mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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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-1000-PFKA-END-4_S28_L001_R1_001.good.fq | 414,462 | 59,608,000 | 100.0% | 143.8 bases | 149 bases | 96.3% |
| errors | Plate-1-BOP-1000-PFKA-END-4_S28_L001_R2_001.good.fq | 414,462 | 59,274,352 | 100.0% | 143.0 bases | 149 bases | 97.1% |
| errors | Plate-1-BOP-1000-PFKA-END-4_S28_L002_R1_001.good.fq | 392,706 | 56,480,096 | 100.0% | 143.8 bases | 149 bases | 96.5% |
| errors | Plate-1-BOP-1000-PFKA-END-4_S28_L002_R2_001.good.fq | 392,706 | 56,198,834 | 100.0% | 143.1 bases | 149 bases | 97.1% |
| errors | Plate-1-BOP-1000-PFKA-END-4_S28_L003_R1_001.good.fq | 405,510 | 58,314,818 | 100.0% | 143.8 bases | 149 bases | 96.2% |
| errors | Plate-1-BOP-1000-PFKA-END-4_S28_L003_R2_001.good.fq | 405,510 | 57,997,997 | 100.0% | 143.0 bases | 149 bases | 97.0% |
| errors | Plate-1-BOP-1000-PFKA-END-4_S28_L004_R1_001.good.fq | 419,915 | 60,354,801 | 100.0% | 143.7 bases | 149 bases | 96.5% |
| errors | Plate-1-BOP-1000-PFKA-END-4_S28_L004_R2_001.good.fq | 419,915 | 60,049,195 | 100.0% | 143.0 bases | 149 bases | 97.2% |
| total | 3,265,186 | 468,278,093 | 100.0% | 143.4 bases | 149 bases | 96.7% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_000913 | 4,641,652 | 96.1 | 4.0 | 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 | 35046 |
| 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 | 44 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.003 |
| reference sequence | pr(no read start) |
|---|---|
| NC_000913 | 0.74971 |
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 | 19:10:20 11 Sep 2020 | 19:11:10 11 Sep 2020 | 50 seconds |
| Read alignment to reference genome | 19:11:10 11 Sep 2020 | 19:17:26 11 Sep 2020 | 6 minutes 16 seconds |
| Preprocessing alignments for candidate junction identification | 19:17:26 11 Sep 2020 | 19:18:16 11 Sep 2020 | 50 seconds |
| Preliminary analysis of coverage distribution | 19:18:16 11 Sep 2020 | 19:20:07 11 Sep 2020 | 1 minute 51 seconds |
| Identifying junction candidates | 19:20:07 11 Sep 2020 | 19:20:28 11 Sep 2020 | 21 seconds |
| Re-alignment to junction candidates | 19:20:28 11 Sep 2020 | 19:22:17 11 Sep 2020 | 1 minute 49 seconds |
| Resolving best read alignments | 19:22:17 11 Sep 2020 | 19:23:36 11 Sep 2020 | 1 minute 19 seconds |
| Creating BAM files | 19:23:36 11 Sep 2020 | 19:25:18 11 Sep 2020 | 1 minute 42 seconds |
| Tabulating error counts | 19:25:18 11 Sep 2020 | 19:25:53 11 Sep 2020 | 35 seconds |
| Re-calibrating base error rates | 19:25:53 11 Sep 2020 | 19:25:56 11 Sep 2020 | 3 seconds |
| Examining read alignment evidence | 19:25:56 11 Sep 2020 | 19:33:17 11 Sep 2020 | 7 minutes 21 seconds |
| Polymorphism statistics | 19:33:17 11 Sep 2020 | 19:33:17 11 Sep 2020 | 0 seconds |
| Output | 19:33:17 11 Sep 2020 | 19:33:32 11 Sep 2020 | 15 seconds |
| Total | 23 minutes 12 seconds | ||
