mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.32.0b
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| read file | reads | bases | passed filters | average | longest | mapped | |
|---|---|---|---|---|---|---|---|
| errors | A12_F037_R1_F18_I40_S2176_L001_R1_001.good.fq | 1,905,514 | 283,921,586 | 100.0% | 149.0 bases | 149 bases | 98.4% |
| errors | A12_F037_R1_F18_I40_S2176_L001_R2_001.good.fq | 1,773,338 | 253,587,334 | 100.0% | 143.0 bases | 143 bases | 97.7% |
| total | 3,678,852 | 537,508,920 | 100.0% | 146.1 bases | 149 bases | 98.0% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | CP009273 | 4,631,469 | 113.1 | 2.2 | 100.0% | Escherichia coli BW25113, complete genome. |
| total | 4,631,469 | 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 | 25600 |
| 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 | 549 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.036 |
| reference sequence | pr(no read start) |
|---|---|
| CP009273 | 0.72152 |
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 | 0.8 |
| Consensus minimum coverage each strand | OFF |
| Polymorphism E-value cutoff | 10 |
| Polymorphism frequency cutoff | 0.2 |
| Polymorphism minimum coverage each strand | 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 | 2.3.2 |
| R | 3.4.2 |
| step | start | end | elapsed |
|---|---|---|---|
| Read and reference sequence file input | 00:27:31 16 Jun 2018 | 00:28:17 16 Jun 2018 | 46 seconds |
| Read alignment to reference genome | 00:28:17 16 Jun 2018 | 00:31:50 16 Jun 2018 | 3 minutes 33 seconds |
| Preprocessing alignments for candidate junction identification | 00:31:50 16 Jun 2018 | 00:32:28 16 Jun 2018 | 38 seconds |
| Preliminary analysis of coverage distribution | 00:32:28 16 Jun 2018 | 00:34:11 16 Jun 2018 | 1 minute 43 seconds |
| Identifying junction candidates | 00:34:11 16 Jun 2018 | 00:34:19 16 Jun 2018 | 8 seconds |
| Re-alignment to junction candidates | 00:34:19 16 Jun 2018 | 00:35:12 16 Jun 2018 | 53 seconds |
| Resolving alignments with junction candidates | 00:35:12 16 Jun 2018 | 00:36:15 16 Jun 2018 | 1 minute 3 seconds |
| Creating BAM files | 00:36:15 16 Jun 2018 | 00:37:49 16 Jun 2018 | 1 minute 34 seconds |
| Tabulating error counts | 00:37:49 16 Jun 2018 | 00:38:33 16 Jun 2018 | 44 seconds |
| Re-calibrating base error rates | 00:38:33 16 Jun 2018 | 00:38:34 16 Jun 2018 | 1 second |
| Examining read alignment evidence | 00:38:34 16 Jun 2018 | 00:47:39 16 Jun 2018 | 9 minutes 5 seconds |
| Polymorphism statistics | 00:47:39 16 Jun 2018 | 00:47:39 16 Jun 2018 | 0 seconds |
| Output | 00:47:39 16 Jun 2018 | 00:47:55 16 Jun 2018 | 16 seconds |
| Total | 20 minutes 24 seconds | ||
