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-1-BOP-27-PFKA-END-4_S36_L001_R1_001.good.fq | 429,229 | 60,638,537 | 100.0% | 141.3 bases | 149 bases | 97.6% |
| errors | Plate-1-BOP-27-PFKA-END-4_S36_L001_R2_001.good.fq | 429,229 | 60,407,026 | 100.0% | 140.7 bases | 149 bases | 97.9% |
| errors | Plate-1-BOP-27-PFKA-END-4_S36_L002_R1_001.good.fq | 400,423 | 56,609,836 | 100.0% | 141.4 bases | 149 bases | 97.7% |
| errors | Plate-1-BOP-27-PFKA-END-4_S36_L002_R2_001.good.fq | 400,423 | 56,403,335 | 100.0% | 140.9 bases | 149 bases | 97.7% |
| errors | Plate-1-BOP-27-PFKA-END-4_S36_L003_R1_001.good.fq | 416,752 | 58,831,131 | 100.0% | 141.2 bases | 149 bases | 97.5% |
| errors | Plate-1-BOP-27-PFKA-END-4_S36_L003_R2_001.good.fq | 416,752 | 58,600,861 | 100.0% | 140.6 bases | 149 bases | 97.8% |
| errors | Plate-1-BOP-27-PFKA-END-4_S36_L004_R1_001.good.fq | 444,513 | 62,785,972 | 100.0% | 141.2 bases | 149 bases | 97.7% |
| errors | Plate-1-BOP-27-PFKA-END-4_S36_L004_R2_001.good.fq | 444,513 | 62,560,005 | 100.0% | 140.7 bases | 149 bases | 97.8% |
| total | 3,381,834 | 476,836,703 | 100.0% | 141.0 bases | 149 bases | 97.7% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_000913 | 4,641,652 | 99.6 | 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 | 22420 |
| 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 | 90 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.006 |
| reference sequence | pr(no read start) |
|---|---|
| NC_000913 | 0.73326 |
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 | ≤ 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 | 22:11:26 10 Sep 2020 | 22:12:18 10 Sep 2020 | 52 seconds |
| Read alignment to reference genome | 22:12:18 10 Sep 2020 | 22:18:48 10 Sep 2020 | 6 minutes 30 seconds |
| Preprocessing alignments for candidate junction identification | 22:18:48 10 Sep 2020 | 22:19:42 10 Sep 2020 | 54 seconds |
| Preliminary analysis of coverage distribution | 22:19:42 10 Sep 2020 | 22:21:39 10 Sep 2020 | 1 minute 57 seconds |
| Identifying junction candidates | 22:21:39 10 Sep 2020 | 22:22:06 10 Sep 2020 | 27 seconds |
| Re-alignment to junction candidates | 22:22:06 10 Sep 2020 | 22:24:05 10 Sep 2020 | 1 minute 59 seconds |
| Resolving best read alignments | 22:24:05 10 Sep 2020 | 22:25:27 10 Sep 2020 | 1 minute 22 seconds |
| Creating BAM files | 22:25:27 10 Sep 2020 | 22:27:15 10 Sep 2020 | 1 minute 48 seconds |
| Tabulating error counts | 22:27:15 10 Sep 2020 | 22:27:52 10 Sep 2020 | 37 seconds |
| Re-calibrating base error rates | 22:27:52 10 Sep 2020 | 22:27:55 10 Sep 2020 | 3 seconds |
| Examining read alignment evidence | 22:27:55 10 Sep 2020 | 22:35:22 10 Sep 2020 | 7 minutes 27 seconds |
| Polymorphism statistics | 22:35:22 10 Sep 2020 | 22:35:23 10 Sep 2020 | 1 second |
| Output | 22:35:23 10 Sep 2020 | 22:35:42 10 Sep 2020 | 19 seconds |
| Total | 24 minutes 16 seconds | ||
