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 | Plate-1-BOP-27-PFKA-END-3_S35_L001_R1_001.good.fq | 440,225 | 62,388,109 | 100.0% | 141.7 bases | 149 bases | 97.2% |
| errors | Plate-1-BOP-27-PFKA-END-3_S35_L001_R2_001.good.fq | 440,225 | 62,168,782 | 100.0% | 141.2 bases | 149 bases | 97.3% |
| errors | Plate-1-BOP-27-PFKA-END-3_S35_L002_R1_001.good.fq | 408,684 | 57,958,528 | 100.0% | 141.8 bases | 149 bases | 97.3% |
| errors | Plate-1-BOP-27-PFKA-END-3_S35_L002_R2_001.good.fq | 408,684 | 57,770,014 | 100.0% | 141.4 bases | 149 bases | 97.0% |
| errors | Plate-1-BOP-27-PFKA-END-3_S35_L003_R1_001.good.fq | 427,446 | 60,526,087 | 100.0% | 141.6 bases | 149 bases | 97.1% |
| errors | Plate-1-BOP-27-PFKA-END-3_S35_L003_R2_001.good.fq | 427,446 | 60,324,771 | 100.0% | 141.1 bases | 149 bases | 97.1% |
| errors | Plate-1-BOP-27-PFKA-END-3_S35_L004_R1_001.good.fq | 437,883 | 62,007,298 | 100.0% | 141.6 bases | 149 bases | 97.3% |
| errors | Plate-1-BOP-27-PFKA-END-3_S35_L004_R2_001.good.fq | 437,883 | 61,815,874 | 100.0% | 141.2 bases | 149 bases | 97.1% |
| total | 3,428,476 | 484,959,463 | 100.0% | 141.5 bases | 149 bases | 97.2% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_000913 | 4,641,652 | 101.0 | 3.3 | 100.0% | Escherichia coli str. K-12 substr. MG1655, complete genome. |
| total | 4,641,652 | 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 | 34512 |
| Coverage evenness (position-hash) score of junction candidates | ≥ 2 | ≥ 3 |
| Test this many junction candidates (n). May be smaller if not enough passed the coverage evenness threshold | 100 ≤ n ≤ 5000 | 77 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.005 |
| reference sequence | pr(no read start) |
|---|---|
| NC_000913 | 0.73039 |
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 | 10:35:02 06 Apr 2022 | 10:36:04 06 Apr 2022 | 1 minute 2 seconds |
| Read alignment to reference genome | 10:36:04 06 Apr 2022 | 10:42:59 06 Apr 2022 | 6 minutes 55 seconds |
| Preprocessing alignments for candidate junction identification | 10:42:59 06 Apr 2022 | 10:43:43 06 Apr 2022 | 44 seconds |
| Preliminary analysis of coverage distribution | 10:43:43 06 Apr 2022 | 10:45:47 06 Apr 2022 | 2 minutes 4 seconds |
| Identifying junction candidates | 10:45:47 06 Apr 2022 | 10:46:25 06 Apr 2022 | 38 seconds |
| Re-alignment to junction candidates | 10:46:25 06 Apr 2022 | 10:48:03 06 Apr 2022 | 1 minute 38 seconds |
| Resolving best read alignments | 10:48:03 06 Apr 2022 | 10:49:05 06 Apr 2022 | 1 minute 2 seconds |
| Creating BAM files | 10:49:05 06 Apr 2022 | 10:50:56 06 Apr 2022 | 1 minute 51 seconds |
| Tabulating error counts | 10:50:56 06 Apr 2022 | 10:51:39 06 Apr 2022 | 43 seconds |
| Re-calibrating base error rates | 10:51:39 06 Apr 2022 | 10:51:42 06 Apr 2022 | 3 seconds |
| Examining read alignment evidence | 10:51:42 06 Apr 2022 | 11:00:42 06 Apr 2022 | 9 minutes 0 seconds |
| Polymorphism statistics | 11:00:42 06 Apr 2022 | 11:00:43 06 Apr 2022 | 1 second |
| Output | 11:00:43 06 Apr 2022 | 11:00:57 06 Apr 2022 | 14 seconds |
| Total | 25 minutes 55 seconds | ||
