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-27-RPE-END-3_S46_L001_R1_001.good.fq | 406,059 | 55,255,484 | 100.0% | 136.1 bases | 148 bases | 98.4% |
| errors | Plate-3-BOP-27-RPE-END-3_S46_L001_R2_001.good.fq | 406,059 | 55,290,075 | 100.0% | 136.2 bases | 148 bases | 97.4% |
| errors | Plate-3-BOP-27-RPE-END-3_S46_L002_R1_001.good.fq | 378,591 | 51,598,809 | 100.0% | 136.3 bases | 148 bases | 98.4% |
| errors | Plate-3-BOP-27-RPE-END-3_S46_L002_R2_001.good.fq | 378,591 | 51,642,854 | 100.0% | 136.4 bases | 148 bases | 97.2% |
| errors | Plate-3-BOP-27-RPE-END-3_S46_L003_R1_001.good.fq | 392,735 | 53,408,364 | 100.0% | 136.0 bases | 148 bases | 98.3% |
| errors | Plate-3-BOP-27-RPE-END-3_S46_L003_R2_001.good.fq | 392,735 | 53,450,781 | 100.0% | 136.1 bases | 148 bases | 97.2% |
| errors | Plate-3-BOP-27-RPE-END-3_S46_L004_R1_001.good.fq | 420,250 | 57,225,486 | 100.0% | 136.2 bases | 148 bases | 98.5% |
| errors | Plate-3-BOP-27-RPE-END-3_S46_L004_R2_001.good.fq | 420,250 | 57,276,087 | 100.0% | 136.3 bases | 148 bases | 97.3% |
| total | 3,195,270 | 435,147,940 | 100.0% | 136.2 bases | 148 bases | 97.9% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_000913 | 4,641,652 | 82.4 | 3.9 | 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 | 37775 |
| 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 | 51 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.003 |
| reference sequence | pr(no read start) |
|---|---|
| NC_000913 | 0.75077 |
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 | 13:41:54 12 Sep 2020 | 13:42:42 12 Sep 2020 | 48 seconds |
| Read alignment to reference genome | 13:42:43 12 Sep 2020 | 13:48:35 12 Sep 2020 | 5 minutes 52 seconds |
| Preprocessing alignments for candidate junction identification | 13:48:35 12 Sep 2020 | 13:49:23 12 Sep 2020 | 48 seconds |
| Preliminary analysis of coverage distribution | 13:49:23 12 Sep 2020 | 13:51:10 12 Sep 2020 | 1 minute 47 seconds |
| Identifying junction candidates | 13:51:10 12 Sep 2020 | 13:52:35 12 Sep 2020 | 1 minute 25 seconds |
| Re-alignment to junction candidates | 13:52:35 12 Sep 2020 | 13:54:21 12 Sep 2020 | 1 minute 46 seconds |
| Resolving best read alignments | 13:54:21 12 Sep 2020 | 13:55:36 12 Sep 2020 | 1 minute 15 seconds |
| Creating BAM files | 13:55:36 12 Sep 2020 | 13:57:14 12 Sep 2020 | 1 minute 38 seconds |
| Tabulating error counts | 13:57:14 12 Sep 2020 | 13:57:47 12 Sep 2020 | 33 seconds |
| Re-calibrating base error rates | 13:57:47 12 Sep 2020 | 13:57:50 12 Sep 2020 | 3 seconds |
| Examining read alignment evidence | 13:57:50 12 Sep 2020 | 14:25:19 12 Sep 2020 | 27 minutes 29 seconds |
| Polymorphism statistics | 14:25:19 12 Sep 2020 | 14:25:20 12 Sep 2020 | 1 second |
| Output | 14:25:20 12 Sep 2020 | 14:25:44 12 Sep 2020 | 24 seconds |
| Total | 43 minutes 49 seconds | ||
