breseq version 0.35.4 revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
read file | reads | bases | passed filters | average | longest | mapped | |
---|---|---|---|---|---|---|---|
errors | c13-Redo-1-23_S7_L001_R1_001.good.fq | 1,104,735 | 306,641,027 | 100.0% | 277.6 bases | 289 bases | 96.2% |
errors | c13-Redo-1-23_S7_L001_R2_001.good.fq | 1,104,735 | 307,014,729 | 100.0% | 277.9 bases | 289 bases | 82.9% |
total | 2,209,470 | 613,655,756 | 100.0% | 277.7 bases | 289 bases | 89.5% |
seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
---|---|---|---|---|---|---|---|
coverage | distribution | NC_000913 | 4,641,652 | 120.7 | 8.0 | 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 | 58167 |
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 | 478 |
Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.060 |
reference sequence | pr(no read start) |
---|---|
NC_000913 | 0.86882 |
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 |
Minimum probablilty assigned that no mapped read will start at a given position and strand for junction prediction | 0.1 |
Junction allow suboptimal matches | FALSE |
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 | 09:30:22 09 Jul 2022 | 09:31:18 09 Jul 2022 | 56 seconds |
Read alignment to reference genome | 09:31:18 09 Jul 2022 | 09:43:33 09 Jul 2022 | 12 minutes 15 seconds |
Preprocessing alignments for candidate junction identification | 09:43:33 09 Jul 2022 | 09:44:12 09 Jul 2022 | 39 seconds |
Preliminary analysis of coverage distribution | 09:44:12 09 Jul 2022 | 09:46:07 09 Jul 2022 | 1 minute 55 seconds |
Identifying junction candidates | 09:46:07 09 Jul 2022 | 09:52:15 09 Jul 2022 | 6 minutes 8 seconds |
Re-alignment to junction candidates | 09:52:15 09 Jul 2022 | 09:54:46 09 Jul 2022 | 2 minutes 31 seconds |
Resolving best read alignments | 09:54:46 09 Jul 2022 | 09:55:40 09 Jul 2022 | 54 seconds |
Creating BAM files | 09:55:40 09 Jul 2022 | 09:57:17 09 Jul 2022 | 1 minute 37 seconds |
Tabulating error counts | 09:57:17 09 Jul 2022 | 09:58:13 09 Jul 2022 | 56 seconds |
Re-calibrating base error rates | 09:58:13 09 Jul 2022 | 09:58:14 09 Jul 2022 | 1 second |
Examining read alignment evidence | 09:58:14 09 Jul 2022 | 10:09:42 09 Jul 2022 | 11 minutes 28 seconds |
Polymorphism statistics | 10:09:42 09 Jul 2022 | 10:09:43 09 Jul 2022 | 1 second |
Output | 10:09:43 09 Jul 2022 | 10:10:00 09 Jul 2022 | 17 seconds |
Total | 39 minutes 38 seconds |