mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.32.0b
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| read file | reads | bases | passed filters | average | longest | mapped | |
|---|---|---|---|---|---|---|---|
| errors | A5_F028_R1_F15_I40_S2157_L001_R2_001.good.fq | 1,057,943 | 154,459,678 | 100.0% | 146.0 bases | 146 bases | 97.8% |
| errors | A5_F028_R1_F15_I40_S2157_L001_R1_001.good.fq | 1,146,727 | 170,862,323 | 100.0% | 149.0 bases | 149 bases | 98.4% |
| total | 2,204,670 | 325,322,001 | 100.0% | 147.6 bases | 149 bases | 98.1% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | CP009273 | 4,631,469 | 67.3 | 3.2 | 100.0% | Escherichia coli BW25113, complete genome. |
| total | 4,631,469 | 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 | 14180 |
| 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 | 233 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.015 |
| reference sequence | pr(no read start) |
|---|---|
| CP009273 | 0.81957 |
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 | 0.8 |
| Consensus minimum coverage each strand | OFF |
| Polymorphism E-value cutoff | 10 |
| Polymorphism frequency cutoff | 0.2 |
| Polymorphism minimum coverage each strand | 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 | 2.3.2 |
| R | 3.4.2 |
| step | start | end | elapsed |
|---|---|---|---|
| Read and reference sequence file input | 23:02:57 15 Jun 2018 | 23:03:25 15 Jun 2018 | 28 seconds |
| Read alignment to reference genome | 23:03:26 15 Jun 2018 | 23:05:28 15 Jun 2018 | 2 minutes 2 seconds |
| Preprocessing alignments for candidate junction identification | 23:05:28 15 Jun 2018 | 23:05:50 15 Jun 2018 | 22 seconds |
| Preliminary analysis of coverage distribution | 23:05:50 15 Jun 2018 | 23:06:53 15 Jun 2018 | 1 minute 3 seconds |
| Identifying junction candidates | 23:06:53 15 Jun 2018 | 23:06:56 15 Jun 2018 | 3 seconds |
| Re-alignment to junction candidates | 23:06:56 15 Jun 2018 | 23:07:20 15 Jun 2018 | 24 seconds |
| Resolving alignments with junction candidates | 23:07:20 15 Jun 2018 | 23:07:56 15 Jun 2018 | 36 seconds |
| Creating BAM files | 23:07:56 15 Jun 2018 | 23:08:51 15 Jun 2018 | 55 seconds |
| Tabulating error counts | 23:08:51 15 Jun 2018 | 23:09:17 15 Jun 2018 | 26 seconds |
| Re-calibrating base error rates | 23:09:17 15 Jun 2018 | 23:09:18 15 Jun 2018 | 1 second |
| Examining read alignment evidence | 23:09:18 15 Jun 2018 | 23:14:42 15 Jun 2018 | 5 minutes 24 seconds |
| Polymorphism statistics | 23:14:42 15 Jun 2018 | 23:14:43 15 Jun 2018 | 1 second |
| Output | 23:14:43 15 Jun 2018 | 23:14:53 15 Jun 2018 | 10 seconds |
| Total | 11 minutes 55 seconds | ||
