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 | 1_S1_L001_R1_001.good.fq | 367,191 | 53,593,054 | 100.0% | 146.0 bases | 149 bases | 99.0% |
| errors | 1_S1_L001_R2_001.good.fq | 367,191 | 53,592,065 | 100.0% | 146.0 bases | 149 bases | 97.8% |
| errors | 1_S1_L002_R1_001.good.fq | 359,520 | 52,482,907 | 100.0% | 146.0 bases | 149 bases | 98.9% |
| errors | 1_S1_L002_R2_001.good.fq | 359,520 | 52,487,741 | 100.0% | 146.0 bases | 149 bases | 97.4% |
| errors | 1_S1_L003_R1_001.good.fq | 370,547 | 54,085,107 | 100.0% | 146.0 bases | 149 bases | 99.0% |
| errors | 1_S1_L003_R2_001.good.fq | 370,547 | 54,083,356 | 100.0% | 146.0 bases | 149 bases | 98.0% |
| errors | 1_S1_L004_R1_001.good.fq | 384,840 | 56,144,232 | 100.0% | 145.9 bases | 149 bases | 99.1% |
| errors | 1_S1_L004_R2_001.good.fq | 384,840 | 56,135,906 | 100.0% | 145.9 bases | 149 bases | 98.3% |
| total | 2,964,196 | 432,604,368 | 100.0% | 145.9 bases | 149 bases | 98.4% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_002947_CJ-RC | 6,184,688 | 69.5 | 1.8 | 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 | 12516 |
| 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 | 866 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.042 |
| reference sequence | pr(no read start) |
|---|---|
| NC_002947_CJ-RC | 0.80839 |
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 | 12:30:27 26 Oct 2024 | 12:31:17 26 Oct 2024 | 50 seconds |
| Read alignment to reference genome | 12:31:17 26 Oct 2024 | 12:36:54 26 Oct 2024 | 5 minutes 37 seconds |
| Preprocessing alignments for candidate junction identification | 12:36:54 26 Oct 2024 | 12:37:31 26 Oct 2024 | 37 seconds |
| Preliminary analysis of coverage distribution | 12:37:31 26 Oct 2024 | 12:39:04 26 Oct 2024 | 1 minute 33 seconds |
| Identifying junction candidates | 12:39:04 26 Oct 2024 | 12:39:07 26 Oct 2024 | 3 seconds |
| Re-alignment to junction candidates | 12:39:07 26 Oct 2024 | 12:40:47 26 Oct 2024 | 1 minute 40 seconds |
| Resolving best read alignments | 12:40:47 26 Oct 2024 | 12:41:39 26 Oct 2024 | 52 seconds |
| Creating BAM files | 12:41:39 26 Oct 2024 | 12:43:02 26 Oct 2024 | 1 minute 23 seconds |
| Tabulating error counts | 12:43:02 26 Oct 2024 | 12:43:40 26 Oct 2024 | 38 seconds |
| Re-calibrating base error rates | 12:43:40 26 Oct 2024 | 12:43:42 26 Oct 2024 | 2 seconds |
| Examining read alignment evidence | 12:43:42 26 Oct 2024 | 12:51:14 26 Oct 2024 | 7 minutes 32 seconds |
| Polymorphism statistics | 12:51:14 26 Oct 2024 | 12:51:14 26 Oct 2024 | 0 seconds |
| Output | 12:51:14 26 Oct 2024 | 12:51:27 26 Oct 2024 | 13 seconds |
| Total | 21 minutes 0 seconds | ||
