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-ACB122-A12-F47-I1-R1_S31_L001_R1_001.good.fq | 354,448 | 46,040,347 | 100.0% | 129.9 bases | 137 bases | 95.2% |
| errors | Putida-Van-ACB122-A12-F47-I1-R1_S31_L001_R2_001.good.fq | 354,448 | 46,040,347 | 100.0% | 129.9 bases | 137 bases | 94.1% |
| errors | Putida-Van-ACB122-A12-F47-I1-R1_S31_L002_R1_001.good.fq | 345,775 | 45,013,886 | 100.0% | 130.2 bases | 137 bases | 95.6% |
| errors | Putida-Van-ACB122-A12-F47-I1-R1_S31_L002_R2_001.good.fq | 345,775 | 45,013,886 | 100.0% | 130.2 bases | 137 bases | 94.4% |
| errors | Putida-Van-ACB122-A12-F47-I1-R1_S31_L003_R1_001.good.fq | 367,535 | 47,924,584 | 100.0% | 130.4 bases | 137 bases | 95.7% |
| errors | Putida-Van-ACB122-A12-F47-I1-R1_S31_L003_R2_001.good.fq | 367,535 | 47,924,584 | 100.0% | 130.4 bases | 137 bases | 94.5% |
| errors | Putida-Van-ACB122-A12-F47-I1-R1_S31_L004_R1_001.good.fq | 359,341 | 46,793,374 | 100.0% | 130.2 bases | 137 bases | 95.7% |
| errors | Putida-Van-ACB122-A12-F47-I1-R1_S31_L004_R2_001.good.fq | 359,341 | 46,793,374 | 100.0% | 130.2 bases | 137 bases | 94.4% |
| total | 2,854,198 | 371,544,382 | 100.0% | 130.2 bases | 137 bases | 94.9% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | ACB122 | 6,184,097 | 58.0 | 2.5 | 100.0% | tig00000001|arrow. |
| total | 6,184,097 | 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 | 1545 |
| 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 | 86 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.004 |
| reference sequence | pr(no read start) |
|---|---|
| ACB122 | 0.86041 |
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 | 11:13:43 28 Apr 2023 | 11:14:31 28 Apr 2023 | 48 seconds |
| Read alignment to reference genome | 11:14:32 28 Apr 2023 | 11:20:39 28 Apr 2023 | 6 minutes 7 seconds |
| Preprocessing alignments for candidate junction identification | 11:20:39 28 Apr 2023 | 11:21:14 28 Apr 2023 | 35 seconds |
| Preliminary analysis of coverage distribution | 11:21:14 28 Apr 2023 | 11:22:52 28 Apr 2023 | 1 minute 38 seconds |
| Identifying junction candidates | 11:22:52 28 Apr 2023 | 11:22:53 28 Apr 2023 | 1 second |
| Re-alignment to junction candidates | 11:22:53 28 Apr 2023 | 11:24:19 28 Apr 2023 | 1 minute 26 seconds |
| Resolving best read alignments | 11:24:19 28 Apr 2023 | 11:25:08 28 Apr 2023 | 49 seconds |
| Creating BAM files | 11:25:08 28 Apr 2023 | 11:26:37 28 Apr 2023 | 1 minute 29 seconds |
| Tabulating error counts | 11:26:37 28 Apr 2023 | 11:27:08 28 Apr 2023 | 31 seconds |
| Re-calibrating base error rates | 11:27:08 28 Apr 2023 | 11:27:11 28 Apr 2023 | 3 seconds |
| Examining read alignment evidence | 11:27:11 28 Apr 2023 | 11:33:54 28 Apr 2023 | 6 minutes 43 seconds |
| Polymorphism statistics | 11:33:54 28 Apr 2023 | 11:33:55 28 Apr 2023 | 1 second |
| Output | 11:33:55 28 Apr 2023 | 11:34:10 28 Apr 2023 | 15 seconds |
| Total | 20 minutes 26 seconds | ||
