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 | PAL131_S129_L001_R1_001.good.fq | 3,083,172 | 417,794,201 | 100.0% | 135.5 bases | 140 bases | 98.9% |
| errors | PAL131_S129_L001_R2_001.good.fq | 3,083,172 | 417,794,201 | 100.0% | 135.5 bases | 140 bases | 98.1% |
| total | 6,166,344 | 835,588,402 | 100.0% | 135.5 bases | 140 bases | 98.5% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NZ_CP034943 | 4,045,538 | 200.6 | 10.3 | 100.0% | Bacillus subtilis subsp. spizizenii ATCC 6633 = JCM 2499 strain |
| total | 4,045,538 | 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 | 2410 |
| 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 | 159 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.011 |
| reference sequence | pr(no read start) |
|---|---|
| NZ_CP034943 | 0.74026 |
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 | 10:58:29 16 May 2023 | 11:00:34 16 May 2023 | 2 minutes 5 seconds |
| Read alignment to reference genome | 11:00:34 16 May 2023 | 11:13:51 16 May 2023 | 13 minutes 17 seconds |
| Preprocessing alignments for candidate junction identification | 11:13:51 16 May 2023 | 11:15:15 16 May 2023 | 1 minute 24 seconds |
| Preliminary analysis of coverage distribution | 11:15:15 16 May 2023 | 11:18:27 16 May 2023 | 3 minutes 12 seconds |
| Identifying junction candidates | 11:18:27 16 May 2023 | 11:18:28 16 May 2023 | 1 second |
| Re-alignment to junction candidates | 11:18:28 16 May 2023 | 11:21:53 16 May 2023 | 3 minutes 25 seconds |
| Resolving best read alignments | 11:21:53 16 May 2023 | 11:23:59 16 May 2023 | 2 minutes 6 seconds |
| Creating BAM files | 11:23:59 16 May 2023 | 11:26:45 16 May 2023 | 2 minutes 46 seconds |
| Tabulating error counts | 11:26:45 16 May 2023 | 11:27:59 16 May 2023 | 1 minute 14 seconds |
| Re-calibrating base error rates | 11:27:59 16 May 2023 | 11:28:01 16 May 2023 | 2 seconds |
| Examining read alignment evidence | 11:28:01 16 May 2023 | 11:43:05 16 May 2023 | 15 minutes 4 seconds |
| Polymorphism statistics | 11:43:05 16 May 2023 | 11:43:05 16 May 2023 | 0 seconds |
| Output | 11:43:05 16 May 2023 | 11:43:20 16 May 2023 | 15 seconds |
| Total | 44 minutes 51 seconds | ||
