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 | SRR2915026_R1.good.fq | 963,110 | 133,321,897 | 100.0% | 138.4 bases | 140 bases | 99.5% |
errors | SRR2915026_R2.good.fq | 963,110 | 133,321,897 | 100.0% | 138.4 bases | 140 bases | 98.7% |
total | 1,926,220 | 266,643,794 | 100.0% | 138.4 bases | 140 bases | 99.1% |
seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
---|---|---|---|---|---|---|---|
coverage | distribution | NC_000913 | 4,641,652 | 57.1 | 3.4 | 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 | 2784 |
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 | 351 |
Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.021 |
reference sequence | pr(no read start) |
---|---|
NC_000913 | 0.84886 |
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 | 15:29:38 14 Jan 2021 | 15:31:29 14 Jan 2021 | 1 minute 51 seconds |
Read alignment to reference genome | 15:31:30 14 Jan 2021 | 15:46:47 14 Jan 2021 | 15 minutes 17 seconds |
Preprocessing alignments for candidate junction identification | 15:46:47 14 Jan 2021 | 15:48:25 14 Jan 2021 | 1 minute 38 seconds |
Preliminary analysis of coverage distribution | 15:48:25 14 Jan 2021 | 15:51:07 14 Jan 2021 | 2 minutes 42 seconds |
Identifying junction candidates | 15:51:07 14 Jan 2021 | 15:51:12 14 Jan 2021 | 5 seconds |
Re-alignment to junction candidates | 15:51:12 14 Jan 2021 | 15:56:01 14 Jan 2021 | 4 minutes 49 seconds |
Resolving best read alignments | 15:56:01 14 Jan 2021 | 15:58:19 14 Jan 2021 | 2 minutes 18 seconds |
Creating BAM files | 15:58:19 14 Jan 2021 | 16:00:40 14 Jan 2021 | 2 minutes 21 seconds |
Tabulating error counts | 16:00:40 14 Jan 2021 | 16:01:50 14 Jan 2021 | 1 minute 10 seconds |
Re-calibrating base error rates | 16:01:50 14 Jan 2021 | 16:01:53 14 Jan 2021 | 3 seconds |
Examining read alignment evidence | 16:01:53 14 Jan 2021 | 16:18:15 14 Jan 2021 | 16 minutes 22 seconds |
Polymorphism statistics | 16:18:15 14 Jan 2021 | 16:18:16 14 Jan 2021 | 1 second |
Output | 16:18:16 14 Jan 2021 | 16:19:16 14 Jan 2021 | 1 minute 0 seconds |
Total | 49 minutes 37 seconds |