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 | JADR50_R1_A17_F55_I0_R1_S51_L001_R1_001.good.fq | 403,423 | 51,191,934 | 100.0% | 126.9 bases | 139 bases | 95.6% |
| errors | JADR50_R1_A17_F55_I0_R1_S51_L001_R2_001.good.fq | 403,423 | 51,193,223 | 100.0% | 126.9 bases | 139 bases | 92.4% |
| errors | JADR50_R1_A17_F55_I0_R1_S51_L002_R1_001.good.fq | 407,136 | 51,753,738 | 100.0% | 127.1 bases | 139 bases | 96.4% |
| errors | JADR50_R1_A17_F55_I0_R1_S51_L002_R2_001.good.fq | 407,136 | 51,754,498 | 100.0% | 127.1 bases | 139 bases | 94.0% |
| errors | JADR50_R1_A17_F55_I0_R1_S51_L003_R1_001.good.fq | 406,443 | 51,614,523 | 100.0% | 127.0 bases | 139 bases | 96.2% |
| errors | JADR50_R1_A17_F55_I0_R1_S51_L003_R2_001.good.fq | 406,443 | 51,614,563 | 100.0% | 127.0 bases | 139 bases | 93.9% |
| errors | JADR50_R1_A17_F55_I0_R1_S51_L004_R1_001.good.fq | 404,670 | 51,177,723 | 100.0% | 126.5 bases | 139 bases | 96.8% |
| errors | JADR50_R1_A17_F55_I0_R1_S51_L004_R2_001.good.fq | 404,670 | 51,177,527 | 100.0% | 126.5 bases | 139 bases | 95.0% |
| total | 3,243,344 | 411,477,729 | 100.0% | 126.9 bases | 139 bases | 95.0% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | CP006881 | 4,033,459 | 81.2 | 6.1 | 85.5% | Bacillus subtilis PY79, complete genome. |
| coverage | distribution | pSIJ663_pHT315_araE_xy | 11,568 | 5326.5 | 199.4 | 14.5% | . |
| total | 4,045,027 | 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 | 8339 |
| 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 | 53 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.004 |
| reference sequence | pr(no read start) |
|---|---|
| CP006881 | 0.82343 |
| pSIJ663_pHT315_araE_xy | 0.18274 |
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 | 10:17:40 04 Jun 2021 | 10:18:35 04 Jun 2021 | 55 seconds |
| Read alignment to reference genome | 10:18:35 04 Jun 2021 | 10:25:21 04 Jun 2021 | 6 minutes 46 seconds |
| Preprocessing alignments for candidate junction identification | 10:25:21 04 Jun 2021 | 10:26:06 04 Jun 2021 | 45 seconds |
| Preliminary analysis of coverage distribution | 10:26:06 04 Jun 2021 | 10:27:59 04 Jun 2021 | 1 minute 53 seconds |
| Identifying junction candidates | 10:27:59 04 Jun 2021 | 10:28:00 04 Jun 2021 | 1 second |
| Re-alignment to junction candidates | 10:28:00 04 Jun 2021 | 10:29:40 04 Jun 2021 | 1 minute 40 seconds |
| Resolving best read alignments | 10:29:40 04 Jun 2021 | 10:30:40 04 Jun 2021 | 1 minute 0 seconds |
| Creating BAM files | 10:30:40 04 Jun 2021 | 10:32:22 04 Jun 2021 | 1 minute 42 seconds |
| Tabulating error counts | 10:32:22 04 Jun 2021 | 10:32:59 04 Jun 2021 | 37 seconds |
| Re-calibrating base error rates | 10:32:59 04 Jun 2021 | 10:33:02 04 Jun 2021 | 3 seconds |
| Examining read alignment evidence | 10:33:02 04 Jun 2021 | 11:09:55 04 Jun 2021 | 36 minutes 53 seconds |
| Polymorphism statistics | 11:09:55 04 Jun 2021 | 11:09:57 04 Jun 2021 | 2 seconds |
| Output | 11:09:57 04 Jun 2021 | 11:10:33 04 Jun 2021 | 36 seconds |
| Total | 52 minutes 53 seconds | ||
