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-57_S57_L001_R1_001.good.fq | 388,385 | 55,674,292 | 100.0% | 143.3 bases | 149 bases | 94.3% |
| errors | ALE-57_S57_L001_R2_001.good.fq | 388,385 | 55,480,218 | 100.0% | 142.8 bases | 149 bases | 94.7% |
| errors | ALE-57_S57_L002_R1_001.good.fq | 379,485 | 54,315,955 | 100.0% | 143.1 bases | 149 bases | 95.7% |
| errors | ALE-57_S57_L002_R2_001.good.fq | 379,485 | 54,166,612 | 100.0% | 142.7 bases | 149 bases | 95.1% |
| errors | ALE-57_S57_L003_R1_001.good.fq | 390,610 | 55,869,222 | 100.0% | 143.0 bases | 149 bases | 95.5% |
| errors | ALE-57_S57_L003_R2_001.good.fq | 390,610 | 55,689,345 | 100.0% | 142.6 bases | 149 bases | 95.6% |
| errors | ALE-57_S57_L004_R1_001.good.fq | 363,597 | 51,988,178 | 100.0% | 143.0 bases | 149 bases | 95.4% |
| errors | ALE-57_S57_L004_R2_001.good.fq | 363,597 | 51,847,876 | 100.0% | 142.6 bases | 149 bases | 94.7% |
| total | 3,044,154 | 435,031,698 | 100.0% | 142.9 bases | 149 bases | 95.1% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_002947 | 6,181,873 | 66.3 | 2.3 | 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 | 54096 |
| 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 | 588 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.029 |
| reference sequence | pr(no read start) |
|---|---|
| NC_002947 | 0.80788 |
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 | 21:56:49 18 Feb 2020 | 21:57:34 18 Feb 2020 | 45 seconds |
| Read alignment to reference genome | 21:57:35 18 Feb 2020 | 22:04:10 18 Feb 2020 | 6 minutes 35 seconds |
| Preprocessing alignments for candidate junction identification | 22:04:10 18 Feb 2020 | 22:04:52 18 Feb 2020 | 42 seconds |
| Preliminary analysis of coverage distribution | 22:04:52 18 Feb 2020 | 22:06:37 18 Feb 2020 | 1 minute 45 seconds |
| Identifying junction candidates | 22:06:37 18 Feb 2020 | 22:11:47 18 Feb 2020 | 5 minutes 10 seconds |
| Re-alignment to junction candidates | 22:11:47 18 Feb 2020 | 22:13:55 18 Feb 2020 | 2 minutes 8 seconds |
| Resolving best read alignments | 22:13:55 18 Feb 2020 | 22:15:01 18 Feb 2020 | 1 minute 6 seconds |
| Creating BAM files | 22:15:01 18 Feb 2020 | 22:16:38 18 Feb 2020 | 1 minute 37 seconds |
| Tabulating error counts | 22:16:38 18 Feb 2020 | 22:17:10 18 Feb 2020 | 32 seconds |
| Re-calibrating base error rates | 22:17:10 18 Feb 2020 | 22:17:13 18 Feb 2020 | 3 seconds |
| Examining read alignment evidence | 22:17:13 18 Feb 2020 | 22:23:24 18 Feb 2020 | 6 minutes 11 seconds |
| Polymorphism statistics | 22:23:24 18 Feb 2020 | 22:23:25 18 Feb 2020 | 1 second |
| Output | 22:23:25 18 Feb 2020 | 22:24:09 18 Feb 2020 | 44 seconds |
| Total | 27 minutes 19 seconds | ||
