mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.33.1 revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| read file | reads | bases | passed filters | average | longest | mapped | |
|---|---|---|---|---|---|---|---|
| errors | R3_Lane1_BC11_R1.good.fq | 6,968,469 | 529,517,060 | 100.0% | 76.0 bases | 76 bases | 96.8% |
| errors | R3_Lane1_BC11_R2.good.fq | 6,968,469 | 529,517,060 | 100.0% | 76.0 bases | 76 bases | 94.4% |
| total | 13,936,938 | 1,059,034,120 | 100.0% | 76.0 bases | 76 bases | 95.6% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | REL606 | 4,629,812 | 221.5 | 5.7 | 100.0% | Escherichia coli strain REL606. |
| total | 4,629,812 | 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 | 12477 |
| 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 | 389 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.013 |
| reference sequence | pr(no read start) |
|---|---|
| REL606 | 0.31589 |
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 | 22:12:52 01 Feb 2019 | 22:15:16 01 Feb 2019 | 2 minutes 24 seconds |
| Read alignment to reference genome | 22:15:17 01 Feb 2019 | 22:36:18 01 Feb 2019 | 21 minutes 1 second |
| Preprocessing alignments for candidate junction identification | 22:36:18 01 Feb 2019 | 22:38:55 01 Feb 2019 | 2 minutes 37 seconds |
| Preliminary analysis of coverage distribution | 22:38:55 01 Feb 2019 | 22:44:26 01 Feb 2019 | 5 minutes 31 seconds |
| Identifying junction candidates | 22:44:26 01 Feb 2019 | 22:44:29 01 Feb 2019 | 3 seconds |
| Re-alignment to junction candidates | 22:44:29 01 Feb 2019 | 22:50:00 01 Feb 2019 | 5 minutes 31 seconds |
| Resolving best read alignments | 22:50:00 01 Feb 2019 | 22:54:01 01 Feb 2019 | 4 minutes 1 second |
| Creating BAM files | 22:54:01 01 Feb 2019 | 22:59:00 01 Feb 2019 | 4 minutes 59 seconds |
| Tabulating error counts | 22:59:00 01 Feb 2019 | 23:00:33 01 Feb 2019 | 1 minute 33 seconds |
| Re-calibrating base error rates | 23:00:33 01 Feb 2019 | 23:00:34 01 Feb 2019 | 1 second |
| Examining read alignment evidence | 23:00:34 01 Feb 2019 | 23:14:21 01 Feb 2019 | 13 minutes 47 seconds |
| Polymorphism statistics | 23:14:21 01 Feb 2019 | 23:14:23 01 Feb 2019 | 2 seconds |
| Output | 23:14:23 01 Feb 2019 | 23:14:49 01 Feb 2019 | 26 seconds |
| Total | 1 hour 1 minute 56 seconds | ||
