mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.39.0
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| read file | reads | bases | passed filters | average | longest | mapped | |
|---|---|---|---|---|---|---|---|
| errors | ME9621_S34_R1_RMDUP_RM-R2-DUP.cutadapt | 884,360 | 262,247,212 | 100.0% | 296.5 bases | 300 bases | 96.1% |
| errors | ME9621_S34_R2_RMDUP_RM-R1-DUP.cutadapt | 884,640 | 260,194,542 | 100.0% | 294.1 bases | 300 bases | 98.5% |
| total | 1,769,000 | 522,441,754 | 100.0% | 295.3 bases | 300 bases | 97.3% |
| seq id | length | fit mean | fit relative_variance | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_000913 | 4,641,652 | 109.8 | 4.8 | 100.0% | Escherichia coli str. K-12 substr. MG1655, complete genome. |
| total | 4,641,652 | 100.0% |
fit relative_variance 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 | 10748 |
| 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 | 188 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.025 |
| reference sequence | pr(no read start) |
|---|---|
| NC_000913 | 0.88602 |
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 | 0.8 |
| 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 | 2.5.1 |
| R | 4.0.3 |
| step | start | end | elapsed |
|---|---|---|---|
| Read and reference sequence file input | 00:01:12 11 Oct 2025 | 00:01:39 11 Oct 2025 | 27 seconds |
| Read alignment to reference genome | 00:01:39 11 Oct 2025 | 00:03:09 11 Oct 2025 | 1 minute 30 seconds |
| Preprocessing alignments for candidate junction identification | 00:03:09 11 Oct 2025 | 00:03:36 11 Oct 2025 | 27 seconds |
| Preliminary analysis of coverage distribution | 00:03:36 11 Oct 2025 | 00:04:47 11 Oct 2025 | 1 minute 11 seconds |
| Identifying junction candidates | 00:04:47 11 Oct 2025 | 00:04:54 11 Oct 2025 | 7 seconds |
| Re-alignment to junction candidates | 00:04:54 11 Oct 2025 | 00:05:09 11 Oct 2025 | 15 seconds |
| Resolving best read alignments | 00:05:09 11 Oct 2025 | 00:06:00 11 Oct 2025 | 51 seconds |
| Creating BAM files | 00:06:00 11 Oct 2025 | 00:07:00 11 Oct 2025 | 1 minute 0 seconds |
| Tabulating error counts | 00:07:00 11 Oct 2025 | 00:07:45 11 Oct 2025 | 45 seconds |
| Re-calibrating base error rates | 00:07:45 11 Oct 2025 | 00:07:46 11 Oct 2025 | 1 second |
| Examining read alignment evidence | 00:07:46 11 Oct 2025 | 00:14:14 11 Oct 2025 | 6 minutes 28 seconds |
| Polymorphism statistics | 00:14:14 11 Oct 2025 | 00:14:14 11 Oct 2025 | 0 seconds |
| Output | 00:14:14 11 Oct 2025 | 00:14:23 11 Oct 2025 | 9 seconds |
| Output :: Mutation Prediction | 00:14:14 11 Oct 2025 | 00:14:15 11 Oct 2025 | 1 second |
| Output :: Mutation Annotation | 00:14:15 11 Oct 2025 | 00:14:15 11 Oct 2025 | 0 seconds |
| Total | 13 minutes 12 seconds | ||
