mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.35.4 revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| read file | reads | bases | passed filters | average | longest | mapped | |
|---|---|---|---|---|---|---|---|
| errors | JADR40_R1_A5_F60_I0_R1_S73_L001_R1_001.good.fq | 292,971 | 37,408,440 | 100.0% | 127.7 bases | 139 bases | 95.9% |
| errors | JADR40_R1_A5_F60_I0_R1_S73_L001_R2_001.good.fq | 292,971 | 37,411,581 | 100.0% | 127.7 bases | 139 bases | 92.6% |
| errors | JADR40_R1_A5_F60_I0_R1_S73_L002_R1_001.good.fq | 297,405 | 38,018,670 | 100.0% | 127.8 bases | 139 bases | 96.7% |
| errors | JADR40_R1_A5_F60_I0_R1_S73_L002_R2_001.good.fq | 297,405 | 38,021,499 | 100.0% | 127.8 bases | 139 bases | 94.2% |
| errors | JADR40_R1_A5_F60_I0_R1_S73_L003_R1_001.good.fq | 295,756 | 37,720,320 | 100.0% | 127.5 bases | 139 bases | 96.6% |
| errors | JADR40_R1_A5_F60_I0_R1_S73_L003_R2_001.good.fq | 295,756 | 37,721,723 | 100.0% | 127.5 bases | 139 bases | 94.2% |
| errors | JADR40_R1_A5_F60_I0_R1_S73_L004_R1_001.good.fq | 294,388 | 37,450,522 | 100.0% | 127.2 bases | 139 bases | 97.0% |
| errors | JADR40_R1_A5_F60_I0_R1_S73_L004_R2_001.good.fq | 294,388 | 37,453,223 | 100.0% | 127.2 bases | 139 bases | 95.3% |
| total | 2,361,040 | 301,205,978 | 100.0% | 127.6 bases | 139 bases | 95.3% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | BS168_reference_genome | 4,215,606 | 34.2 | 3.5 | 53.0% | Bacillus subtilis subsp. subtilis str. 168 complete genome. |
| coverage | distribution | Exported | 6,538 | 23131.1 | 722.3 | 47.0% | natural circular DNA |
| total | 4,222,144 | 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 | 44572 |
| 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 | 42 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.003 |
| reference sequence | pr(no read start) |
|---|---|
| BS168_reference_genome | 0.90413 |
| Exported | 0.17819 |
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 |
| Minimum probablilty assigned that no mapped read will start at a given position and strand for junction prediction | 0.1 |
| Junction allow suboptimal matches | FALSE |
| 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 | 10:15:29 04 Jun 2021 | 10:16:08 04 Jun 2021 | 39 seconds |
| Read alignment to reference genome | 10:16:08 04 Jun 2021 | 10:21:03 04 Jun 2021 | 4 minutes 55 seconds |
| Preprocessing alignments for candidate junction identification | 10:21:03 04 Jun 2021 | 10:21:34 04 Jun 2021 | 31 seconds |
| Preliminary analysis of coverage distribution | 10:21:34 04 Jun 2021 | 10:22:56 04 Jun 2021 | 1 minute 22 seconds |
| Identifying junction candidates | 10:22:56 04 Jun 2021 | 10:22:57 04 Jun 2021 | 1 second |
| Re-alignment to junction candidates | 10:22:57 04 Jun 2021 | 10:24:56 04 Jun 2021 | 1 minute 59 seconds |
| Resolving best read alignments | 10:24:56 04 Jun 2021 | 10:25:44 04 Jun 2021 | 48 seconds |
| Creating BAM files | 10:25:44 04 Jun 2021 | 10:26:56 04 Jun 2021 | 1 minute 12 seconds |
| Tabulating error counts | 10:26:56 04 Jun 2021 | 10:27:37 04 Jun 2021 | 41 seconds |
| Re-calibrating base error rates | 10:27:37 04 Jun 2021 | 10:27:41 04 Jun 2021 | 4 seconds |
| Examining read alignment evidence | 10:27:41 04 Jun 2021 | 11:04:56 04 Jun 2021 | 37 minutes 15 seconds |
| Polymorphism statistics | 11:04:56 04 Jun 2021 | 11:05:00 04 Jun 2021 | 4 seconds |
| Output | 11:05:00 04 Jun 2021 | 11:06:08 04 Jun 2021 | 1 minute 8 seconds |
| Total | 50 minutes 39 seconds | ||
