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_R3_A7_F57_I0_R1_S85_L001_R1_001.good.fq | 300,729 | 38,052,508 | 100.0% | 126.5 bases | 139 bases | 95.7% |
| errors | JADR40_R3_A7_F57_I0_R1_S85_L001_R2_001.good.fq | 300,729 | 38,052,991 | 100.0% | 126.5 bases | 139 bases | 92.5% |
| errors | JADR40_R3_A7_F57_I0_R1_S85_L002_R1_001.good.fq | 302,694 | 38,345,471 | 100.0% | 126.7 bases | 139 bases | 96.4% |
| errors | JADR40_R3_A7_F57_I0_R1_S85_L002_R2_001.good.fq | 302,694 | 38,346,180 | 100.0% | 126.7 bases | 139 bases | 94.2% |
| errors | JADR40_R3_A7_F57_I0_R1_S85_L003_R1_001.good.fq | 302,278 | 38,239,684 | 100.0% | 126.5 bases | 139 bases | 96.4% |
| errors | JADR40_R3_A7_F57_I0_R1_S85_L003_R2_001.good.fq | 302,278 | 38,240,971 | 100.0% | 126.5 bases | 139 bases | 94.2% |
| errors | JADR40_R3_A7_F57_I0_R1_S85_L004_R1_001.good.fq | 300,421 | 37,838,369 | 100.0% | 126.0 bases | 139 bases | 96.9% |
| errors | JADR40_R3_A7_F57_I0_R1_S85_L004_R2_001.good.fq | 300,421 | 37,839,692 | 100.0% | 126.0 bases | 139 bases | 95.3% |
| total | 2,412,244 | 304,955,866 | 100.0% | 126.4 bases | 139 bases | 95.2% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | BS168_reference_genome | 4,215,606 | 54.6 | 4.6 | 81.1% | Bacillus subtilis subsp. subtilis str. 168 complete genome. |
| coverage | distribution | Exported | 6,538 | 8612.3 | 284.2 | 18.9% | 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 | 11514 |
| 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 | 70 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.005 |
| reference sequence | pr(no read start) |
|---|---|
| BS168_reference_genome | 0.86343 |
| Exported | 0.13835 |
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 | 10:16:45 04 Jun 2021 | 10:17:26 04 Jun 2021 | 41 seconds |
| Read alignment to reference genome | 10:17:26 04 Jun 2021 | 10:22:54 04 Jun 2021 | 5 minutes 28 seconds |
| Preprocessing alignments for candidate junction identification | 10:22:54 04 Jun 2021 | 10:23:28 04 Jun 2021 | 34 seconds |
| Preliminary analysis of coverage distribution | 10:23:28 04 Jun 2021 | 10:24:52 04 Jun 2021 | 1 minute 24 seconds |
| Identifying junction candidates | 10:24:52 04 Jun 2021 | 10:24:53 04 Jun 2021 | 1 second |
| Re-alignment to junction candidates | 10:24:53 04 Jun 2021 | 10:26:36 04 Jun 2021 | 1 minute 43 seconds |
| Resolving best read alignments | 10:26:36 04 Jun 2021 | 10:27:23 04 Jun 2021 | 47 seconds |
| Creating BAM files | 10:27:23 04 Jun 2021 | 10:28:38 04 Jun 2021 | 1 minute 15 seconds |
| Tabulating error counts | 10:28:38 04 Jun 2021 | 10:29:13 04 Jun 2021 | 35 seconds |
| Re-calibrating base error rates | 10:29:13 04 Jun 2021 | 10:29:17 04 Jun 2021 | 4 seconds |
| Examining read alignment evidence | 10:29:17 04 Jun 2021 | 10:56:11 04 Jun 2021 | 26 minutes 54 seconds |
| Polymorphism statistics | 10:56:11 04 Jun 2021 | 10:56:14 04 Jun 2021 | 3 seconds |
| Output | 10:56:14 04 Jun 2021 | 10:56:52 04 Jun 2021 | 38 seconds |
| Total | 40 minutes 7 seconds | ||
