.2 | 42.4% | Ralstonia eutropha H16 chromosome 2. |
| coverage | distribution | AY305378 | 452,156 | 19.6 | 3.7 | 4.3% | Ralstonia eutropha H16 megaplasmid pHG1, complete sequence. |
| total | 7,416,678 | 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 | 9486 |
| 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 | 73 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.003 |
| reference sequence | pr(no read start) |
|---|---|
| AM260479 | 0.89994 |
| AM260480 | 0.89115 |
| AY305378 | 0.92418 |
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 | 08:33:42 01 May 2023 | 08:34:27 01 May 2023 | 45 seconds |
| Read alignment to reference genome | 08:34:28 01 May 2023 | 08:40:49 01 May 2023 | 6 minutes 21 seconds |
| Preprocessing alignments for candidate junction identification | 08:40:49 01 May 2023 | 08:41:25 01 May 2023 | 36 seconds |
| Preliminary analysis of coverage distribution | 08:41:25 01 May 2023 | 08:42:42 01 May 2023 | 1 minute 17 seconds |
| Identifying junction candidates | 08:42:42 01 May 2023 | 08:42:57 01 May 2023 | 15 seconds |
| Re-alignment to junction candidates | 08:42:57 01 May 2023 | 08:44:30 01 May 2023 | 1 minute 33 seconds |
| Resolving best read alignments | 08:44:30 01 May 2023 | 08:45:18 01 May 2023 | 48 seconds |
| Creating BAM files | 08:45:18 01 May 2023 | 08:46:25 01 May 2023 | 1 minute 7 seconds |
| Tabulating error counts | 08:46:25 01 May 2023 | 08:46:57 01 May 2023 | 32 seconds |
| Re-calibrating base error rates | 08:46:57 01 May 2023 | 08:46:59 01 May 2023 | 2 seconds |
| Examining read alignment evidence | 08:46:59 01 May 2023 | 08:52:06 01 May 2023 | 5 minutes 7 seconds |
| Polymorphism statistics | 08:52:06 01 May 2023 | 08:52:06 01 May 2023 | 0 seconds |
| Output | 08:52:06 01 May 2023 | 08:52:58 01 May 2023 | 52 seconds |
| Total | 19 minutes 15 seconds | ||
