mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.32.1 revision 5f2cb669173e
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| read file | reads | bases | passed filters | average | longest | mapped | |
|---|---|---|---|---|---|---|---|
| errors | SNFR_5_58_0_S2338_L001_R1_001.good.fq | 611,081 | 86,133,926 | 100.0% | 141.0 bases | 141 bases | 97.8% |
| errors | SNFR_5_58_0_S2338_L001_R2_001.good.fq | 611,081 | 86,133,926 | 100.0% | 141.0 bases | 141 bases | 93.9% |
| total | 1,222,162 | 172,267,852 | 100.0% | 141.0 bases | 141 bases | 95.8% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | CP000730 | 2,872,915 | 56.9 | 1.9 | 100.0% | Staphylococcus aureus subsp. aureus USA300_TCH1516, complete |
| total | 2,872,915 | 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 | 2397 |
| 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 | 51 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.005 |
| reference sequence | pr(no read start) |
|---|---|
| CP000730 | 0.84208 |
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 | ≤ 0 |
| Number of bases that at least one read must overlap each uniquely aligned side of a predicted junction | ≥ 6 |
| option | value |
|---|---|
| Mode | Full Polymorphism |
| Ploidy | 1 (haploid) |
| Consensus mutation E-value cutoff | 10 |
| Consensus frequency cutoff | OFF |
| 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 | 2 |
| Polymorphism frequency cutoff | 0.025 |
| Polymorphism minimum variant coverage each strand | 2 |
| 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 | ≥3 bases |
| Skip base substitutions when they create a homopolymer flanked on each side by | ≥5 bases |
| program | version |
|---|---|
| bowtie2 | 2.3.4.1 |
| R | 3.5.0 |
| step | start | end | elapsed |
|---|---|---|---|
| Read and reference sequence file input | 22:04:29 22 Jun 2018 | 22:05:13 22 Jun 2018 | 44 seconds |
| Read alignment to reference genome | 22:05:13 22 Jun 2018 | 22:07:44 22 Jun 2018 | 2 minutes 31 seconds |
| Preprocessing alignments for candidate junction identification | 22:07:44 22 Jun 2018 | 22:08:19 22 Jun 2018 | 35 seconds |
| Preliminary analysis of coverage distribution | 22:08:19 22 Jun 2018 | 22:09:13 22 Jun 2018 | 54 seconds |
| Identifying junction candidates | 22:09:13 22 Jun 2018 | 22:09:13 22 Jun 2018 | 0 seconds |
| Re-alignment to junction candidates | 22:09:13 22 Jun 2018 | 22:09:54 22 Jun 2018 | 41 seconds |
| Resolving best read alignments | 22:09:54 22 Jun 2018 | 22:10:50 22 Jun 2018 | 56 seconds |
| Creating BAM files | 22:10:50 22 Jun 2018 | 22:11:31 22 Jun 2018 | 41 seconds |
| Tabulating error counts | 22:11:31 22 Jun 2018 | 22:11:48 22 Jun 2018 | 17 seconds |
| Re-calibrating base error rates | 22:11:48 22 Jun 2018 | 22:11:51 22 Jun 2018 | 3 seconds |
| Examining read alignment evidence | 22:11:51 22 Jun 2018 | 22:24:47 22 Jun 2018 | 12 minutes 56 seconds |
| Polymorphism statistics | 22:24:47 22 Jun 2018 | 22:24:47 22 Jun 2018 | 0 seconds |
| Output | 22:24:47 22 Jun 2018 | 22:24:54 22 Jun 2018 | 7 seconds |
| Total | 20 minutes 25 seconds | ||
