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 | SRR4302518_R1.good.fq | 14,433,899 | 1,385,175,051 | 100.0% | 96.0 bases | 96 bases | 97.4% |
| errors | SRR4302518_R2.good.fq | 14,433,899 | 1,385,175,051 | 100.0% | 96.0 bases | 96 bases | 98.1% |
| total | 28,867,798 | 2,770,350,102 | 100.0% | 96.0 bases | 96 bases | 97.7% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_000913 | 4,639,221 | 579.6 | 9.3 | 100.0% | Escherichia coli K12, complete genome. |
| total | 4,639,221 | 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 | 30503 |
| 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 | 996 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.043 |
| reference sequence | pr(no read start) |
|---|---|
| NC_000913 | 0.08348 |
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 | 10:27:54 17 Jan 2023 | 10:34:52 17 Jan 2023 | 6 minutes 58 seconds |
| Read alignment to reference genome | 10:34:52 17 Jan 2023 | 11:16:03 17 Jan 2023 | 41 minutes 11 seconds |
| Preprocessing alignments for candidate junction identification | 11:16:03 17 Jan 2023 | 11:22:22 17 Jan 2023 | 6 minutes 19 seconds |
| Preliminary analysis of coverage distribution | 11:22:22 17 Jan 2023 | 11:35:46 17 Jan 2023 | 13 minutes 24 seconds |
| Identifying junction candidates | 11:35:46 17 Jan 2023 | 11:35:52 17 Jan 2023 | 6 seconds |
| Re-alignment to junction candidates | 11:35:52 17 Jan 2023 | 11:47:19 17 Jan 2023 | 11 minutes 27 seconds |
| Resolving best read alignments | 11:47:19 17 Jan 2023 | 11:55:37 17 Jan 2023 | 8 minutes 18 seconds |
| Creating BAM files | 11:55:37 17 Jan 2023 | 12:07:43 17 Jan 2023 | 12 minutes 6 seconds |
| Tabulating error counts | 12:07:43 17 Jan 2023 | 12:11:39 17 Jan 2023 | 3 minutes 56 seconds |
| Re-calibrating base error rates | 12:11:39 17 Jan 2023 | 12:11:40 17 Jan 2023 | 1 second |
| Examining read alignment evidence | 12:11:40 17 Jan 2023 | 12:57:56 17 Jan 2023 | 46 minutes 16 seconds |
| Polymorphism statistics | 12:57:56 17 Jan 2023 | 12:57:57 17 Jan 2023 | 1 second |
| Output | 12:57:57 17 Jan 2023 | 12:59:34 17 Jan 2023 | 1 minute 37 seconds |
| Total | 2 hours 31 minutes 40 seconds | ||
