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 | 57_S57_L001_R1_001.good.fq | 288,591 | 40,798,929 | 100.0% | 141.4 bases | 149 bases | 98.1% |
| errors | 57_S57_L001_R2_001.good.fq | 288,591 | 40,770,823 | 100.0% | 141.3 bases | 149 bases | 97.4% |
| errors | 57_S57_L002_R1_001.good.fq | 280,914 | 39,716,814 | 100.0% | 141.4 bases | 149 bases | 98.0% |
| errors | 57_S57_L002_R2_001.good.fq | 280,914 | 39,705,063 | 100.0% | 141.3 bases | 149 bases | 96.9% |
| errors | 57_S57_L003_R1_001.good.fq | 293,873 | 41,572,223 | 100.0% | 141.5 bases | 149 bases | 98.1% |
| errors | 57_S57_L003_R2_001.good.fq | 293,873 | 41,540,669 | 100.0% | 141.4 bases | 149 bases | 97.5% |
| errors | 57_S57_L004_R1_001.good.fq | 302,724 | 42,760,011 | 100.0% | 141.3 bases | 149 bases | 98.2% |
| errors | 57_S57_L004_R2_001.good.fq | 302,724 | 42,714,811 | 100.0% | 141.1 bases | 149 bases | 97.9% |
| total | 2,332,204 | 329,579,343 | 100.0% | 141.3 bases | 149 bases | 97.8% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_002947_CJ-RC | 6,184,688 | 52.7 | 2.3 | 100.0% | Pseudomonas putida KT2440 chromosome, complete genome. |
| total | 6,184,688 | 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 | 18593 |
| 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 | 23 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.001 |
| reference sequence | pr(no read start) |
|---|---|
| NC_002947_CJ-RC | 0.84232 |
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 | 14:40:18 25 Oct 2024 | 14:41:01 25 Oct 2024 | 43 seconds |
| Read alignment to reference genome | 14:41:01 25 Oct 2024 | 14:45:43 25 Oct 2024 | 4 minutes 42 seconds |
| Preprocessing alignments for candidate junction identification | 14:45:43 25 Oct 2024 | 14:46:13 25 Oct 2024 | 30 seconds |
| Preliminary analysis of coverage distribution | 14:46:13 25 Oct 2024 | 14:47:26 25 Oct 2024 | 1 minute 13 seconds |
| Identifying junction candidates | 14:47:26 25 Oct 2024 | 14:47:34 25 Oct 2024 | 8 seconds |
| Re-alignment to junction candidates | 14:47:34 25 Oct 2024 | 14:48:40 25 Oct 2024 | 1 minute 6 seconds |
| Resolving best read alignments | 14:48:40 25 Oct 2024 | 14:49:22 25 Oct 2024 | 42 seconds |
| Creating BAM files | 14:49:22 25 Oct 2024 | 14:50:27 25 Oct 2024 | 1 minute 5 seconds |
| Tabulating error counts | 14:50:27 25 Oct 2024 | 14:50:58 25 Oct 2024 | 31 seconds |
| Re-calibrating base error rates | 14:50:58 25 Oct 2024 | 14:51:01 25 Oct 2024 | 3 seconds |
| Examining read alignment evidence | 14:51:01 25 Oct 2024 | 14:57:08 25 Oct 2024 | 6 minutes 7 seconds |
| Polymorphism statistics | 14:57:08 25 Oct 2024 | 14:57:09 25 Oct 2024 | 1 second |
| Output | 14:57:09 25 Oct 2024 | 14:57:21 25 Oct 2024 | 12 seconds |
| Total | 17 minutes 3 seconds | ||
