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-1000-PFKA-END-1_S25_L001_R1_001.good.fq | 437,332 | 60,006,190 | 100.0% | 137.2 bases | 149 bases | 96.5% |
| errors | Plate-1-BOP-1000-PFKA-END-1_S25_L001_R2_001.good.fq | 437,332 | 59,687,846 | 100.0% | 136.5 bases | 149 bases | 97.4% |
| errors | Plate-1-BOP-1000-PFKA-END-1_S25_L002_R1_001.good.fq | 396,951 | 54,515,574 | 100.0% | 137.3 bases | 149 bases | 96.6% |
| errors | Plate-1-BOP-1000-PFKA-END-1_S25_L002_R2_001.good.fq | 396,951 | 54,247,068 | 100.0% | 136.7 bases | 149 bases | 97.2% |
| errors | Plate-1-BOP-1000-PFKA-END-1_S25_L003_R1_001.good.fq | 425,660 | 58,388,935 | 100.0% | 137.2 bases | 149 bases | 96.4% |
| errors | Plate-1-BOP-1000-PFKA-END-1_S25_L003_R2_001.good.fq | 425,660 | 58,084,896 | 100.0% | 136.5 bases | 149 bases | 97.3% |
| errors | Plate-1-BOP-1000-PFKA-END-1_S25_L004_R1_001.good.fq | 439,278 | 60,254,312 | 100.0% | 137.2 bases | 149 bases | 96.6% |
| errors | Plate-1-BOP-1000-PFKA-END-1_S25_L004_R2_001.good.fq | 439,278 | 59,965,291 | 100.0% | 136.5 bases | 149 bases | 97.2% |
| total | 3,398,442 | 465,150,112 | 100.0% | 136.9 bases | 149 bases | 96.9% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_000913 | 4,641,652 | 95.2 | 3.6 | 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 | 41151 |
| 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 | 159 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.010 |
| reference sequence | pr(no read start) |
|---|---|
| NC_000913 | 0.73539 |
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 | 05:28:28 12 Sep 2020 | 05:29:19 12 Sep 2020 | 51 seconds |
| Read alignment to reference genome | 05:29:20 12 Sep 2020 | 05:35:38 12 Sep 2020 | 6 minutes 18 seconds |
| Preprocessing alignments for candidate junction identification | 05:35:38 12 Sep 2020 | 05:36:30 12 Sep 2020 | 52 seconds |
| Preliminary analysis of coverage distribution | 05:36:30 12 Sep 2020 | 05:38:20 12 Sep 2020 | 1 minute 50 seconds |
| Identifying junction candidates | 05:38:20 12 Sep 2020 | 05:39:50 12 Sep 2020 | 1 minute 30 seconds |
| Re-alignment to junction candidates | 05:39:50 12 Sep 2020 | 05:41:48 12 Sep 2020 | 1 minute 58 seconds |
| Resolving best read alignments | 05:41:48 12 Sep 2020 | 05:43:09 12 Sep 2020 | 1 minute 21 seconds |
| Creating BAM files | 05:43:09 12 Sep 2020 | 05:44:51 12 Sep 2020 | 1 minute 42 seconds |
| Tabulating error counts | 05:44:51 12 Sep 2020 | 05:45:26 12 Sep 2020 | 35 seconds |
| Re-calibrating base error rates | 05:45:26 12 Sep 2020 | 05:45:29 12 Sep 2020 | 3 seconds |
| Examining read alignment evidence | 05:45:29 12 Sep 2020 | 05:52:32 12 Sep 2020 | 7 minutes 3 seconds |
| Polymorphism statistics | 05:52:32 12 Sep 2020 | 05:52:32 12 Sep 2020 | 0 seconds |
| Output | 05:52:32 12 Sep 2020 | 05:52:49 12 Sep 2020 | 17 seconds |
| Total | 24 minutes 20 seconds | ||
