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-1_S69_L001_R1_001.good.fq | 358,656 | 51,587,163 | 100.0% | 143.8 bases | 149 bases | 97.9% |
| errors | Plate-3-BOP-1000-PFKA-END-1_S69_L001_R2_001.good.fq | 358,656 | 51,457,826 | 100.0% | 143.5 bases | 149 bases | 97.6% |
| errors | Plate-3-BOP-1000-PFKA-END-1_S69_L002_R1_001.good.fq | 334,341 | 48,102,675 | 100.0% | 143.9 bases | 149 bases | 97.9% |
| errors | Plate-3-BOP-1000-PFKA-END-1_S69_L002_R2_001.good.fq | 334,341 | 47,996,370 | 100.0% | 143.6 bases | 149 bases | 97.3% |
| errors | Plate-3-BOP-1000-PFKA-END-1_S69_L003_R1_001.good.fq | 346,123 | 49,725,727 | 100.0% | 143.7 bases | 149 bases | 97.8% |
| errors | Plate-3-BOP-1000-PFKA-END-1_S69_L003_R2_001.good.fq | 346,123 | 49,603,296 | 100.0% | 143.3 bases | 149 bases | 97.4% |
| errors | Plate-3-BOP-1000-PFKA-END-1_S69_L004_R1_001.good.fq | 351,182 | 50,444,308 | 100.0% | 143.6 bases | 149 bases | 98.0% |
| errors | Plate-3-BOP-1000-PFKA-END-1_S69_L004_R2_001.good.fq | 351,182 | 50,329,211 | 100.0% | 143.3 bases | 149 bases | 97.5% |
| total | 2,780,604 | 399,246,576 | 100.0% | 143.6 bases | 149 bases | 97.7% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_000913 | 4,641,652 | 83.1 | 2.9 | 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 | 19202 |
| 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 | 40 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.003 |
| reference sequence | pr(no read start) |
|---|---|
| NC_000913 | 0.77308 |
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 | 2.3.4.1 |
| R | 3.4.4 |
| step | start | end | elapsed |
|---|---|---|---|
| Read and reference sequence file input | 01:27:28 27 Feb 2020 | 01:28:10 27 Feb 2020 | 42 seconds |
| Read alignment to reference genome | 01:28:10 27 Feb 2020 | 01:33:49 27 Feb 2020 | 5 minutes 39 seconds |
| Preprocessing alignments for candidate junction identification | 01:33:49 27 Feb 2020 | 01:34:28 27 Feb 2020 | 39 seconds |
| Preliminary analysis of coverage distribution | 01:34:28 27 Feb 2020 | 01:36:10 27 Feb 2020 | 1 minute 42 seconds |
| Identifying junction candidates | 01:36:10 27 Feb 2020 | 01:36:18 27 Feb 2020 | 8 seconds |
| Re-alignment to junction candidates | 01:36:18 27 Feb 2020 | 01:37:59 27 Feb 2020 | 1 minute 41 seconds |
| Resolving best read alignments | 01:37:59 27 Feb 2020 | 01:39:01 27 Feb 2020 | 1 minute 2 seconds |
| Creating BAM files | 01:39:01 27 Feb 2020 | 01:40:34 27 Feb 2020 | 1 minute 33 seconds |
| Tabulating error counts | 01:40:34 27 Feb 2020 | 01:41:05 27 Feb 2020 | 31 seconds |
| Re-calibrating base error rates | 01:41:05 27 Feb 2020 | 01:41:08 27 Feb 2020 | 3 seconds |
| Examining read alignment evidence | 01:41:08 27 Feb 2020 | 02:05:39 27 Feb 2020 | 24 minutes 31 seconds |
| Polymorphism statistics | 02:05:39 27 Feb 2020 | 02:05:40 27 Feb 2020 | 1 second |
| Output | 02:05:40 27 Feb 2020 | 02:06:01 27 Feb 2020 | 21 seconds |
| Total | 38 minutes 33 seconds | ||
