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-ACB143-A15-F16-I1-R1_S67_L001_R1_001.good.fq | 373,216 | 48,745,357 | 100.0% | 130.6 bases | 137 bases | 95.7% |
| errors | Putida-Van-ACB143-A15-F16-I1-R1_S67_L001_R2_001.good.fq | 373,216 | 48,745,357 | 100.0% | 130.6 bases | 137 bases | 94.5% |
| errors | Putida-Van-ACB143-A15-F16-I1-R1_S67_L002_R1_001.good.fq | 363,839 | 47,645,301 | 100.0% | 131.0 bases | 137 bases | 96.1% |
| errors | Putida-Van-ACB143-A15-F16-I1-R1_S67_L002_R2_001.good.fq | 363,839 | 47,645,301 | 100.0% | 131.0 bases | 137 bases | 94.8% |
| errors | Putida-Van-ACB143-A15-F16-I1-R1_S67_L003_R1_001.good.fq | 383,076 | 50,155,062 | 100.0% | 130.9 bases | 137 bases | 96.2% |
| errors | Putida-Van-ACB143-A15-F16-I1-R1_S67_L003_R2_001.good.fq | 383,076 | 50,155,062 | 100.0% | 130.9 bases | 137 bases | 95.0% |
| errors | Putida-Van-ACB143-A15-F16-I1-R1_S67_L004_R1_001.good.fq | 375,670 | 49,163,809 | 100.0% | 130.9 bases | 137 bases | 96.1% |
| errors | Putida-Van-ACB143-A15-F16-I1-R1_S67_L004_R2_001.good.fq | 375,670 | 49,163,809 | 100.0% | 130.9 bases | 137 bases | 94.9% |
| total | 2,991,602 | 391,419,058 | 100.0% | 130.8 bases | 137 bases | 95.4% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | ACB143 | 6,188,635 | 61.0 | 2.5 | 100.0% | tig00000001_arrow. |
| total | 6,188,635 | 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 | 1859 |
| 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 | 130 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.006 |
| reference sequence | pr(no read start) |
|---|---|
| ACB143 | 0.85508 |
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 | 11:15:44 28 Apr 2023 | 11:16:35 28 Apr 2023 | 51 seconds |
| Read alignment to reference genome | 11:16:35 28 Apr 2023 | 11:23:01 28 Apr 2023 | 6 minutes 26 seconds |
| Preprocessing alignments for candidate junction identification | 11:23:01 28 Apr 2023 | 11:23:38 28 Apr 2023 | 37 seconds |
| Preliminary analysis of coverage distribution | 11:23:38 28 Apr 2023 | 11:25:22 28 Apr 2023 | 1 minute 44 seconds |
| Identifying junction candidates | 11:25:22 28 Apr 2023 | 11:25:23 28 Apr 2023 | 1 second |
| Re-alignment to junction candidates | 11:25:23 28 Apr 2023 | 11:26:55 28 Apr 2023 | 1 minute 32 seconds |
| Resolving best read alignments | 11:26:55 28 Apr 2023 | 11:27:47 28 Apr 2023 | 52 seconds |
| Creating BAM files | 11:27:47 28 Apr 2023 | 11:29:21 28 Apr 2023 | 1 minute 34 seconds |
| Tabulating error counts | 11:29:21 28 Apr 2023 | 11:29:56 28 Apr 2023 | 35 seconds |
| Re-calibrating base error rates | 11:29:56 28 Apr 2023 | 11:29:59 28 Apr 2023 | 3 seconds |
| Examining read alignment evidence | 11:29:59 28 Apr 2023 | 11:37:05 28 Apr 2023 | 7 minutes 6 seconds |
| Polymorphism statistics | 11:37:05 28 Apr 2023 | 11:37:05 28 Apr 2023 | 0 seconds |
| Output | 11:37:05 28 Apr 2023 | 11:37:24 28 Apr 2023 | 19 seconds |
| Total | 21 minutes 40 seconds | ||
