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-48_S48_L001_R1_001.good.fq | 465,780 | 67,110,922 | 100.0% | 144.1 bases | 149 bases | 94.2% |
| errors | ALE-48_S48_L001_R2_001.good.fq | 465,780 | 66,907,878 | 100.0% | 143.6 bases | 149 bases | 94.5% |
| errors | ALE-48_S48_L002_R1_001.good.fq | 455,387 | 65,527,198 | 100.0% | 143.9 bases | 149 bases | 95.7% |
| errors | ALE-48_S48_L002_R2_001.good.fq | 455,387 | 65,372,557 | 100.0% | 143.6 bases | 149 bases | 95.0% |
| errors | ALE-48_S48_L003_R1_001.good.fq | 464,791 | 66,813,698 | 100.0% | 143.7 bases | 149 bases | 95.5% |
| errors | ALE-48_S48_L003_R2_001.good.fq | 464,791 | 66,629,254 | 100.0% | 143.4 bases | 149 bases | 95.5% |
| errors | ALE-48_S48_L004_R1_001.good.fq | 436,431 | 62,755,709 | 100.0% | 143.8 bases | 149 bases | 95.4% |
| errors | ALE-48_S48_L004_R2_001.good.fq | 436,431 | 62,602,176 | 100.0% | 143.4 bases | 149 bases | 94.6% |
| total | 3,644,778 | 523,719,392 | 100.0% | 143.7 bases | 149 bases | 95.0% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_002947 | 6,181,873 | 81.2 | 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 | 70015 |
| 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 | 858 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.043 |
| reference sequence | pr(no read start) |
|---|---|
| NC_002947 | 0.77598 |
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 | 20:41:37 17 Feb 2020 | 20:42:31 17 Feb 2020 | 54 seconds |
| Read alignment to reference genome | 20:42:32 17 Feb 2020 | 20:50:31 17 Feb 2020 | 7 minutes 59 seconds |
| Preprocessing alignments for candidate junction identification | 20:50:31 17 Feb 2020 | 20:51:21 17 Feb 2020 | 50 seconds |
| Preliminary analysis of coverage distribution | 20:51:21 17 Feb 2020 | 20:53:27 17 Feb 2020 | 2 minutes 6 seconds |
| Identifying junction candidates | 20:53:27 17 Feb 2020 | 21:00:42 17 Feb 2020 | 7 minutes 15 seconds |
| Re-alignment to junction candidates | 21:00:42 17 Feb 2020 | 21:03:24 17 Feb 2020 | 2 minutes 42 seconds |
| Resolving best read alignments | 21:03:24 17 Feb 2020 | 21:04:42 17 Feb 2020 | 1 minute 18 seconds |
| Creating BAM files | 21:04:42 17 Feb 2020 | 21:06:40 17 Feb 2020 | 1 minute 58 seconds |
| Tabulating error counts | 21:06:40 17 Feb 2020 | 21:07:18 17 Feb 2020 | 38 seconds |
| Re-calibrating base error rates | 21:07:18 17 Feb 2020 | 21:07:21 17 Feb 2020 | 3 seconds |
| Examining read alignment evidence | 21:07:21 17 Feb 2020 | 21:14:48 17 Feb 2020 | 7 minutes 27 seconds |
| Polymorphism statistics | 21:14:48 17 Feb 2020 | 21:14:48 17 Feb 2020 | 0 seconds |
| Output | 21:14:48 17 Feb 2020 | 21:15:46 17 Feb 2020 | 58 seconds |
| Total | 34 minutes 8 seconds | ||
