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-3-BOP-1000-SUCB-END-3_S59_L001_R1_001.good.fq | 471,572 | 65,535,349 | 100.0% | 139.0 bases | 148 bases | 99.1% |
| errors | Plate-3-BOP-1000-SUCB-END-3_S59_L001_R2_001.good.fq | 471,572 | 65,556,364 | 100.0% | 139.0 bases | 148 bases | 98.3% |
| errors | Plate-3-BOP-1000-SUCB-END-3_S59_L002_R1_001.good.fq | 443,601 | 61,680,616 | 100.0% | 139.0 bases | 148 bases | 99.2% |
| errors | Plate-3-BOP-1000-SUCB-END-3_S59_L002_R2_001.good.fq | 443,601 | 61,708,965 | 100.0% | 139.1 bases | 148 bases | 98.1% |
| errors | Plate-3-BOP-1000-SUCB-END-3_S59_L003_R1_001.good.fq | 459,028 | 63,709,668 | 100.0% | 138.8 bases | 148 bases | 99.1% |
| errors | Plate-3-BOP-1000-SUCB-END-3_S59_L003_R2_001.good.fq | 459,028 | 63,739,224 | 100.0% | 138.9 bases | 148 bases | 98.1% |
| errors | Plate-3-BOP-1000-SUCB-END-3_S59_L004_R1_001.good.fq | 485,050 | 67,357,544 | 100.0% | 138.9 bases | 148 bases | 99.2% |
| errors | Plate-3-BOP-1000-SUCB-END-3_S59_L004_R2_001.good.fq | 485,050 | 67,394,468 | 100.0% | 138.9 bases | 148 bases | 98.2% |
| total | 3,718,502 | 516,682,198 | 100.0% | 138.9 bases | 148 bases | 98.6% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_000913 | 4,641,652 | 105.5 | 4.7 | 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 | 19515 |
| 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 | 42 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.003 |
| reference sequence | pr(no read start) |
|---|---|
| NC_000913 | 0.71846 |
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 | ≤ 0 |
| Number of bases that at least one read must overlap each uniquely aligned side of a predicted junction | ≥ 6 |
| option | value |
|---|---|
| Mode | Full Polymorphism |
| 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 | 2 |
| Polymorphism frequency cutoff | 0.05 |
| Polymorphism minimum variant coverage each strand | 2 |
| 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 | ≥3 bases |
| Skip base substitutions when they create a homopolymer flanked on each side by | ≥5 bases |
| program | version |
|---|---|
| bowtie2 | 2.2.6 |
| R | 3.4.4 |
| step | start | end | elapsed |
|---|---|---|---|
| Read and reference sequence file input | 10:34:57 06 Apr 2022 | 10:36:02 06 Apr 2022 | 1 minute 5 seconds |
| Read alignment to reference genome | 10:36:02 06 Apr 2022 | 10:42:55 06 Apr 2022 | 6 minutes 53 seconds |
| Preprocessing alignments for candidate junction identification | 10:42:55 06 Apr 2022 | 10:43:41 06 Apr 2022 | 46 seconds |
| Preliminary analysis of coverage distribution | 10:43:41 06 Apr 2022 | 10:45:48 06 Apr 2022 | 2 minutes 7 seconds |
| Identifying junction candidates | 10:45:48 06 Apr 2022 | 10:46:10 06 Apr 2022 | 22 seconds |
| Re-alignment to junction candidates | 10:46:10 06 Apr 2022 | 10:47:45 06 Apr 2022 | 1 minute 35 seconds |
| Resolving best read alignments | 10:47:45 06 Apr 2022 | 10:48:49 06 Apr 2022 | 1 minute 4 seconds |
| Creating BAM files | 10:48:49 06 Apr 2022 | 10:50:41 06 Apr 2022 | 1 minute 52 seconds |
| Tabulating error counts | 10:50:41 06 Apr 2022 | 10:51:25 06 Apr 2022 | 44 seconds |
| Re-calibrating base error rates | 10:51:25 06 Apr 2022 | 10:51:27 06 Apr 2022 | 2 seconds |
| Examining read alignment evidence | 10:51:27 06 Apr 2022 | 11:31:03 06 Apr 2022 | 39 minutes 36 seconds |
| Polymorphism statistics | 11:31:03 06 Apr 2022 | 11:31:04 06 Apr 2022 | 1 second |
| Output | 11:31:04 06 Apr 2022 | 11:31:20 06 Apr 2022 | 16 seconds |
| Total | 56 minutes 23 seconds | ||
