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 | JADR49_R3_A15_F58_I0_R1_S86_L001_R1_001.good.fq | 350,244 | 44,407,466 | 100.0% | 126.8 bases | 139 bases | 95.5% |
| errors | JADR49_R3_A15_F58_I0_R1_S86_L001_R2_001.good.fq | 350,244 | 44,409,700 | 100.0% | 126.8 bases | 139 bases | 92.1% |
| errors | JADR49_R3_A15_F58_I0_R1_S86_L002_R1_001.good.fq | 353,161 | 44,855,865 | 100.0% | 127.0 bases | 139 bases | 96.2% |
| errors | JADR49_R3_A15_F58_I0_R1_S86_L002_R2_001.good.fq | 353,161 | 44,856,010 | 100.0% | 127.0 bases | 139 bases | 93.7% |
| errors | JADR49_R3_A15_F58_I0_R1_S86_L003_R1_001.good.fq | 353,074 | 44,782,677 | 100.0% | 126.8 bases | 139 bases | 96.1% |
| errors | JADR49_R3_A15_F58_I0_R1_S86_L003_R2_001.good.fq | 353,074 | 44,783,815 | 100.0% | 126.8 bases | 139 bases | 93.7% |
| errors | JADR49_R3_A15_F58_I0_R1_S86_L004_R1_001.good.fq | 351,358 | 44,397,350 | 100.0% | 126.4 bases | 139 bases | 96.7% |
| errors | JADR49_R3_A15_F58_I0_R1_S86_L004_R2_001.good.fq | 351,358 | 44,398,313 | 100.0% | 126.4 bases | 139 bases | 94.9% |
| total | 2,815,674 | 356,891,196 | 100.0% | 126.8 bases | 139 bases | 94.9% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | CP006881 | 4,033,459 | 66.2 | 5.2 | 81.7% | Bacillus subtilis PY79, complete genome. |
| coverage | distribution | pSIJ663_pHT315_araE_xy | 11,568 | 10360.1 | 482.0 | 18.3% | . |
| 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 | 19699 |
| 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 | 60 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.004 |
| reference sequence | pr(no read start) |
|---|---|
| CP006881 | 0.84453 |
| pSIJ663_pHT315_araE_xy | 0.43910 |
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 | 10:16:23 04 Jun 2021 | 10:17:10 04 Jun 2021 | 47 seconds |
| Read alignment to reference genome | 10:17:10 04 Jun 2021 | 10:22:58 04 Jun 2021 | 5 minutes 48 seconds |
| Preprocessing alignments for candidate junction identification | 10:22:58 04 Jun 2021 | 10:23:36 04 Jun 2021 | 38 seconds |
| Preliminary analysis of coverage distribution | 10:23:36 04 Jun 2021 | 10:25:15 04 Jun 2021 | 1 minute 39 seconds |
| Identifying junction candidates | 10:25:15 04 Jun 2021 | 10:25:16 04 Jun 2021 | 1 second |
| Re-alignment to junction candidates | 10:25:16 04 Jun 2021 | 10:26:58 04 Jun 2021 | 1 minute 42 seconds |
| Resolving best read alignments | 10:26:58 04 Jun 2021 | 10:27:51 04 Jun 2021 | 53 seconds |
| Creating BAM files | 10:27:51 04 Jun 2021 | 10:29:19 04 Jun 2021 | 1 minute 28 seconds |
| Tabulating error counts | 10:29:19 04 Jun 2021 | 10:29:53 04 Jun 2021 | 34 seconds |
| Re-calibrating base error rates | 10:29:53 04 Jun 2021 | 10:29:57 04 Jun 2021 | 4 seconds |
| Examining read alignment evidence | 10:29:57 04 Jun 2021 | 11:02:29 04 Jun 2021 | 32 minutes 32 seconds |
| Polymorphism statistics | 11:02:29 04 Jun 2021 | 11:02:30 04 Jun 2021 | 1 second |
| Output | 11:02:30 04 Jun 2021 | 11:03:13 04 Jun 2021 | 43 seconds |
| Total | 46 minutes 50 seconds | ||
