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-72_S72_L001_R1_001.good.fq | 372,578 | 52,847,788 | 100.0% | 141.8 bases | 149 bases | 95.4% |
| errors | ALE-72_S72_L001_R2_001.good.fq | 372,578 | 52,622,533 | 100.0% | 141.2 bases | 149 bases | 96.1% |
| errors | ALE-72_S72_L002_R1_001.good.fq | 367,479 | 52,029,602 | 100.0% | 141.6 bases | 149 bases | 96.8% |
| errors | ALE-72_S72_L002_R2_001.good.fq | 367,479 | 51,854,374 | 100.0% | 141.1 bases | 149 bases | 96.7% |
| errors | ALE-72_S72_L003_R1_001.good.fq | 376,690 | 53,299,001 | 100.0% | 141.5 bases | 149 bases | 96.7% |
| errors | ALE-72_S72_L003_R2_001.good.fq | 376,690 | 53,097,797 | 100.0% | 141.0 bases | 149 bases | 97.2% |
| errors | ALE-72_S72_L004_R1_001.good.fq | 353,654 | 50,036,732 | 100.0% | 141.5 bases | 149 bases | 96.6% |
| errors | ALE-72_S72_L004_R2_001.good.fq | 353,654 | 49,862,304 | 100.0% | 141.0 bases | 149 bases | 96.3% |
| total | 2,940,802 | 415,650,131 | 100.0% | 141.3 bases | 149 bases | 96.5% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_002947 | 6,181,873 | 64.9 | 2.0 | 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 | 34373 |
| 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 | 272 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.014 |
| reference sequence | pr(no read start) |
|---|---|
| NC_002947 | 0.81080 |
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 | 18:59:16 17 Feb 2020 | 19:00:02 17 Feb 2020 | 46 seconds |
| Read alignment to reference genome | 19:00:02 17 Feb 2020 | 19:07:08 17 Feb 2020 | 7 minutes 6 seconds |
| Preprocessing alignments for candidate junction identification | 19:07:08 17 Feb 2020 | 19:07:50 17 Feb 2020 | 42 seconds |
| Preliminary analysis of coverage distribution | 19:07:50 17 Feb 2020 | 19:09:35 17 Feb 2020 | 1 minute 45 seconds |
| Identifying junction candidates | 19:09:35 17 Feb 2020 | 19:11:47 17 Feb 2020 | 2 minutes 12 seconds |
| Re-alignment to junction candidates | 19:11:47 17 Feb 2020 | 19:13:58 17 Feb 2020 | 2 minutes 11 seconds |
| Resolving best read alignments | 19:13:58 17 Feb 2020 | 19:15:06 17 Feb 2020 | 1 minute 8 seconds |
| Creating BAM files | 19:15:06 17 Feb 2020 | 19:16:42 17 Feb 2020 | 1 minute 36 seconds |
| Tabulating error counts | 19:16:42 17 Feb 2020 | 19:17:13 17 Feb 2020 | 31 seconds |
| Re-calibrating base error rates | 19:17:13 17 Feb 2020 | 19:17:16 17 Feb 2020 | 3 seconds |
| Examining read alignment evidence | 19:17:16 17 Feb 2020 | 19:23:30 17 Feb 2020 | 6 minutes 14 seconds |
| Polymorphism statistics | 19:23:30 17 Feb 2020 | 19:23:31 17 Feb 2020 | 1 second |
| Output | 19:23:31 17 Feb 2020 | 19:23:58 17 Feb 2020 | 27 seconds |
| Total | 24 minutes 42 seconds | ||
