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-SUCB-END-3_S59_L001_R1_001.good.fq | 471,572 | 65,535,349 | 100.0% | 139.0 bases | 148 bases | 99.1% |
| errors | Plate-3-BOP-1000-SUCB-END-3_S59_L001_R2_001.good.fq | 471,572 | 65,556,364 | 100.0% | 139.0 bases | 148 bases | 98.3% |
| errors | Plate-3-BOP-1000-SUCB-END-3_S59_L002_R1_001.good.fq | 443,601 | 61,680,616 | 100.0% | 139.0 bases | 148 bases | 99.2% |
| errors | Plate-3-BOP-1000-SUCB-END-3_S59_L002_R2_001.good.fq | 443,601 | 61,708,965 | 100.0% | 139.1 bases | 148 bases | 98.1% |
| errors | Plate-3-BOP-1000-SUCB-END-3_S59_L003_R1_001.good.fq | 459,028 | 63,709,668 | 100.0% | 138.8 bases | 148 bases | 99.1% |
| errors | Plate-3-BOP-1000-SUCB-END-3_S59_L003_R2_001.good.fq | 459,028 | 63,739,224 | 100.0% | 138.9 bases | 148 bases | 98.1% |
| errors | Plate-3-BOP-1000-SUCB-END-3_S59_L004_R1_001.good.fq | 485,050 | 67,357,544 | 100.0% | 138.9 bases | 148 bases | 99.2% |
| errors | Plate-3-BOP-1000-SUCB-END-3_S59_L004_R2_001.good.fq | 485,050 | 67,394,468 | 100.0% | 138.9 bases | 148 bases | 98.2% |
| total | 3,718,502 | 516,682,198 | 100.0% | 138.9 bases | 148 bases | 98.6% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_000913 | 4,641,652 | 105.5 | 4.7 | 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 | 19515 |
| 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 | 42 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.003 |
| reference sequence | pr(no read start) |
|---|---|
| NC_000913 | 0.71846 |
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 | 2.2.6 |
| R | 3.4.4 |
| step | start | end | elapsed |
|---|---|---|---|
| Read and reference sequence file input | 19:45:50 12 Sep 2020 | 19:46:47 12 Sep 2020 | 57 seconds |
| Read alignment to reference genome | 19:46:47 12 Sep 2020 | 19:53:43 12 Sep 2020 | 6 minutes 56 seconds |
| Preprocessing alignments for candidate junction identification | 19:53:43 12 Sep 2020 | 19:54:41 12 Sep 2020 | 58 seconds |
| Preliminary analysis of coverage distribution | 19:54:41 12 Sep 2020 | 19:56:48 12 Sep 2020 | 2 minutes 7 seconds |
| Identifying junction candidates | 19:56:48 12 Sep 2020 | 19:57:17 12 Sep 2020 | 29 seconds |
| Re-alignment to junction candidates | 19:57:17 12 Sep 2020 | 19:59:23 12 Sep 2020 | 2 minutes 6 seconds |
| Resolving best read alignments | 19:59:23 12 Sep 2020 | 20:00:51 12 Sep 2020 | 1 minute 28 seconds |
| Creating BAM files | 20:00:51 12 Sep 2020 | 20:02:48 12 Sep 2020 | 1 minute 57 seconds |
| Tabulating error counts | 20:02:48 12 Sep 2020 | 20:03:28 12 Sep 2020 | 40 seconds |
| Re-calibrating base error rates | 20:03:28 12 Sep 2020 | 20:03:31 12 Sep 2020 | 3 seconds |
| Examining read alignment evidence | 20:03:31 12 Sep 2020 | 20:38:56 12 Sep 2020 | 35 minutes 25 seconds |
| Polymorphism statistics | 20:38:56 12 Sep 2020 | 20:38:57 12 Sep 2020 | 1 second |
| Output | 20:38:57 12 Sep 2020 | 20:39:19 12 Sep 2020 | 22 seconds |
| Total | 53 minutes 29 seconds | ||
