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-ACNB-END-1_S12_L001_R1_001.good.fq | 384,652 | 54,698,830 | 100.0% | 142.2 bases | 149 bases | 98.4% |
| errors | Plate-1-BOP-1000-ACNB-END-1_S12_L001_R2_001.good.fq | 384,652 | 54,530,468 | 100.0% | 141.8 bases | 149 bases | 98.4% |
| errors | Plate-1-BOP-1000-ACNB-END-1_S12_L002_R1_001.good.fq | 357,981 | 50,914,805 | 100.0% | 142.2 bases | 149 bases | 98.4% |
| errors | Plate-1-BOP-1000-ACNB-END-1_S12_L002_R2_001.good.fq | 357,981 | 50,771,976 | 100.0% | 141.8 bases | 149 bases | 98.2% |
| errors | Plate-1-BOP-1000-ACNB-END-1_S12_L003_R1_001.good.fq | 373,718 | 53,133,801 | 100.0% | 142.2 bases | 149 bases | 98.2% |
| errors | Plate-1-BOP-1000-ACNB-END-1_S12_L003_R2_001.good.fq | 373,718 | 52,974,680 | 100.0% | 141.8 bases | 149 bases | 98.3% |
| errors | Plate-1-BOP-1000-ACNB-END-1_S12_L004_R1_001.good.fq | 393,503 | 55,904,077 | 100.0% | 142.1 bases | 149 bases | 98.4% |
| errors | Plate-1-BOP-1000-ACNB-END-1_S12_L004_R2_001.good.fq | 393,503 | 55,746,373 | 100.0% | 141.7 bases | 149 bases | 98.3% |
| total | 3,019,708 | 428,675,010 | 100.0% | 142.0 bases | 149 bases | 98.3% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_000913 | 4,641,652 | 89.3 | 8.0 | 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 | 7766 |
| 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 | 706 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.046 |
| reference sequence | pr(no read start) |
|---|---|
| NC_000913 | 0.75639 |
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 | 2.3.4.1 |
| R | 3.4.4 |
| step | start | end | elapsed |
|---|---|---|---|
| Read and reference sequence file input | 20:54:43 29 Feb 2020 | 20:55:27 29 Feb 2020 | 44 seconds |
| Read alignment to reference genome | 20:55:28 29 Feb 2020 | 21:01:31 29 Feb 2020 | 6 minutes 3 seconds |
| Preprocessing alignments for candidate junction identification | 21:01:31 29 Feb 2020 | 21:02:14 29 Feb 2020 | 43 seconds |
| Preliminary analysis of coverage distribution | 21:02:14 29 Feb 2020 | 21:04:03 29 Feb 2020 | 1 minute 49 seconds |
| Identifying junction candidates | 21:04:03 29 Feb 2020 | 21:04:10 29 Feb 2020 | 7 seconds |
| Re-alignment to junction candidates | 21:04:10 29 Feb 2020 | 21:06:22 29 Feb 2020 | 2 minutes 12 seconds |
| Resolving best read alignments | 21:06:22 29 Feb 2020 | 21:07:28 29 Feb 2020 | 1 minute 6 seconds |
| Creating BAM files | 21:07:28 29 Feb 2020 | 21:09:09 29 Feb 2020 | 1 minute 41 seconds |
| Tabulating error counts | 21:09:09 29 Feb 2020 | 21:09:42 29 Feb 2020 | 33 seconds |
| Re-calibrating base error rates | 21:09:42 29 Feb 2020 | 21:09:45 29 Feb 2020 | 3 seconds |
| Examining read alignment evidence | 21:09:45 29 Feb 2020 | 21:16:04 29 Feb 2020 | 6 minutes 19 seconds |
| Polymorphism statistics | 21:16:04 29 Feb 2020 | 21:16:04 29 Feb 2020 | 0 seconds |
| Output | 21:16:04 29 Feb 2020 | 21:16:21 29 Feb 2020 | 17 seconds |
| Total | 21 minutes 37 seconds | ||
