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 | TF_KALE_crp_A2_F19_I1_R1_S16_L001_R1_001.good.fq | 286,457 | 37,623,631 | 100.0% | 131.3 bases | 139 bases | 97.9% |
| errors | TF_KALE_crp_A2_F19_I1_R1_S16_L001_R2_001.good.fq | 286,457 | 37,624,180 | 100.0% | 131.3 bases | 139 bases | 96.1% |
| errors | TF_KALE_crp_A2_F19_I1_R1_S16_L002_R1_001.good.fq | 285,867 | 36,978,347 | 100.0% | 129.4 bases | 137 bases | 98.4% |
| errors | TF_KALE_crp_A2_F19_I1_R1_S16_L002_R2_001.good.fq | 285,867 | 36,978,592 | 100.0% | 129.4 bases | 137 bases | 97.0% |
| errors | TF_KALE_crp_A2_F19_I1_R1_S16_L003_R1_001.good.fq | 285,845 | 36,920,609 | 100.0% | 129.2 bases | 137 bases | 98.3% |
| errors | TF_KALE_crp_A2_F19_I1_R1_S16_L003_R2_001.good.fq | 285,845 | 36,920,553 | 100.0% | 129.2 bases | 137 bases | 97.3% |
| errors | TF_KALE_crp_A2_F19_I1_R1_S16_L004_R1_001.good.fq | 293,451 | 37,877,826 | 100.0% | 129.1 bases | 137 bases | 98.6% |
| errors | TF_KALE_crp_A2_F19_I1_R1_S16_L004_R2_001.good.fq | 293,451 | 37,878,390 | 100.0% | 129.1 bases | 137 bases | 97.8% |
| total | 2,303,240 | 298,802,128 | 100.0% | 129.7 bases | 139 bases | 97.7% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_000913 | 4,641,652 | 62.5 | 3.4 | 100.0% | Escherichia coli str. K-12 substr. MG1655, complete genome. |
| total | 4,641,652 | 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 | 1371 |
| 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 | 99 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.006 |
| reference sequence | pr(no read start) |
|---|---|
| NC_000913 | 0.84350 |
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 | 21:18:20 22 Apr 2021 | 21:18:59 22 Apr 2021 | 39 seconds |
| Read alignment to reference genome | 21:18:59 22 Apr 2021 | 21:23:43 22 Apr 2021 | 4 minutes 44 seconds |
| Preprocessing alignments for candidate junction identification | 21:23:43 22 Apr 2021 | 21:24:10 22 Apr 2021 | 27 seconds |
| Preliminary analysis of coverage distribution | 21:24:10 22 Apr 2021 | 21:25:29 22 Apr 2021 | 1 minute 19 seconds |
| Identifying junction candidates | 21:25:29 22 Apr 2021 | 21:25:30 22 Apr 2021 | 1 second |
| Re-alignment to junction candidates | 21:25:30 22 Apr 2021 | 21:26:39 22 Apr 2021 | 1 minute 9 seconds |
| Resolving best read alignments | 21:26:39 22 Apr 2021 | 21:27:18 22 Apr 2021 | 39 seconds |
| Creating BAM files | 21:27:18 22 Apr 2021 | 21:28:30 22 Apr 2021 | 1 minute 12 seconds |
| Tabulating error counts | 21:28:30 22 Apr 2021 | 21:28:57 22 Apr 2021 | 27 seconds |
| Re-calibrating base error rates | 21:28:57 22 Apr 2021 | 21:29:00 22 Apr 2021 | 3 seconds |
| Examining read alignment evidence | 21:29:00 22 Apr 2021 | 21:34:29 22 Apr 2021 | 5 minutes 29 seconds |
| Polymorphism statistics | 21:34:29 22 Apr 2021 | 21:34:30 22 Apr 2021 | 1 second |
| Output | 21:34:30 22 Apr 2021 | 21:34:38 22 Apr 2021 | 8 seconds |
| Total | 16 minutes 18 seconds | ||
