mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.33.1 revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| read file | reads | bases | passed filters | average | longest | mapped | |
|---|---|---|---|---|---|---|---|
| errors | ALE-50_S50_L001_R1_001.good.fq | 410,446 | 58,644,311 | 100.0% | 142.9 bases | 149 bases | 96.6% |
| errors | ALE-50_S50_L001_R2_001.good.fq | 410,446 | 58,506,507 | 100.0% | 142.5 bases | 149 bases | 96.7% |
| errors | ALE-50_S50_L002_R1_001.good.fq | 405,375 | 57,410,368 | 100.0% | 141.6 bases | 148 bases | 98.0% |
| errors | ALE-50_S50_L002_R2_001.good.fq | 405,375 | 57,325,758 | 100.0% | 141.4 bases | 148 bases | 97.2% |
| errors | ALE-50_S50_L003_R1_001.good.fq | 417,811 | 59,150,511 | 100.0% | 141.6 bases | 148 bases | 97.9% |
| errors | ALE-50_S50_L003_R2_001.good.fq | 417,811 | 59,038,129 | 100.0% | 141.3 bases | 148 bases | 97.8% |
| errors | ALE-50_S50_L004_R1_001.good.fq | 388,331 | 55,352,250 | 100.0% | 142.5 bases | 149 bases | 97.8% |
| errors | ALE-50_S50_L004_R2_001.good.fq | 388,331 | 55,266,701 | 100.0% | 142.3 bases | 149 bases | 96.8% |
| total | 3,243,926 | 460,694,535 | 100.0% | 142.0 bases | 149 bases | 97.4% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_002947 | 6,181,873 | 77.1 | 3.9 | 100.0% | Pseudomonas putida KT2440 chromosome, complete genome. |
| total | 6,181,873 | 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 | 31793 |
| Coverage evenness (position-hash) score of junction candidates | ≥ 2 | ≥ 3 |
| Test this many junction candidates (n). May be smaller if not enough passed the coverage evenness threshold | 100 ≤ n ≤ 5000 | 239 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.012 |
| reference sequence | pr(no read start) |
|---|---|
| NC_002947 | 0.78916 |
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 |
| 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 | 2.3.4.1 |
| R | 3.4.4 |
| step | start | end | elapsed |
|---|---|---|---|
| Read and reference sequence file input | 18:30:58 18 Feb 2020 | 18:31:46 18 Feb 2020 | 48 seconds |
| Read alignment to reference genome | 18:31:46 18 Feb 2020 | 18:38:31 18 Feb 2020 | 6 minutes 45 seconds |
| Preprocessing alignments for candidate junction identification | 18:38:31 18 Feb 2020 | 18:39:16 18 Feb 2020 | 45 seconds |
| Preliminary analysis of coverage distribution | 18:39:16 18 Feb 2020 | 18:41:07 18 Feb 2020 | 1 minute 51 seconds |
| Identifying junction candidates | 18:41:07 18 Feb 2020 | 18:44:08 18 Feb 2020 | 3 minutes 1 second |
| Re-alignment to junction candidates | 18:44:08 18 Feb 2020 | 18:46:18 18 Feb 2020 | 2 minutes 10 seconds |
| Resolving best read alignments | 18:46:18 18 Feb 2020 | 18:47:29 18 Feb 2020 | 1 minute 11 seconds |
| Creating BAM files | 18:47:29 18 Feb 2020 | 18:49:13 18 Feb 2020 | 1 minute 44 seconds |
| Tabulating error counts | 18:49:13 18 Feb 2020 | 18:49:48 18 Feb 2020 | 35 seconds |
| Re-calibrating base error rates | 18:49:48 18 Feb 2020 | 18:49:51 18 Feb 2020 | 3 seconds |
| Examining read alignment evidence | 18:49:51 18 Feb 2020 | 18:56:41 18 Feb 2020 | 6 minutes 50 seconds |
| Polymorphism statistics | 18:56:41 18 Feb 2020 | 18:56:41 18 Feb 2020 | 0 seconds |
| Output | 18:56:41 18 Feb 2020 | 18:57:01 18 Feb 2020 | 20 seconds |
| Total | 26 minutes 3 seconds | ||
