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 | ALE-54_S54_L001_R1_001.good.fq | 374,976 | 52,215,060 | 100.0% | 139.2 bases | 149 bases | 92.3% |
| errors | ALE-54_S54_L001_R2_001.good.fq | 374,976 | 51,978,703 | 100.0% | 138.6 bases | 149 bases | 92.9% |
| errors | ALE-54_S54_L002_R1_001.good.fq | 373,053 | 51,811,917 | 100.0% | 138.9 bases | 149 bases | 93.6% |
| errors | ALE-54_S54_L002_R2_001.good.fq | 373,053 | 51,650,045 | 100.0% | 138.5 bases | 149 bases | 93.5% |
| errors | ALE-54_S54_L003_R1_001.good.fq | 384,282 | 53,334,716 | 100.0% | 138.8 bases | 149 bases | 93.6% |
| errors | ALE-54_S54_L003_R2_001.good.fq | 384,282 | 53,134,061 | 100.0% | 138.3 bases | 149 bases | 94.1% |
| errors | ALE-54_S54_L004_R1_001.good.fq | 357,033 | 49,549,949 | 100.0% | 138.8 bases | 149 bases | 93.5% |
| errors | ALE-54_S54_L004_R2_001.good.fq | 357,033 | 49,403,959 | 100.0% | 138.4 bases | 149 bases | 93.2% |
| total | 2,978,688 | 413,078,410 | 100.0% | 138.7 bases | 149 bases | 93.3% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_002947 | 6,181,873 | 62.6 | 2.4 | 100.0% | Pseudomonas putida KT2440 chromosome, complete genome. |
| total | 6,181,873 | 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 | 100000 |
| Coverage evenness (position-hash) score of junction candidates | ≥ 2 | ≥ 3 |
| Test this many junction candidates (n). May be smaller if not enough passed the coverage evenness threshold | 100 ≤ n ≤ 5000 | 507 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.025 |
| reference sequence | pr(no read start) |
|---|---|
| NC_002947 | 0.81518 |
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 | ≤ 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 | 2.3.4.1 |
| R | 3.4.4 |
| step | start | end | elapsed |
|---|---|---|---|
| Read and reference sequence file input | 04:05:02 19 Feb 2020 | 04:05:45 19 Feb 2020 | 43 seconds |
| Read alignment to reference genome | 04:05:46 19 Feb 2020 | 04:12:14 19 Feb 2020 | 6 minutes 28 seconds |
| Preprocessing alignments for candidate junction identification | 04:12:14 19 Feb 2020 | 04:12:56 19 Feb 2020 | 42 seconds |
| Preliminary analysis of coverage distribution | 04:12:56 19 Feb 2020 | 04:14:33 19 Feb 2020 | 1 minute 37 seconds |
| Identifying junction candidates | 04:14:33 19 Feb 2020 | 04:31:09 19 Feb 2020 | 16 minutes 36 seconds |
| Re-alignment to junction candidates | 04:31:09 19 Feb 2020 | 04:33:09 19 Feb 2020 | 2 minutes 0 seconds |
| Resolving best read alignments | 04:33:09 19 Feb 2020 | 04:34:13 19 Feb 2020 | 1 minute 4 seconds |
| Creating BAM files | 04:34:13 19 Feb 2020 | 04:35:42 19 Feb 2020 | 1 minute 29 seconds |
| Tabulating error counts | 04:35:42 19 Feb 2020 | 04:36:12 19 Feb 2020 | 30 seconds |
| Re-calibrating base error rates | 04:36:12 19 Feb 2020 | 04:36:15 19 Feb 2020 | 3 seconds |
| Examining read alignment evidence | 04:36:15 19 Feb 2020 | 04:41:56 19 Feb 2020 | 5 minutes 41 seconds |
| Polymorphism statistics | 04:41:56 19 Feb 2020 | 04:41:56 19 Feb 2020 | 0 seconds |
| Output | 04:41:56 19 Feb 2020 | 04:42:37 19 Feb 2020 | 41 seconds |
| Total | 37 minutes 34 seconds | ||
