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 | Putida-Van-KT2440-A1-F42-I1-R1_S89_L001_R1_001.good.fq | 351,405 | 45,893,962 | 100.0% | 130.6 bases | 137 bases | 96.2% |
| errors | Putida-Van-KT2440-A1-F42-I1-R1_S89_L001_R2_001.good.fq | 351,405 | 45,893,962 | 100.0% | 130.6 bases | 137 bases | 95.2% |
| errors | Putida-Van-KT2440-A1-F42-I1-R1_S89_L002_R1_001.good.fq | 342,389 | 44,849,868 | 100.0% | 131.0 bases | 137 bases | 96.5% |
| errors | Putida-Van-KT2440-A1-F42-I1-R1_S89_L002_R2_001.good.fq | 342,389 | 44,849,868 | 100.0% | 131.0 bases | 137 bases | 95.4% |
| errors | Putida-Van-KT2440-A1-F42-I1-R1_S89_L003_R1_001.good.fq | 361,379 | 47,405,261 | 100.0% | 131.2 bases | 137 bases | 96.6% |
| errors | Putida-Van-KT2440-A1-F42-I1-R1_S89_L003_R2_001.good.fq | 361,379 | 47,405,261 | 100.0% | 131.2 bases | 137 bases | 95.5% |
| errors | Putida-Van-KT2440-A1-F42-I1-R1_S89_L004_R1_001.good.fq | 355,827 | 46,613,596 | 100.0% | 131.0 bases | 137 bases | 96.6% |
| errors | Putida-Van-KT2440-A1-F42-I1-R1_S89_L004_R2_001.good.fq | 355,827 | 46,613,596 | 100.0% | 131.0 bases | 137 bases | 95.4% |
| total | 2,822,000 | 369,525,374 | 100.0% | 130.9 bases | 137 bases | 95.9% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | KT2440 | 6,185,276 | 58.0 | 2.5 | 100.0% | tig00000001|arrow. |
| total | 6,185,276 | 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 | 1665 |
| 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 | 65 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.003 |
| reference sequence | pr(no read start) |
|---|---|
| KT2440 | 0.86086 |
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 | 11:15:10 28 Apr 2023 | 11:15:59 28 Apr 2023 | 49 seconds |
| Read alignment to reference genome | 11:15:59 28 Apr 2023 | 11:22:18 28 Apr 2023 | 6 minutes 19 seconds |
| Preprocessing alignments for candidate junction identification | 11:22:18 28 Apr 2023 | 11:22:53 28 Apr 2023 | 35 seconds |
| Preliminary analysis of coverage distribution | 11:22:53 28 Apr 2023 | 11:24:31 28 Apr 2023 | 1 minute 38 seconds |
| Identifying junction candidates | 11:24:31 28 Apr 2023 | 11:24:31 28 Apr 2023 | 0 seconds |
| Re-alignment to junction candidates | 11:24:31 28 Apr 2023 | 11:25:58 28 Apr 2023 | 1 minute 27 seconds |
| Resolving best read alignments | 11:25:58 28 Apr 2023 | 11:26:47 28 Apr 2023 | 49 seconds |
| Creating BAM files | 11:26:47 28 Apr 2023 | 11:28:17 28 Apr 2023 | 1 minute 30 seconds |
| Tabulating error counts | 11:28:17 28 Apr 2023 | 11:28:48 28 Apr 2023 | 31 seconds |
| Re-calibrating base error rates | 11:28:48 28 Apr 2023 | 11:28:51 28 Apr 2023 | 3 seconds |
| Examining read alignment evidence | 11:28:51 28 Apr 2023 | 11:35:37 28 Apr 2023 | 6 minutes 46 seconds |
| Polymorphism statistics | 11:35:37 28 Apr 2023 | 11:35:38 28 Apr 2023 | 1 second |
| Output | 11:35:38 28 Apr 2023 | 11:35:52 28 Apr 2023 | 14 seconds |
| Total | 20 minutes 42 seconds | ||
