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 | SRR16019042_R1.good.fq | 11,388,670 | 1,694,225,286 | 100.0% | 148.8 bases | 149 bases | 99.9% |
| errors | SRR16019042_R2.good.fq | 11,388,670 | 1,694,225,286 | 100.0% | 148.8 bases | 149 bases | 97.1% |
| total | 22,777,340 | 3,388,450,572 | 100.0% | 148.8 bases | 149 bases | 98.5% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | AM406671 | 2,529,478 | 1307.8 | 45.6 | 100.0% | Lactococcus lactis subsp. cremoris MG1363, complete genome. |
| total | 2,529,478 | 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 | 32828 |
| 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 | 141 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.017 |
| reference sequence | pr(no read start) |
|---|---|
| AM406671 | 0.03634 |
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 | 11:06:02 08 Feb 2023 | 11:11:51 08 Feb 2023 | 5 minutes 49 seconds |
| Read alignment to reference genome | 11:11:52 08 Feb 2023 | 12:01:42 08 Feb 2023 | 49 minutes 50 seconds |
| Preprocessing alignments for candidate junction identification | 12:01:43 08 Feb 2023 | 12:08:53 08 Feb 2023 | 7 minutes 10 seconds |
| Preliminary analysis of coverage distribution | 12:08:53 08 Feb 2023 | 12:23:30 08 Feb 2023 | 14 minutes 37 seconds |
| Identifying junction candidates | 12:23:30 08 Feb 2023 | 12:23:33 08 Feb 2023 | 3 seconds |
| Re-alignment to junction candidates | 12:23:33 08 Feb 2023 | 12:36:04 08 Feb 2023 | 12 minutes 31 seconds |
| Resolving best read alignments | 12:36:04 08 Feb 2023 | 12:45:17 08 Feb 2023 | 9 minutes 13 seconds |
| Creating BAM files | 12:45:17 08 Feb 2023 | 12:57:45 08 Feb 2023 | 12 minutes 28 seconds |
| Tabulating error counts | 12:57:45 08 Feb 2023 | 13:03:17 08 Feb 2023 | 5 minutes 32 seconds |
| Re-calibrating base error rates | 13:03:17 08 Feb 2023 | 13:03:18 08 Feb 2023 | 1 second |
| Examining read alignment evidence | 13:03:18 08 Feb 2023 | 14:07:23 08 Feb 2023 | 1 hour 4 minutes 5 seconds |
| Polymorphism statistics | 14:07:23 08 Feb 2023 | 14:07:26 08 Feb 2023 | 3 seconds |
| Output | 14:07:26 08 Feb 2023 | 14:09:15 08 Feb 2023 | 1 minute 49 seconds |
| Total | 3 hours 3 minutes 11 seconds | ||
