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_109_0_S2331_L001_R1_001.good.fq | 1,202,374 | 169,482,910 | 100.0% | 141.0 bases | 141 bases | 97.3% |
| errors | SNFR_5_109_0_S2331_L001_R2_001.good.fq | 1,202,374 | 169,482,910 | 100.0% | 141.0 bases | 141 bases | 93.9% |
| total | 2,404,748 | 338,965,820 | 100.0% | 141.0 bases | 141 bases | 95.6% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | CP000730 | 2,872,915 | 111.8 | 3.0 | 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 | 5619 |
| 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 | 275 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.027 |
| reference sequence | pr(no read start) |
|---|---|
| CP000730 | 0.73732 |
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 | 23:30:23 22 Jun 2018 | 23:31:43 22 Jun 2018 | 1 minute 20 seconds |
| Read alignment to reference genome | 23:31:43 22 Jun 2018 | 23:37:01 22 Jun 2018 | 5 minutes 18 seconds |
| Preprocessing alignments for candidate junction identification | 23:37:01 22 Jun 2018 | 23:38:11 22 Jun 2018 | 1 minute 10 seconds |
| Preliminary analysis of coverage distribution | 23:38:11 22 Jun 2018 | 23:39:49 22 Jun 2018 | 1 minute 38 seconds |
| Identifying junction candidates | 23:39:49 22 Jun 2018 | 23:39:52 22 Jun 2018 | 3 seconds |
| Re-alignment to junction candidates | 23:39:52 22 Jun 2018 | 23:41:09 22 Jun 2018 | 1 minute 17 seconds |
| Resolving best read alignments | 23:41:09 22 Jun 2018 | 23:42:59 22 Jun 2018 | 1 minute 50 seconds |
| Creating BAM files | 23:42:59 22 Jun 2018 | 23:44:23 22 Jun 2018 | 1 minute 24 seconds |
| Tabulating error counts | 23:44:23 22 Jun 2018 | 23:44:57 22 Jun 2018 | 34 seconds |
| Re-calibrating base error rates | 23:44:57 22 Jun 2018 | 23:44:59 22 Jun 2018 | 2 seconds |
| Examining read alignment evidence | 23:44:59 22 Jun 2018 | 00:17:36 23 Jun 2018 | 32 minutes 37 seconds |
| Polymorphism statistics | 00:17:36 23 Jun 2018 | 00:17:37 23 Jun 2018 | 1 second |
| Output | 00:17:37 23 Jun 2018 | 00:17:52 23 Jun 2018 | 15 seconds |
| Total | 47 minutes 29 seconds | ||
