mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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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-ACEF-END-2_S72_L001_R1_001.good.fq | 472,463 | 65,257,362 | 100.0% | 138.1 bases | 149 bases | 93.6% |
| errors | Plate-3-BOP-27-ACEF-END-2_S72_L001_R2_001.good.fq | 472,463 | 64,982,145 | 100.0% | 137.5 bases | 149 bases | 94.2% |
| errors | Plate-3-BOP-27-ACEF-END-2_S72_L002_R1_001.good.fq | 432,086 | 59,711,980 | 100.0% | 138.2 bases | 149 bases | 93.7% |
| errors | Plate-3-BOP-27-ACEF-END-2_S72_L002_R2_001.good.fq | 432,086 | 59,478,645 | 100.0% | 137.7 bases | 149 bases | 94.0% |
| errors | Plate-3-BOP-27-ACEF-END-2_S72_L003_R1_001.good.fq | 459,657 | 63,463,281 | 100.0% | 138.1 bases | 149 bases | 93.5% |
| errors | Plate-3-BOP-27-ACEF-END-2_S72_L003_R2_001.good.fq | 459,657 | 63,198,885 | 100.0% | 137.5 bases | 149 bases | 94.0% |
| errors | Plate-3-BOP-27-ACEF-END-2_S72_L004_R1_001.good.fq | 475,526 | 65,658,812 | 100.0% | 138.1 bases | 149 bases | 93.7% |
| errors | Plate-3-BOP-27-ACEF-END-2_S72_L004_R2_001.good.fq | 475,526 | 65,418,212 | 100.0% | 137.6 bases | 149 bases | 94.0% |
| total | 3,679,464 | 507,169,322 | 100.0% | 137.8 bases | 149 bases | 93.8% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_000913 | 4,641,652 | 101.7 | 3.5 | 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 | 29822 |
| 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 | 204 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.013 |
| reference sequence | pr(no read start) |
|---|---|
| NC_000913 | 0.72502 |
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 | 18:59:15 12 Sep 2020 | 19:00:11 12 Sep 2020 | 56 seconds |
| Read alignment to reference genome | 19:00:11 12 Sep 2020 | 19:07:04 12 Sep 2020 | 6 minutes 53 seconds |
| Preprocessing alignments for candidate junction identification | 19:07:04 12 Sep 2020 | 19:07:59 12 Sep 2020 | 55 seconds |
| Preliminary analysis of coverage distribution | 19:07:59 12 Sep 2020 | 19:09:59 12 Sep 2020 | 2 minutes 0 seconds |
| Identifying junction candidates | 19:09:59 12 Sep 2020 | 19:11:20 12 Sep 2020 | 1 minute 21 seconds |
| Re-alignment to junction candidates | 19:11:20 12 Sep 2020 | 19:13:32 12 Sep 2020 | 2 minutes 12 seconds |
| Resolving best read alignments | 19:13:32 12 Sep 2020 | 19:14:59 12 Sep 2020 | 1 minute 27 seconds |
| Creating BAM files | 19:14:59 12 Sep 2020 | 19:16:49 12 Sep 2020 | 1 minute 50 seconds |
| Tabulating error counts | 19:16:49 12 Sep 2020 | 19:17:27 12 Sep 2020 | 38 seconds |
| Re-calibrating base error rates | 19:17:27 12 Sep 2020 | 19:17:30 12 Sep 2020 | 3 seconds |
| Examining read alignment evidence | 19:17:30 12 Sep 2020 | 19:44:56 12 Sep 2020 | 27 minutes 26 seconds |
| Polymorphism statistics | 19:44:56 12 Sep 2020 | 19:44:58 12 Sep 2020 | 2 seconds |
| Output | 19:44:58 12 Sep 2020 | 19:45:49 12 Sep 2020 | 51 seconds |
| Total | 46 minutes 34 seconds | ||
