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 | ERR1711319_R1.good.fq | 1,286,192 | 257,391,932 | 100.0% | 200.1 bases | 236 bases | 98.4% |
errors | ERR1711319_R2.good.fq | 1,286,189 | 204,494,832 | 100.0% | 159.0 bases | 236 bases | 96.7% |
total | 2,572,381 | 461,886,764 | 100.0% | 179.6 bases | 236 bases | 97.5% |
seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
---|---|---|---|---|---|---|---|
coverage | distribution | AE015451 | 6,181,873 | 74.2 | 3.9 | 100.0% | Pseudomonas putida KT2440 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 | 17223 |
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 | 222 |
Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.017 |
reference sequence | pr(no read start) |
---|---|
AE015451 | 0.85011 |
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 | ≤ 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 | 2.2.6 |
R | 3.4.4 |
step | start | end | elapsed |
---|---|---|---|
Read and reference sequence file input | 16:14:11 24 Jan 2023 | 16:15:06 24 Jan 2023 | 55 seconds |
Read alignment to reference genome | 16:15:06 24 Jan 2023 | 16:24:53 24 Jan 2023 | 9 minutes 47 seconds |
Preprocessing alignments for candidate junction identification | 16:24:53 24 Jan 2023 | 16:25:28 24 Jan 2023 | 35 seconds |
Preliminary analysis of coverage distribution | 16:25:28 24 Jan 2023 | 16:27:26 24 Jan 2023 | 1 minute 58 seconds |
Identifying junction candidates | 16:27:26 24 Jan 2023 | 16:27:41 24 Jan 2023 | 15 seconds |
Re-alignment to junction candidates | 16:27:41 24 Jan 2023 | 16:29:25 24 Jan 2023 | 1 minute 44 seconds |
Resolving best read alignments | 16:29:25 24 Jan 2023 | 16:30:15 24 Jan 2023 | 50 seconds |
Creating BAM files | 16:30:15 24 Jan 2023 | 16:31:59 24 Jan 2023 | 1 minute 44 seconds |
Tabulating error counts | 16:31:59 24 Jan 2023 | 16:32:40 24 Jan 2023 | 41 seconds |
Re-calibrating base error rates | 16:32:40 24 Jan 2023 | 16:32:42 24 Jan 2023 | 2 seconds |
Examining read alignment evidence | 16:32:42 24 Jan 2023 | 16:56:01 24 Jan 2023 | 23 minutes 19 seconds |
Polymorphism statistics | 16:56:01 24 Jan 2023 | 16:56:02 24 Jan 2023 | 1 second |
Output | 16:56:02 24 Jan 2023 | 16:56:49 24 Jan 2023 | 47 seconds |
Total | 42 minutes 38 seconds |