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_A1_F86_I4_R1_S79_L001_R1_001.good.fq | 363,265 | 46,898,163 | 100.0% | 129.1 bases | 137 bases | 97.7% |
| errors | TF_KALE_crp_A1_F86_I4_R1_S79_L001_R2_001.good.fq | 363,265 | 46,897,896 | 100.0% | 129.1 bases | 137 bases | 96.0% |
| errors | TF_KALE_crp_A1_F86_I4_R1_S79_L002_R1_001.good.fq | 363,163 | 46,942,852 | 100.0% | 129.3 bases | 137 bases | 98.3% |
| errors | TF_KALE_crp_A1_F86_I4_R1_S79_L002_R2_001.good.fq | 363,163 | 46,945,243 | 100.0% | 129.3 bases | 137 bases | 97.2% |
| errors | TF_KALE_crp_A1_F86_I4_R1_S79_L003_R1_001.good.fq | 363,189 | 46,862,995 | 100.0% | 129.0 bases | 137 bases | 98.3% |
| errors | TF_KALE_crp_A1_F86_I4_R1_S79_L003_R2_001.good.fq | 363,189 | 46,864,686 | 100.0% | 129.0 bases | 137 bases | 97.4% |
| errors | TF_KALE_crp_A1_F86_I4_R1_S79_L004_R1_001.good.fq | 373,261 | 48,108,263 | 100.0% | 128.9 bases | 137 bases | 98.7% |
| errors | TF_KALE_crp_A1_F86_I4_R1_S79_L004_R2_001.good.fq | 373,261 | 48,109,466 | 100.0% | 128.9 bases | 137 bases | 97.9% |
| total | 2,925,756 | 377,629,564 | 100.0% | 129.1 bases | 137 bases | 97.7% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_000913 | 4,641,652 | 78.8 | 4.2 | 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 | 1500 |
| 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 | 93 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.006 |
| reference sequence | pr(no read start) |
|---|---|
| NC_000913 | 0.82822 |
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 | 21:20:23 22 Apr 2021 | 21:21:12 22 Apr 2021 | 49 seconds |
| Read alignment to reference genome | 21:21:12 22 Apr 2021 | 21:27:14 22 Apr 2021 | 6 minutes 2 seconds |
| Preprocessing alignments for candidate junction identification | 21:27:14 22 Apr 2021 | 21:27:50 22 Apr 2021 | 36 seconds |
| Preliminary analysis of coverage distribution | 21:27:50 22 Apr 2021 | 21:29:28 22 Apr 2021 | 1 minute 38 seconds |
| Identifying junction candidates | 21:29:28 22 Apr 2021 | 21:29:29 22 Apr 2021 | 1 second |
| Re-alignment to junction candidates | 21:29:29 22 Apr 2021 | 21:30:57 22 Apr 2021 | 1 minute 28 seconds |
| Resolving best read alignments | 21:30:57 22 Apr 2021 | 21:31:46 22 Apr 2021 | 49 seconds |
| Creating BAM files | 21:31:46 22 Apr 2021 | 21:33:17 22 Apr 2021 | 1 minute 31 seconds |
| Tabulating error counts | 21:33:17 22 Apr 2021 | 21:33:49 22 Apr 2021 | 32 seconds |
| Re-calibrating base error rates | 21:33:49 22 Apr 2021 | 21:33:52 22 Apr 2021 | 3 seconds |
| Examining read alignment evidence | 21:33:52 22 Apr 2021 | 21:40:47 22 Apr 2021 | 6 minutes 55 seconds |
| Polymorphism statistics | 21:40:47 22 Apr 2021 | 21:40:47 22 Apr 2021 | 0 seconds |
| Output | 21:40:47 22 Apr 2021 | 21:40:57 22 Apr 2021 | 10 seconds |
| Total | 20 minutes 34 seconds | ||
