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 | JADR46_R3_A11_F58_I1_R1_S88_L001_R1_001.good.fq | 294,793 | 37,477,018 | 100.0% | 127.1 bases | 139 bases | 95.8% |
| errors | JADR46_R3_A11_F58_I1_R1_S88_L001_R2_001.good.fq | 294,793 | 37,478,990 | 100.0% | 127.1 bases | 139 bases | 92.9% |
| errors | JADR46_R3_A11_F58_I1_R1_S88_L002_R1_001.good.fq | 298,423 | 37,995,757 | 100.0% | 127.3 bases | 139 bases | 96.5% |
| errors | JADR46_R3_A11_F58_I1_R1_S88_L002_R2_001.good.fq | 298,423 | 37,996,853 | 100.0% | 127.3 bases | 139 bases | 94.3% |
| errors | JADR46_R3_A11_F58_I1_R1_S88_L003_R1_001.good.fq | 296,257 | 37,650,348 | 100.0% | 127.1 bases | 139 bases | 96.5% |
| errors | JADR46_R3_A11_F58_I1_R1_S88_L003_R2_001.good.fq | 296,257 | 37,651,724 | 100.0% | 127.1 bases | 139 bases | 94.4% |
| errors | JADR46_R3_A11_F58_I1_R1_S88_L004_R1_001.good.fq | 295,054 | 37,383,977 | 100.0% | 126.7 bases | 139 bases | 97.0% |
| errors | JADR46_R3_A11_F58_I1_R1_S88_L004_R2_001.good.fq | 295,054 | 37,386,040 | 100.0% | 126.7 bases | 139 bases | 95.4% |
| total | 2,369,054 | 301,020,707 | 100.0% | 127.1 bases | 139 bases | 95.4% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | CP006881 | 4,033,459 | 63.0 | 5.0 | 89.7% | Bacillus subtilis PY79, complete genome. |
| coverage | distribution | Exported | 6,538 | 4580.8 | 172.0 | 10.3% | natural circular DNA |
| total | 4,039,997 | 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 | 6142 |
| 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 | 28 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.002 |
| reference sequence | pr(no read start) |
|---|---|
| CP006881 | 0.84997 |
| Exported | 0.19693 |
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 | ≤ 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 | 0.75 |
| 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 | 10 |
| Polymorphism frequency cutoff | 0.2 |
| Polymorphism minimum variant coverage each strand | OFF |
| 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 | OFF |
| Skip base substitutions when they create a homopolymer flanked on each side by | OFF |
| program | version |
|---|---|
| bowtie2 | 2.2.6 |
| R | 3.4.4 |
| step | start | end | elapsed |
|---|---|---|---|
| Read and reference sequence file input | 10:15:20 04 Jun 2021 | 10:16:00 04 Jun 2021 | 40 seconds |
| Read alignment to reference genome | 10:16:00 04 Jun 2021 | 10:20:48 04 Jun 2021 | 4 minutes 48 seconds |
| Preprocessing alignments for candidate junction identification | 10:20:48 04 Jun 2021 | 10:21:19 04 Jun 2021 | 31 seconds |
| Preliminary analysis of coverage distribution | 10:21:19 04 Jun 2021 | 10:22:40 04 Jun 2021 | 1 minute 21 seconds |
| Identifying junction candidates | 10:22:40 04 Jun 2021 | 10:22:41 04 Jun 2021 | 1 second |
| Re-alignment to junction candidates | 10:22:41 04 Jun 2021 | 10:23:52 04 Jun 2021 | 1 minute 11 seconds |
| Resolving best read alignments | 10:23:52 04 Jun 2021 | 10:24:36 04 Jun 2021 | 44 seconds |
| Creating BAM files | 10:24:36 04 Jun 2021 | 10:25:49 04 Jun 2021 | 1 minute 13 seconds |
| Tabulating error counts | 10:25:49 04 Jun 2021 | 10:26:15 04 Jun 2021 | 26 seconds |
| Re-calibrating base error rates | 10:26:15 04 Jun 2021 | 10:26:19 04 Jun 2021 | 4 seconds |
| Examining read alignment evidence | 10:26:19 04 Jun 2021 | 10:31:52 04 Jun 2021 | 5 minutes 33 seconds |
| Polymorphism statistics | 10:31:52 04 Jun 2021 | 10:31:53 04 Jun 2021 | 1 second |
| Output | 10:31:53 04 Jun 2021 | 10:32:13 04 Jun 2021 | 20 seconds |
| Total | 16 minutes 53 seconds | ||
