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-5_S5_L001_R1_001.good.fq | 409,433 | 58,533,427 | 100.0% | 143.0 bases | 149 bases | 94.0% |
| errors | ALE-5_S5_L001_R2_001.good.fq | 409,433 | 58,373,405 | 100.0% | 142.6 bases | 149 bases | 94.2% |
| errors | ALE-5_S5_L002_R1_001.good.fq | 404,703 | 57,759,605 | 100.0% | 142.7 bases | 149 bases | 95.2% |
| errors | ALE-5_S5_L002_R2_001.good.fq | 404,703 | 57,645,813 | 100.0% | 142.4 bases | 149 bases | 94.5% |
| errors | ALE-5_S5_L003_R1_001.good.fq | 419,841 | 59,899,488 | 100.0% | 142.7 bases | 149 bases | 95.1% |
| errors | ALE-5_S5_L003_R2_001.good.fq | 419,841 | 59,763,855 | 100.0% | 142.3 bases | 149 bases | 95.1% |
| errors | ALE-5_S5_L004_R1_001.good.fq | 387,478 | 55,247,296 | 100.0% | 142.6 bases | 149 bases | 95.0% |
| errors | ALE-5_S5_L004_R2_001.good.fq | 387,478 | 55,136,230 | 100.0% | 142.3 bases | 149 bases | 94.2% |
| total | 3,242,910 | 462,359,119 | 100.0% | 142.6 bases | 149 bases | 94.6% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_002947 | 6,181,873 | 71.6 | 3.0 | 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 | 77809 |
| 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 | 809 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.040 |
| reference sequence | pr(no read start) |
|---|---|
| NC_002947 | 0.79941 |
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 | ≤ 0 |
| Number of bases that at least one read must overlap each uniquely aligned side of a predicted junction | ≥ 6 |
| option | value |
|---|---|
| Mode | Full Polymorphism |
| 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 | 2 |
| Polymorphism frequency cutoff | 0.05 |
| Polymorphism minimum variant coverage each strand | 2 |
| 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 | ≥3 bases |
| Skip base substitutions when they create a homopolymer flanked on each side by | ≥5 bases |
| program | version |
|---|---|
| bowtie2 | 2.3.4.1 |
| R | 3.4.4 |
| step | start | end | elapsed |
|---|---|---|---|
| Read and reference sequence file input | 15:59:06 17 Feb 2020 | 15:59:59 17 Feb 2020 | 53 seconds |
| Read alignment to reference genome | 16:00:00 17 Feb 2020 | 16:07:04 17 Feb 2020 | 7 minutes 4 seconds |
| Preprocessing alignments for candidate junction identification | 16:07:04 17 Feb 2020 | 16:07:49 17 Feb 2020 | 45 seconds |
| Preliminary analysis of coverage distribution | 16:07:49 17 Feb 2020 | 16:09:38 17 Feb 2020 | 1 minute 49 seconds |
| Identifying junction candidates | 16:09:38 17 Feb 2020 | 16:21:09 17 Feb 2020 | 11 minutes 31 seconds |
| Re-alignment to junction candidates | 16:21:09 17 Feb 2020 | 16:23:31 17 Feb 2020 | 2 minutes 22 seconds |
| Resolving best read alignments | 16:23:31 17 Feb 2020 | 16:24:41 17 Feb 2020 | 1 minute 10 seconds |
| Creating BAM files | 16:24:41 17 Feb 2020 | 16:26:23 17 Feb 2020 | 1 minute 42 seconds |
| Tabulating error counts | 16:26:23 17 Feb 2020 | 16:26:57 17 Feb 2020 | 34 seconds |
| Re-calibrating base error rates | 16:26:57 17 Feb 2020 | 16:27:00 17 Feb 2020 | 3 seconds |
| Examining read alignment evidence | 16:27:00 17 Feb 2020 | 16:46:33 17 Feb 2020 | 19 minutes 33 seconds |
| Polymorphism statistics | 16:46:33 17 Feb 2020 | 16:46:36 17 Feb 2020 | 3 seconds |
| Output | 16:46:36 17 Feb 2020 | 16:51:41 17 Feb 2020 | 5 minutes 5 seconds |
| Total | 52 minutes 34 seconds | ||
