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 | PAL203_S201_L001_R1_001.good.fq | 7,769,584 | 1,059,917,714 | 100.0% | 136.4 bases | 140 bases | 95.6% |
| errors | PAL203_S201_L001_R2_001.good.fq | 7,769,584 | 1,059,917,714 | 100.0% | 136.4 bases | 140 bases | 95.1% |
| total | 15,539,168 | 2,119,835,428 | 100.0% | 136.4 bases | 140 bases | 95.3% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NZ_CP034943 | 4,045,538 | 475.9 | 39.4 | 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 | 5652 |
| 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 | 160 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.011 |
| reference sequence | pr(no read start) |
|---|---|
| NZ_CP034943 | 0.64747 |
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 | ≤ 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 | 2.2.6 |
| R | 3.4.4 |
| step | start | end | elapsed |
|---|---|---|---|
| Read and reference sequence file input | 11:22:32 16 May 2023 | 11:26:59 16 May 2023 | 4 minutes 27 seconds |
| Read alignment to reference genome | 11:26:59 16 May 2023 | 12:00:45 16 May 2023 | 33 minutes 46 seconds |
| Preprocessing alignments for candidate junction identification | 12:00:45 16 May 2023 | 12:04:41 16 May 2023 | 3 minutes 56 seconds |
| Preliminary analysis of coverage distribution | 12:04:41 16 May 2023 | 12:12:49 16 May 2023 | 8 minutes 8 seconds |
| Identifying junction candidates | 12:12:49 16 May 2023 | 12:12:50 16 May 2023 | 1 second |
| Re-alignment to junction candidates | 12:12:50 16 May 2023 | 12:21:26 16 May 2023 | 8 minutes 36 seconds |
| Resolving best read alignments | 12:21:26 16 May 2023 | 12:27:06 16 May 2023 | 5 minutes 40 seconds |
| Creating BAM files | 12:27:06 16 May 2023 | 12:34:12 16 May 2023 | 7 minutes 6 seconds |
| Tabulating error counts | 12:34:12 16 May 2023 | 12:37:27 16 May 2023 | 3 minutes 15 seconds |
| Re-calibrating base error rates | 12:37:27 16 May 2023 | 12:37:28 16 May 2023 | 1 second |
| Examining read alignment evidence | 12:37:28 16 May 2023 | 17:57:49 16 May 2023 | 5 hours 20 minutes 21 seconds |
| Polymorphism statistics | 17:57:49 16 May 2023 | 17:57:57 16 May 2023 | 8 seconds |
| Output | 17:57:57 16 May 2023 | 17:58:49 16 May 2023 | 52 seconds |
| Total | 6 hours 36 minutes 17 seconds | ||
