mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.35.4 revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| read file | reads | bases | passed filters | average | longest | mapped | |
|---|---|---|---|---|---|---|---|
| errors | ERR1957971_R1.good.fq | 1,182,531 | 265,401,516 | 100.0% | 224.4 bases | 240 bases | 99.6% |
| errors | ERR1957971_R2.good.fq | 1,182,525 | 242,648,799 | 100.0% | 205.2 bases | 240 bases | 97.5% |
| total | 2,365,056 | 508,050,315 | 100.0% | 214.8 bases | 240 bases | 98.5% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_000913 | 4,641,652 | 103.2 | 4.8 | 95.5% | Escherichia coli str. K-12 substr. MG1655, complete genome. |
| coverage | distribution | BN000925 | 60,096 | 397.6 | 11.4 | 4.5% | TPA_exp: Birmingham IncP-alpha plasmid, complete sequence, isolate |
| total | 4,701,748 | 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 | 4078 |
| 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 | 100 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.010 |
| reference sequence | pr(no read start) |
|---|---|
| NC_000913 | 0.83887 |
| BN000925 | 0.61598 |
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 |
| Minimum probablilty assigned that no mapped read will start at a given position and strand for junction prediction | 0.1 |
| Junction allow suboptimal matches | FALSE |
| 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 | 2.2.6 |
| R | 3.4.4 |
| step | start | end | elapsed |
|---|---|---|---|
| Read and reference sequence file input | 15:04:06 08 Dec 2020 | 15:07:10 08 Dec 2020 | 3 minutes 4 seconds |
| Read alignment to reference genome | 15:07:11 08 Dec 2020 | 15:34:09 08 Dec 2020 | 26 minutes 58 seconds |
| Preprocessing alignments for candidate junction identification | 15:34:09 08 Dec 2020 | 15:36:40 08 Dec 2020 | 2 minutes 31 seconds |
| Preliminary analysis of coverage distribution | 15:36:40 08 Dec 2020 | 15:44:46 08 Dec 2020 | 8 minutes 6 seconds |
| Identifying junction candidates | 15:44:46 08 Dec 2020 | 15:44:52 08 Dec 2020 | 6 seconds |
| Re-alignment to junction candidates | 15:44:52 08 Dec 2020 | 15:51:42 08 Dec 2020 | 6 minutes 50 seconds |
| Resolving best read alignments | 15:51:42 08 Dec 2020 | 15:54:59 08 Dec 2020 | 3 minutes 17 seconds |
| Creating BAM files | 15:54:59 08 Dec 2020 | 16:02:27 08 Dec 2020 | 7 minutes 28 seconds |
| Tabulating error counts | 16:02:27 08 Dec 2020 | 16:04:53 08 Dec 2020 | 2 minutes 26 seconds |
| Re-calibrating base error rates | 16:04:53 08 Dec 2020 | 16:04:58 08 Dec 2020 | 5 seconds |
| Examining read alignment evidence | 16:04:58 08 Dec 2020 | 16:35:59 08 Dec 2020 | 31 minutes 1 second |
| Polymorphism statistics | 16:35:59 08 Dec 2020 | 16:36:00 08 Dec 2020 | 1 second |
| Output | 16:36:00 08 Dec 2020 | 16:37:06 08 Dec 2020 | 1 minute 6 seconds |
| Total | 1 hour 32 minutes 59 seconds | ||
