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 | SRR9723003_R1.good.fq | 1,249,050 | 311,048,676 | 100.0% | 249.0 bases | 250 bases | 99.6% |
errors | SRR9723003_R2.good.fq | 1,249,050 | 311,130,272 | 100.0% | 249.1 bases | 250 bases | 93.1% |
total | 2,498,100 | 622,178,948 | 100.0% | 249.1 bases | 250 bases | 96.4% |
seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
---|---|---|---|---|---|---|---|
coverage | distribution | NZ_CP009273 | 4,631,469 | 128.3 | 2.1 | 100.0% | Escherichia coli BW25113 strain K-12 chromosome, complete genome. |
total | 4,631,469 | 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 | 2752 |
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 | 60 |
Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.007 |
reference sequence | pr(no read start) |
---|---|
NZ_CP009273 | 0.78822 |
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 | 16:54:37 16 Mar 2023 | 16:55:27 16 Mar 2023 | 50 seconds |
Read alignment to reference genome | 16:55:27 16 Mar 2023 | 17:04:42 16 Mar 2023 | 9 minutes 15 seconds |
Preprocessing alignments for candidate junction identification | 17:04:42 16 Mar 2023 | 17:05:19 16 Mar 2023 | 37 seconds |
Preliminary analysis of coverage distribution | 17:05:19 16 Mar 2023 | 17:07:36 16 Mar 2023 | 2 minutes 17 seconds |
Identifying junction candidates | 17:07:36 16 Mar 2023 | 17:07:37 16 Mar 2023 | 1 second |
Re-alignment to junction candidates | 17:07:37 16 Mar 2023 | 17:09:47 16 Mar 2023 | 2 minutes 10 seconds |
Resolving best read alignments | 17:09:47 16 Mar 2023 | 17:10:43 16 Mar 2023 | 56 seconds |
Creating BAM files | 17:10:43 16 Mar 2023 | 17:12:41 16 Mar 2023 | 1 minute 58 seconds |
Tabulating error counts | 17:12:41 16 Mar 2023 | 17:13:35 16 Mar 2023 | 54 seconds |
Re-calibrating base error rates | 17:13:35 16 Mar 2023 | 17:13:36 16 Mar 2023 | 1 second |
Examining read alignment evidence | 17:13:36 16 Mar 2023 | 17:25:04 16 Mar 2023 | 11 minutes 28 seconds |
Polymorphism statistics | 17:25:04 16 Mar 2023 | 17:25:05 16 Mar 2023 | 1 second |
Output | 17:25:05 16 Mar 2023 | 17:25:17 16 Mar 2023 | 12 seconds |
Total | 30 minutes 40 seconds |