mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.33.1 revision 8505477f25b3
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-PFKA-END-2_S70_L001_R1_001.good.fq | 376,238 | 53,820,364 | 100.0% | 143.0 bases | 149 bases | 98.2% |
| errors | Plate-3-BOP-1000-PFKA-END-2_S70_L001_R2_001.good.fq | 376,238 | 53,674,429 | 100.0% | 142.7 bases | 149 bases | 98.2% |
| errors | Plate-3-BOP-1000-PFKA-END-2_S70_L002_R1_001.good.fq | 350,633 | 50,176,269 | 100.0% | 143.1 bases | 149 bases | 98.3% |
| errors | Plate-3-BOP-1000-PFKA-END-2_S70_L002_R2_001.good.fq | 350,633 | 50,044,689 | 100.0% | 142.7 bases | 149 bases | 98.0% |
| errors | Plate-3-BOP-1000-PFKA-END-2_S70_L003_R1_001.good.fq | 365,250 | 52,232,269 | 100.0% | 143.0 bases | 149 bases | 98.1% |
| errors | Plate-3-BOP-1000-PFKA-END-2_S70_L003_R2_001.good.fq | 365,250 | 52,091,092 | 100.0% | 142.6 bases | 149 bases | 98.0% |
| errors | Plate-3-BOP-1000-PFKA-END-2_S70_L004_R1_001.good.fq | 386,043 | 55,214,034 | 100.0% | 143.0 bases | 149 bases | 98.3% |
| errors | Plate-3-BOP-1000-PFKA-END-2_S70_L004_R2_001.good.fq | 386,043 | 55,074,079 | 100.0% | 142.7 bases | 149 bases | 98.1% |
| total | 2,956,328 | 422,327,225 | 100.0% | 142.9 bases | 149 bases | 98.2% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_000913 | 4,641,652 | 88.6 | 3.9 | 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 | 13490 |
| 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 | 1339 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.087 |
| reference sequence | pr(no read start) |
|---|---|
| NC_000913 | 0.76002 |
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 |
| 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 | 22:15:15 11 Sep 2020 | 22:16:01 11 Sep 2020 | 46 seconds |
| Read alignment to reference genome | 22:16:01 11 Sep 2020 | 22:21:38 11 Sep 2020 | 5 minutes 37 seconds |
| Preprocessing alignments for candidate junction identification | 22:21:38 11 Sep 2020 | 22:22:25 11 Sep 2020 | 47 seconds |
| Preliminary analysis of coverage distribution | 22:22:25 11 Sep 2020 | 22:24:08 11 Sep 2020 | 1 minute 43 seconds |
| Identifying junction candidates | 22:24:08 11 Sep 2020 | 22:24:15 11 Sep 2020 | 7 seconds |
| Re-alignment to junction candidates | 22:24:15 11 Sep 2020 | 22:26:28 11 Sep 2020 | 2 minutes 13 seconds |
| Resolving best read alignments | 22:26:28 11 Sep 2020 | 22:27:41 11 Sep 2020 | 1 minute 13 seconds |
| Creating BAM files | 22:27:41 11 Sep 2020 | 22:29:17 11 Sep 2020 | 1 minute 36 seconds |
| Tabulating error counts | 22:29:17 11 Sep 2020 | 22:29:49 11 Sep 2020 | 32 seconds |
| Re-calibrating base error rates | 22:29:49 11 Sep 2020 | 22:29:52 11 Sep 2020 | 3 seconds |
| Examining read alignment evidence | 22:29:52 11 Sep 2020 | 22:56:01 11 Sep 2020 | 26 minutes 9 seconds |
| Polymorphism statistics | 22:56:01 11 Sep 2020 | 22:56:02 11 Sep 2020 | 1 second |
| Output | 22:56:02 11 Sep 2020 | 22:56:30 11 Sep 2020 | 28 seconds |
| Total | 41 minutes 15 seconds | ||
