mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.33.2 revision caddc01d3be9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| read file | reads | bases | passed filters | average | longest | mapped | |
|---|---|---|---|---|---|---|---|
| errors | Pputida_HGL_57_S199_L002_R1_001.good.fq | 1,500,194 | 203,981,438 | 100.0% | 136.0 bases | 150 bases | 93.8% |
| errors | Pputida_HGL_57_S199_L002_R2_001.good.fq | 1,500,194 | 203,981,438 | 100.0% | 136.0 bases | 150 bases | 92.0% |
| total | 3,000,388 | 407,962,876 | 100.0% | 136.0 bases | 150 bases | 92.9% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_002947 | 6,181,929 | 61.2 | 2.8 | 100.0% | Pseudomonas putida KT2440 chromosome, complete genome. |
| total | 6,181,929 | 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 | 61063 |
| 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 | 1242 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.062 |
| reference sequence | pr(no read start) |
|---|---|
| NC_002947 | 0.81473 |
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 | 2.3.4.1 |
| R | 3.4.4 |
| step | start | end | elapsed |
|---|---|---|---|
| Read and reference sequence file input | 04:04:51 21 Aug 2019 | 04:06:05 21 Aug 2019 | 1 minute 14 seconds |
| Read alignment to reference genome | 04:06:06 21 Aug 2019 | 04:17:24 21 Aug 2019 | 11 minutes 18 seconds |
| Preprocessing alignments for candidate junction identification | 04:17:24 21 Aug 2019 | 04:18:30 21 Aug 2019 | 1 minute 6 seconds |
| Preliminary analysis of coverage distribution | 04:18:30 21 Aug 2019 | 04:20:38 21 Aug 2019 | 2 minutes 8 seconds |
| Identifying junction candidates | 04:20:38 21 Aug 2019 | 05:06:23 21 Aug 2019 | 45 minutes 45 seconds |
| Re-alignment to junction candidates | 05:06:23 21 Aug 2019 | 05:09:53 21 Aug 2019 | 3 minutes 30 seconds |
| Resolving best read alignments | 05:09:53 21 Aug 2019 | 05:11:32 21 Aug 2019 | 1 minute 39 seconds |
| Creating BAM files | 05:11:32 21 Aug 2019 | 05:13:27 21 Aug 2019 | 1 minute 55 seconds |
| Tabulating error counts | 05:13:27 21 Aug 2019 | 05:14:24 21 Aug 2019 | 57 seconds |
| Re-calibrating base error rates | 05:14:24 21 Aug 2019 | 05:14:26 21 Aug 2019 | 2 seconds |
| Examining read alignment evidence | 05:14:26 21 Aug 2019 | 05:26:15 21 Aug 2019 | 11 minutes 49 seconds |
| Polymorphism statistics | 05:26:15 21 Aug 2019 | 05:26:16 21 Aug 2019 | 1 second |
| Output | 05:26:16 21 Aug 2019 | 05:27:27 21 Aug 2019 | 1 minute 11 seconds |
| Total | 1 hour 22 minutes 35 seconds | ||
