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 | SRR12748536_R1.good.fq | 7,223,990 | 1,075,967,336 | 100.0% | 148.9 bases | 151 bases | 99.4% |
errors | SRR12748536_R2.good.fq | 7,223,990 | 1,056,711,025 | 100.0% | 146.3 bases | 151 bases | 99.2% |
total | 14,447,980 | 2,132,678,361 | 100.0% | 147.6 bases | 151 bases | 99.3% |
seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
---|---|---|---|---|---|---|---|
coverage | distribution | AE015451 | 6,181,873 | 348.6 | 2.9 | 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 | 1367 |
Coverage evenness (position-hash) score of junction candidates | ≥ 2 | ≥ 2 |
Test this many junction candidates (n). May be smaller if not enough passed the coverage evenness threshold | 100 ≤ n ≤ 5000 | 73 |
Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.004 |
reference sequence | pr(no read start) |
---|---|
AE015451 | 0.33790 |
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 | 13:54:27 23 Jan 2023 | 13:57:54 23 Jan 2023 | 3 minutes 27 seconds |
Read alignment to reference genome | 13:57:54 23 Jan 2023 | 14:22:05 23 Jan 2023 | 24 minutes 11 seconds |
Preprocessing alignments for candidate junction identification | 14:22:05 23 Jan 2023 | 14:24:53 23 Jan 2023 | 2 minutes 48 seconds |
Preliminary analysis of coverage distribution | 14:24:53 23 Jan 2023 | 14:32:04 23 Jan 2023 | 7 minutes 11 seconds |
Identifying junction candidates | 14:32:04 23 Jan 2023 | 14:32:04 23 Jan 2023 | 0 seconds |
Re-alignment to junction candidates | 14:32:04 23 Jan 2023 | 14:38:33 23 Jan 2023 | 6 minutes 29 seconds |
Resolving best read alignments | 14:38:33 23 Jan 2023 | 14:43:03 23 Jan 2023 | 4 minutes 30 seconds |
Creating BAM files | 14:43:03 23 Jan 2023 | 14:49:30 23 Jan 2023 | 6 minutes 27 seconds |
Tabulating error counts | 14:49:30 23 Jan 2023 | 14:52:27 23 Jan 2023 | 2 minutes 57 seconds |
Re-calibrating base error rates | 14:52:27 23 Jan 2023 | 14:52:28 23 Jan 2023 | 1 second |
Examining read alignment evidence | 14:52:28 23 Jan 2023 | 15:28:16 23 Jan 2023 | 35 minutes 48 seconds |
Polymorphism statistics | 15:28:16 23 Jan 2023 | 15:28:16 23 Jan 2023 | 0 seconds |
Output | 15:28:16 23 Jan 2023 | 15:29:08 23 Jan 2023 | 52 seconds |
Total | 1 hour 34 minutes 41 seconds |