mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.38.1
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| read file | reads | bases | passed filters | average | longest | mapped | |
|---|---|---|---|---|---|---|---|
| errors | F.nNCl_Unknown_CL297-ZX01-010004_1.fq | 3,588,195 | 538,229,250 | 100.0% | 150.0 bases | 150 bases | 98.5% |
| errors | F.nNCl_Unknown_CL297-ZX01-010004_2.fq | 3,574,765 | 536,214,750 | 99.6% | 150.0 bases | 150 bases | 96.7% |
| total | 7,162,960 | 1,074,444,000 | 99.8% | 150.0 bases | 150 bases | 97.6% |
| seq id | length | fit mean | fit relative_variance | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | CP028101 | 2,180,101 | 475.1 | 13.5 | 100.0% | Fusobacterium nucleatum subsp. nucleatum ATCC 25586 chromosome, |
| total | 2,180,101 | 100.0% |
fit relative_variance 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 | 31876 |
| 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 | 540 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.076 |
| reference sequence | pr(no read start) |
|---|---|
| CP028101 | 0.40713 |
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 | 0.8 |
| 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 | s.2023.01/rocky8/x86_64/amd/zen3/software/Bowtie2/2.4.5-GCC-11.3.0/bin/bowtie2-align-s |
| R | 4.2.1 |
| step | start | end | elapsed |
|---|---|---|---|
| Read and reference sequence file input | 20:49:07 08 Jan 2025 | 20:50:38 08 Jan 2025 | 1 minute 31 seconds |
| Read alignment to reference genome | 20:50:38 08 Jan 2025 | 20:54:38 08 Jan 2025 | 4 minutes 0 seconds |
| Preprocessing alignments for candidate junction identification | 20:54:38 08 Jan 2025 | 20:55:46 08 Jan 2025 | 1 minute 8 seconds |
| Preliminary analysis of coverage distribution | 20:55:46 08 Jan 2025 | 20:57:48 08 Jan 2025 | 2 minutes 2 seconds |
| Identifying junction candidates | 20:57:48 08 Jan 2025 | 20:57:53 08 Jan 2025 | 5 seconds |
| Re-alignment to junction candidates | 20:57:53 08 Jan 2025 | 20:59:03 08 Jan 2025 | 1 minute 10 seconds |
| Resolving best read alignments | 20:59:03 08 Jan 2025 | 21:00:47 08 Jan 2025 | 1 minute 44 seconds |
| Creating BAM files | 21:00:47 08 Jan 2025 | 21:02:25 08 Jan 2025 | 1 minute 38 seconds |
| Tabulating error counts | 21:02:25 08 Jan 2025 | 21:04:17 08 Jan 2025 | 1 minute 52 seconds |
| Re-calibrating base error rates | 21:04:17 08 Jan 2025 | 21:04:19 08 Jan 2025 | 2 seconds |
| Examining read alignment evidence | 21:04:19 08 Jan 2025 | 21:17:35 08 Jan 2025 | 13 minutes 16 seconds |
| Polymorphism statistics | 21:17:35 08 Jan 2025 | 21:17:37 08 Jan 2025 | 2 seconds |
| Output | 21:17:37 08 Jan 2025 | 21:17:56 08 Jan 2025 | 19 seconds |
| Output :: Mutation Prediction | 21:17:37 08 Jan 2025 | 21:17:41 08 Jan 2025 | 4 seconds |
| Output :: Mutation Annotation | 21:17:41 08 Jan 2025 | 21:17:41 08 Jan 2025 | 0 seconds |
| Total | 28 minutes 53 seconds | ||
