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-22_S22_L001_R1_001.good.fq | 395,850 | 57,210,189 | 100.0% | 144.5 bases | 149 bases | 93.9% |
| errors | ALE-22_S22_L001_R2_001.good.fq | 395,850 | 57,068,818 | 100.0% | 144.2 bases | 149 bases | 94.1% |
| errors | ALE-22_S22_L002_R1_001.good.fq | 391,862 | 56,572,145 | 100.0% | 144.4 bases | 149 bases | 95.3% |
| errors | ALE-22_S22_L002_R2_001.good.fq | 391,862 | 56,460,044 | 100.0% | 144.1 bases | 149 bases | 94.4% |
| errors | ALE-22_S22_L003_R1_001.good.fq | 401,325 | 57,893,538 | 100.0% | 144.3 bases | 149 bases | 95.3% |
| errors | ALE-22_S22_L003_R2_001.good.fq | 401,325 | 57,756,276 | 100.0% | 143.9 bases | 149 bases | 95.1% |
| errors | ALE-22_S22_L004_R1_001.good.fq | 374,350 | 54,010,555 | 100.0% | 144.3 bases | 149 bases | 95.1% |
| errors | ALE-22_S22_L004_R2_001.good.fq | 374,350 | 53,906,990 | 100.0% | 144.0 bases | 149 bases | 94.0% |
| total | 3,126,774 | 450,878,555 | 100.0% | 144.2 bases | 149 bases | 94.7% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_002947 | 6,181,873 | 68.5 | 2.8 | 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 | 72637 |
| 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 | 480 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.024 |
| reference sequence | pr(no read start) |
|---|---|
| NC_002947 | 0.80757 |
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 | 10:17:03 18 Feb 2020 | 10:17:50 18 Feb 2020 | 47 seconds |
| Read alignment to reference genome | 10:17:50 18 Feb 2020 | 10:24:50 18 Feb 2020 | 7 minutes 0 seconds |
| Preprocessing alignments for candidate junction identification | 10:24:50 18 Feb 2020 | 10:25:34 18 Feb 2020 | 44 seconds |
| Preliminary analysis of coverage distribution | 10:25:34 18 Feb 2020 | 10:27:24 18 Feb 2020 | 1 minute 50 seconds |
| Identifying junction candidates | 10:27:24 18 Feb 2020 | 10:33:52 18 Feb 2020 | 6 minutes 28 seconds |
| Re-alignment to junction candidates | 10:33:52 18 Feb 2020 | 10:36:02 18 Feb 2020 | 2 minutes 10 seconds |
| Resolving best read alignments | 10:36:02 18 Feb 2020 | 10:37:09 18 Feb 2020 | 1 minute 7 seconds |
| Creating BAM files | 10:37:09 18 Feb 2020 | 10:38:51 18 Feb 2020 | 1 minute 42 seconds |
| Tabulating error counts | 10:38:51 18 Feb 2020 | 10:39:24 18 Feb 2020 | 33 seconds |
| Re-calibrating base error rates | 10:39:24 18 Feb 2020 | 10:39:27 18 Feb 2020 | 3 seconds |
| Examining read alignment evidence | 10:39:27 18 Feb 2020 | 11:00:14 18 Feb 2020 | 20 minutes 47 seconds |
| Polymorphism statistics | 11:00:14 18 Feb 2020 | 11:00:16 18 Feb 2020 | 2 seconds |
| Output | 11:00:16 18 Feb 2020 | 11:03:44 18 Feb 2020 | 3 minutes 28 seconds |
| Total | 46 minutes 41 seconds | ||
