mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.32.1 revision aa8f2595a244
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| read file | reads | bases | passed filters | average | longest | mapped | |
|---|---|---|---|---|---|---|---|
| errors | T1000_778_CCACGGCC-TGTAATGA.R1.good.fq | 1,315,729 | 144,584,168 | 100.0% | 109.9 bases | 139 bases | 94.8% |
| errors | T1000_778_CCACGGCC-TGTAATGA.R2.good.fq | 1,315,729 | 144,584,168 | 100.0% | 109.9 bases | 139 bases | 94.7% |
| total | 2,631,458 | 289,168,336 | 100.0% | 109.9 bases | 139 bases | 94.7% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_000913 | 4,641,652 | 55.6 | 4.8 | 100.0% | Escherichia coli str. K-12 substr. MG1655, complete genome. |
| total | 4,641,652 | 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 | 3654 |
| 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 | 540 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.033 |
| reference sequence | pr(no read start) |
|---|---|
| NC_000913 | 0.81436 |
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 |
| 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 | 2.2.8 |
| R | 3.3.1 |
| step | start | end | elapsed |
|---|---|---|---|
| Read and reference sequence file input | 05:46:38 20 Jul 2018 | 05:47:07 20 Jul 2018 | 29 seconds |
| Read alignment to reference genome | 05:47:07 20 Jul 2018 | 05:48:34 20 Jul 2018 | 1 minute 27 seconds |
| Preprocessing alignments for candidate junction identification | 05:48:34 20 Jul 2018 | 05:49:07 20 Jul 2018 | 33 seconds |
| Preliminary analysis of coverage distribution | 05:49:07 20 Jul 2018 | 05:50:05 20 Jul 2018 | 58 seconds |
| Identifying junction candidates | 05:50:05 20 Jul 2018 | 05:50:08 20 Jul 2018 | 3 seconds |
| Re-alignment to junction candidates | 05:50:08 20 Jul 2018 | 05:50:27 20 Jul 2018 | 19 seconds |
| Resolving best read alignments | 05:50:27 20 Jul 2018 | 05:51:25 20 Jul 2018 | 58 seconds |
| Creating BAM files | 05:51:25 20 Jul 2018 | 05:52:16 20 Jul 2018 | 51 seconds |
| Tabulating error counts | 05:52:16 20 Jul 2018 | 05:52:39 20 Jul 2018 | 23 seconds |
| Re-calibrating base error rates | 05:52:39 20 Jul 2018 | 05:52:39 20 Jul 2018 | 0 seconds |
| Examining read alignment evidence | 05:52:39 20 Jul 2018 | 05:57:01 20 Jul 2018 | 4 minutes 22 seconds |
| Polymorphism statistics | 05:57:01 20 Jul 2018 | 05:57:02 20 Jul 2018 | 1 second |
| Output | 05:57:02 20 Jul 2018 | 05:57:59 20 Jul 2018 | 57 seconds |
| Total | 11 minutes 21 seconds | ||
