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 | Plate-2-BOP-1000-PFKA-ALE-2-flask-16_S52_L001_R1_001.good.fq | 146,771 | 19,873,920 | 100.0% | 135.4 bases | 149 bases | 92.5% |
errors | Plate-2-BOP-1000-PFKA-ALE-2-flask-16_S52_L001_R2_001.good.fq | 146,771 | 19,529,568 | 100.0% | 133.1 bases | 149 bases | 97.2% |
errors | Plate-2-BOP-1000-PFKA-ALE-2-flask-16_S52_L002_R1_001.good.fq | 118,260 | 15,987,376 | 100.0% | 135.2 bases | 149 bases | 92.0% |
errors | Plate-2-BOP-1000-PFKA-ALE-2-flask-16_S52_L002_R2_001.good.fq | 118,260 | 15,694,901 | 100.0% | 132.7 bases | 149 bases | 96.8% |
errors | Plate-2-BOP-1000-PFKA-ALE-2-flask-16_S52_L003_R1_001.good.fq | 134,172 | 18,146,842 | 100.0% | 135.3 bases | 149 bases | 92.2% |
errors | Plate-2-BOP-1000-PFKA-ALE-2-flask-16_S52_L003_R2_001.good.fq | 134,172 | 17,814,198 | 100.0% | 132.8 bases | 149 bases | 97.1% |
errors | Plate-2-BOP-1000-PFKA-ALE-2-flask-16_S52_L004_R1_001.good.fq | 115,389 | 15,567,382 | 100.0% | 134.9 bases | 149 bases | 92.0% |
errors | Plate-2-BOP-1000-PFKA-ALE-2-flask-16_S52_L004_R2_001.good.fq | 115,389 | 15,290,139 | 100.0% | 132.5 bases | 149 bases | 96.5% |
total | 1,029,184 | 137,904,326 | 100.0% | 134.0 bases | 149 bases | 94.6% |
seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
---|---|---|---|---|---|---|---|
coverage | distribution | NC_000913 | 4,641,652 | 28.0 | 2.4 | 100.0% | Escherichia coli str. K-12 substr. MG1655, complete genome. |
total | 4,641,652 | 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 | 13908 |
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 | 69 |
Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.005 |
reference sequence | pr(no read start) |
---|---|
NC_000913 | 0.90540 |
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 | 2.2.6 |
R | 3.4.4 |
step | start | end | elapsed |
---|---|---|---|
Read and reference sequence file input | 09:17:29 11 Sep 2020 | 09:17:45 11 Sep 2020 | 16 seconds |
Read alignment to reference genome | 09:17:46 11 Sep 2020 | 09:19:44 11 Sep 2020 | 1 minute 58 seconds |
Preprocessing alignments for candidate junction identification | 09:19:44 11 Sep 2020 | 09:20:00 11 Sep 2020 | 16 seconds |
Preliminary analysis of coverage distribution | 09:20:00 11 Sep 2020 | 09:20:28 11 Sep 2020 | 28 seconds |
Identifying junction candidates | 09:20:28 11 Sep 2020 | 09:20:40 11 Sep 2020 | 12 seconds |
Re-alignment to junction candidates | 09:20:40 11 Sep 2020 | 09:21:15 11 Sep 2020 | 35 seconds |
Resolving best read alignments | 09:21:15 11 Sep 2020 | 09:21:38 11 Sep 2020 | 23 seconds |
Creating BAM files | 09:21:38 11 Sep 2020 | 09:22:04 11 Sep 2020 | 26 seconds |
Tabulating error counts | 09:22:04 11 Sep 2020 | 09:22:14 11 Sep 2020 | 10 seconds |
Re-calibrating base error rates | 09:22:14 11 Sep 2020 | 09:22:16 11 Sep 2020 | 2 seconds |
Examining read alignment evidence | 09:22:16 11 Sep 2020 | 09:24:34 11 Sep 2020 | 2 minutes 18 seconds |
Polymorphism statistics | 09:24:34 11 Sep 2020 | 09:24:34 11 Sep 2020 | 0 seconds |
Output | 09:24:34 11 Sep 2020 | 09:24:44 11 Sep 2020 | 10 seconds |
Total | 7 minutes 14 seconds |