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 | pgi-9-1_S16_L001_R1_001.good.fq | 1,523,947 | 402,588,230 | 100.0% | 264.2 bases | 289 bases | 99.5% |
| errors | pgi-9-1_S16_L001_R2_001.good.fq | 1,523,947 | 403,061,665 | 100.0% | 264.5 bases | 289 bases | 94.8% |
| total | 3,047,894 | 805,649,895 | 100.0% | 264.3 bases | 289 bases | 97.2% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_000913 | 4,641,652 | 167.4 | 4.3 | 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 | 7463 |
| 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 | 501 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.063 |
| reference sequence | pr(no read start) |
|---|---|
| NC_000913 | 0.80918 |
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 | 08:18:32 25 Feb 2020 | 08:19:21 25 Feb 2020 | 49 seconds |
| Read alignment to reference genome | 08:19:21 25 Feb 2020 | 08:33:19 25 Feb 2020 | 13 minutes 58 seconds |
| Preprocessing alignments for candidate junction identification | 08:33:19 25 Feb 2020 | 08:34:12 25 Feb 2020 | 53 seconds |
| Preliminary analysis of coverage distribution | 08:34:12 25 Feb 2020 | 08:36:58 25 Feb 2020 | 2 minutes 46 seconds |
| Identifying junction candidates | 08:36:58 25 Feb 2020 | 08:37:11 25 Feb 2020 | 13 seconds |
| Re-alignment to junction candidates | 08:37:11 25 Feb 2020 | 08:41:33 25 Feb 2020 | 4 minutes 22 seconds |
| Resolving best read alignments | 08:41:33 25 Feb 2020 | 08:43:00 25 Feb 2020 | 1 minute 27 seconds |
| Creating BAM files | 08:43:00 25 Feb 2020 | 08:45:24 25 Feb 2020 | 2 minutes 24 seconds |
| Tabulating error counts | 08:45:24 25 Feb 2020 | 08:46:42 25 Feb 2020 | 1 minute 18 seconds |
| Re-calibrating base error rates | 08:46:42 25 Feb 2020 | 08:46:43 25 Feb 2020 | 1 second |
| Examining read alignment evidence | 08:46:43 25 Feb 2020 | 10:14:24 25 Feb 2020 | 1 hour 27 minutes 41 seconds |
| Polymorphism statistics | 10:14:24 25 Feb 2020 | 10:14:24 25 Feb 2020 | 0 seconds |
| Output | 10:14:24 25 Feb 2020 | 10:14:50 25 Feb 2020 | 26 seconds |
| Total | 1 hour 56 minutes 18 seconds | ||
