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 | Evo04pgiEvo02EP_S2_L001_R1_001.good.fq | 929,099 | 249,435,214 | 100.0% | 268.5 bases | 289 bases | 99.3% |
| errors | Evo04pgiEvo02EP_S2_L001_R2_001.good.fq | 929,099 | 249,564,219 | 100.0% | 268.6 bases | 289 bases | 95.9% |
| total | 1,858,198 | 498,999,433 | 100.0% | 268.5 bases | 289 bases | 97.6% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_000913 | 4,641,652 | 107.5 | 4.2 | 100.0% | Escherichia coli str. K-12 substr. MG1655, complete genome. |
| total | 4,641,652 | 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 | 11623 |
| 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 | 34 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.004 |
| reference sequence | pr(no read start) |
|---|---|
| NC_000913 | 0.86651 |
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 | 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 | 2 |
| Polymorphism frequency cutoff | 0.05 |
| 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 | 3.4.4 |
| step | start | end | elapsed |
|---|---|---|---|
| Read and reference sequence file input | 05:18:16 29 Feb 2020 | 05:18:45 29 Feb 2020 | 29 seconds |
| Read alignment to reference genome | 05:18:46 29 Feb 2020 | 05:26:41 29 Feb 2020 | 7 minutes 55 seconds |
| Preprocessing alignments for candidate junction identification | 05:26:41 29 Feb 2020 | 05:27:13 29 Feb 2020 | 32 seconds |
| Preliminary analysis of coverage distribution | 05:27:13 29 Feb 2020 | 05:28:42 29 Feb 2020 | 1 minute 29 seconds |
| Identifying junction candidates | 05:28:42 29 Feb 2020 | 05:29:08 29 Feb 2020 | 26 seconds |
| Re-alignment to junction candidates | 05:29:08 29 Feb 2020 | 05:31:05 29 Feb 2020 | 1 minute 57 seconds |
| Resolving best read alignments | 05:31:05 29 Feb 2020 | 05:31:57 29 Feb 2020 | 52 seconds |
| Creating BAM files | 05:31:57 29 Feb 2020 | 05:33:14 29 Feb 2020 | 1 minute 17 seconds |
| Tabulating error counts | 05:33:14 29 Feb 2020 | 05:34:03 29 Feb 2020 | 49 seconds |
| Re-calibrating base error rates | 05:34:03 29 Feb 2020 | 05:34:04 29 Feb 2020 | 1 second |
| Examining read alignment evidence | 05:34:04 29 Feb 2020 | 06:09:15 29 Feb 2020 | 35 minutes 11 seconds |
| Polymorphism statistics | 06:09:15 29 Feb 2020 | 06:09:16 29 Feb 2020 | 1 second |
| Output | 06:09:16 29 Feb 2020 | 06:09:35 29 Feb 2020 | 19 seconds |
| Total | 51 minutes 18 seconds | ||
