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 | SRR13416473_R1.good.fq | 1,509,821 | 375,937,546 | 100.0% | 249.0 bases | 249 bases | 64.5% |
| errors | SRR13416473_R2.good.fq | 1,509,821 | 375,937,546 | 100.0% | 249.0 bases | 249 bases | 63.7% |
| total | 3,019,642 | 751,875,092 | 100.0% | 249.0 bases | 249 bases | 64.1% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | CP025533 | 3,316,624 | 156.9 | 1.5 | 100.0% | Corynebacterium glutamicum strain ATCC 13032 chromosome, complete |
| total | 3,316,624 | 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 | 6420 |
| 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 | 67 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.010 |
| reference sequence | pr(no read start) |
|---|---|
| CP025533 | 0.76678 |
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 | 12:54:46 13 Feb 2023 | 12:55:48 13 Feb 2023 | 1 minute 2 seconds |
| Read alignment to reference genome | 12:55:48 13 Feb 2023 | 13:04:34 13 Feb 2023 | 8 minutes 46 seconds |
| Preprocessing alignments for candidate junction identification | 13:04:34 13 Feb 2023 | 13:05:06 13 Feb 2023 | 32 seconds |
| Preliminary analysis of coverage distribution | 13:05:06 13 Feb 2023 | 13:06:54 13 Feb 2023 | 1 minute 48 seconds |
| Identifying junction candidates | 13:06:54 13 Feb 2023 | 13:06:55 13 Feb 2023 | 1 second |
| Re-alignment to junction candidates | 13:06:55 13 Feb 2023 | 13:09:17 13 Feb 2023 | 2 minutes 22 seconds |
| Resolving best read alignments | 13:09:17 13 Feb 2023 | 13:10:18 13 Feb 2023 | 1 minute 1 second |
| Creating BAM files | 13:10:18 13 Feb 2023 | 13:11:54 13 Feb 2023 | 1 minute 36 seconds |
| Tabulating error counts | 13:11:54 13 Feb 2023 | 13:12:34 13 Feb 2023 | 40 seconds |
| Re-calibrating base error rates | 13:12:34 13 Feb 2023 | 13:12:35 13 Feb 2023 | 1 second |
| Examining read alignment evidence | 13:12:35 13 Feb 2023 | 13:21:03 13 Feb 2023 | 8 minutes 28 seconds |
| Polymorphism statistics | 13:21:03 13 Feb 2023 | 13:21:03 13 Feb 2023 | 0 seconds |
| Output | 13:21:03 13 Feb 2023 | 13:21:29 13 Feb 2023 | 26 seconds |
| Total | 26 minutes 43 seconds | ||
