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-78_S78_L001_R1_001.good.fq | 420,465 | 59,377,872 | 100.0% | 141.2 bases | 149 bases | 90.1% |
| errors | ALE-78_S78_L001_R2_001.good.fq | 420,465 | 59,188,208 | 100.0% | 140.8 bases | 149 bases | 90.3% |
| errors | ALE-78_S78_L002_R1_001.good.fq | 410,577 | 57,856,766 | 100.0% | 140.9 bases | 149 bases | 91.4% |
| errors | ALE-78_S78_L002_R2_001.good.fq | 410,577 | 57,722,717 | 100.0% | 140.6 bases | 149 bases | 91.1% |
| errors | ALE-78_S78_L003_R1_001.good.fq | 433,117 | 61,026,463 | 100.0% | 140.9 bases | 149 bases | 91.4% |
| errors | ALE-78_S78_L003_R2_001.good.fq | 433,117 | 60,855,927 | 100.0% | 140.5 bases | 149 bases | 91.6% |
| errors | ALE-78_S78_L004_R1_001.good.fq | 396,175 | 55,784,604 | 100.0% | 140.8 bases | 149 bases | 91.2% |
| errors | ALE-78_S78_L004_R2_001.good.fq | 396,175 | 55,657,338 | 100.0% | 140.5 bases | 149 bases | 90.6% |
| total | 3,320,668 | 467,469,895 | 100.0% | 140.8 bases | 149 bases | 91.0% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_002947 | 6,181,873 | 69.1 | 2.5 | 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 | 100052 |
| Coverage evenness (position-hash) score of junction candidates | ≥ 2 | ≥ 4 |
| Test this many junction candidates (n). May be smaller if not enough passed the coverage evenness threshold | 100 ≤ n ≤ 5000 | 784 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.039 |
| reference sequence | pr(no read start) |
|---|---|
| NC_002947 | 0.80030 |
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 | 21:31:50 18 Feb 2020 | 21:32:39 18 Feb 2020 | 49 seconds |
| Read alignment to reference genome | 21:32:39 18 Feb 2020 | 21:40:10 18 Feb 2020 | 7 minutes 31 seconds |
| Preprocessing alignments for candidate junction identification | 21:40:10 18 Feb 2020 | 21:40:56 18 Feb 2020 | 46 seconds |
| Preliminary analysis of coverage distribution | 21:40:56 18 Feb 2020 | 21:42:41 18 Feb 2020 | 1 minute 45 seconds |
| Identifying junction candidates | 21:42:41 18 Feb 2020 | 21:43:43 18 Feb 2020 | 1 minute 2 seconds |
| Re-alignment to junction candidates | 21:43:43 18 Feb 2020 | 21:46:09 18 Feb 2020 | 2 minutes 26 seconds |
| Resolving best read alignments | 21:46:09 18 Feb 2020 | 21:47:21 18 Feb 2020 | 1 minute 12 seconds |
| Creating BAM files | 21:47:21 18 Feb 2020 | 21:48:58 18 Feb 2020 | 1 minute 37 seconds |
| Tabulating error counts | 21:48:58 18 Feb 2020 | 21:49:31 18 Feb 2020 | 33 seconds |
| Re-calibrating base error rates | 21:49:31 18 Feb 2020 | 21:49:34 18 Feb 2020 | 3 seconds |
| Examining read alignment evidence | 21:49:34 18 Feb 2020 | 21:55:50 18 Feb 2020 | 6 minutes 16 seconds |
| Polymorphism statistics | 21:55:50 18 Feb 2020 | 21:55:53 18 Feb 2020 | 3 seconds |
| Output | 21:55:53 18 Feb 2020 | 21:56:48 18 Feb 2020 | 55 seconds |
| Total | 24 minutes 58 seconds | ||
