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-9-3_S17_L001_R1_001.good.fq | 1,218,830 | 324,353,953 | 100.0% | 266.1 bases | 289 bases | 99.5% |
| errors | pgi-9-3_S17_L001_R2_001.good.fq | 1,218,830 | 324,577,308 | 100.0% | 266.3 bases | 289 bases | 96.1% |
| total | 2,437,660 | 648,931,261 | 100.0% | 266.2 bases | 289 bases | 97.8% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_000913 | 4,641,652 | 139.7 | 3.9 | 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 | 4979 |
| 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 | 396 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.050 |
| reference sequence | pr(no read start) |
|---|---|
| NC_000913 | 0.83605 |
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 | 17:38:27 25 Feb 2020 | 17:39:06 25 Feb 2020 | 39 seconds |
| Read alignment to reference genome | 17:39:06 25 Feb 2020 | 17:50:41 25 Feb 2020 | 11 minutes 35 seconds |
| Preprocessing alignments for candidate junction identification | 17:50:41 25 Feb 2020 | 17:51:25 25 Feb 2020 | 44 seconds |
| Preliminary analysis of coverage distribution | 17:51:25 25 Feb 2020 | 17:53:45 25 Feb 2020 | 2 minutes 20 seconds |
| Identifying junction candidates | 17:53:45 25 Feb 2020 | 17:53:53 25 Feb 2020 | 8 seconds |
| Re-alignment to junction candidates | 17:53:53 25 Feb 2020 | 17:57:16 25 Feb 2020 | 3 minutes 23 seconds |
| Resolving best read alignments | 17:57:16 25 Feb 2020 | 17:58:28 25 Feb 2020 | 1 minute 12 seconds |
| Creating BAM files | 17:58:28 25 Feb 2020 | 18:00:30 25 Feb 2020 | 2 minutes 2 seconds |
| Tabulating error counts | 18:00:30 25 Feb 2020 | 18:01:34 25 Feb 2020 | 1 minute 4 seconds |
| Re-calibrating base error rates | 18:01:34 25 Feb 2020 | 18:01:36 25 Feb 2020 | 2 seconds |
| Examining read alignment evidence | 18:01:36 25 Feb 2020 | 19:06:08 25 Feb 2020 | 1 hour 4 minutes 32 seconds |
| Polymorphism statistics | 19:06:08 25 Feb 2020 | 19:06:09 25 Feb 2020 | 1 second |
| Output | 19:06:09 25 Feb 2020 | 19:06:30 25 Feb 2020 | 21 seconds |
| Total | 1 hour 28 minutes 3 seconds | ||
