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-A10-F28-I1-R1_S7_L001_R1_001.good.fq | 441,082 | 57,560,673 | 100.0% | 130.5 bases | 137 bases | 96.3% |
| errors | Putida-Van-ACB122-A10-F28-I1-R1_S7_L001_R2_001.good.fq | 441,082 | 57,560,673 | 100.0% | 130.5 bases | 137 bases | 95.0% |
| errors | Putida-Van-ACB122-A10-F28-I1-R1_S7_L002_R1_001.good.fq | 429,802 | 56,219,166 | 100.0% | 130.8 bases | 137 bases | 96.7% |
| errors | Putida-Van-ACB122-A10-F28-I1-R1_S7_L002_R2_001.good.fq | 429,802 | 56,219,166 | 100.0% | 130.8 bases | 137 bases | 95.4% |
| errors | Putida-Van-ACB122-A10-F28-I1-R1_S7_L003_R1_001.good.fq | 453,403 | 59,368,622 | 100.0% | 130.9 bases | 137 bases | 96.8% |
| errors | Putida-Van-ACB122-A10-F28-I1-R1_S7_L003_R2_001.good.fq | 453,403 | 59,368,622 | 100.0% | 130.9 bases | 137 bases | 95.5% |
| errors | Putida-Van-ACB122-A10-F28-I1-R1_S7_L004_R1_001.good.fq | 444,870 | 58,169,770 | 100.0% | 130.8 bases | 137 bases | 96.7% |
| errors | Putida-Van-ACB122-A10-F28-I1-R1_S7_L004_R2_001.good.fq | 444,870 | 58,169,770 | 100.0% | 130.8 bases | 137 bases | 95.4% |
| total | 3,538,314 | 462,636,462 | 100.0% | 130.8 bases | 137 bases | 96.0% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | ACB122 | 6,184,097 | 72.3 | 3.0 | 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 | 2001 |
| 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 | 148 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.007 |
| reference sequence | pr(no read start) |
|---|---|
| ACB122 | 0.83696 |
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 | 11:15:30 28 Apr 2023 | 11:16:30 28 Apr 2023 | 1 minute 0 seconds |
| Read alignment to reference genome | 11:16:30 28 Apr 2023 | 11:24:11 28 Apr 2023 | 7 minutes 41 seconds |
| Preprocessing alignments for candidate junction identification | 11:24:11 28 Apr 2023 | 11:24:56 28 Apr 2023 | 45 seconds |
| Preliminary analysis of coverage distribution | 11:24:56 28 Apr 2023 | 11:26:59 28 Apr 2023 | 2 minutes 3 seconds |
| Identifying junction candidates | 11:26:59 28 Apr 2023 | 11:27:00 28 Apr 2023 | 1 second |
| Re-alignment to junction candidates | 11:27:00 28 Apr 2023 | 11:28:51 28 Apr 2023 | 1 minute 51 seconds |
| Resolving best read alignments | 11:28:51 28 Apr 2023 | 11:29:52 28 Apr 2023 | 1 minute 1 second |
| Creating BAM files | 11:29:52 28 Apr 2023 | 11:31:43 28 Apr 2023 | 1 minute 51 seconds |
| Tabulating error counts | 11:31:43 28 Apr 2023 | 11:32:22 28 Apr 2023 | 39 seconds |
| Re-calibrating base error rates | 11:32:22 28 Apr 2023 | 11:32:25 28 Apr 2023 | 3 seconds |
| Examining read alignment evidence | 11:32:25 28 Apr 2023 | 11:40:46 28 Apr 2023 | 8 minutes 21 seconds |
| Polymorphism statistics | 11:40:46 28 Apr 2023 | 11:40:46 28 Apr 2023 | 0 seconds |
| Output | 11:40:46 28 Apr 2023 | 11:41:03 28 Apr 2023 | 17 seconds |
| Total | 25 minutes 33 seconds | ||
