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 | DRR075696_R1.good.fq | 5,016,931 | 752,059,860 | 100.0% | 149.9 bases | 150 bases | 99.5% |
errors | DRR075696_R2.good.fq | 5,016,931 | 752,059,860 | 100.0% | 149.9 bases | 150 bases | 96.6% |
total | 10,033,862 | 1,504,119,720 | 100.0% | 149.9 bases | 150 bases | 98.0% |
seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
---|---|---|---|---|---|---|---|
coverage | distribution | AP012306 | 3,976,195 | 376.8 | 12.6 | 100.0% | Escherichia coli str. K-12 substr. MDS42 DNA, complete genome. |
total | 3,976,195 | 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 | 30875 |
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 | 195 |
Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.015 |
reference sequence | pr(no read start) |
---|---|
AP012306 | 0.33535 |
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 | 12:21:30 24 Mar 2023 | 12:24:07 24 Mar 2023 | 2 minutes 37 seconds |
Read alignment to reference genome | 12:24:07 24 Mar 2023 | 12:42:52 24 Mar 2023 | 18 minutes 45 seconds |
Preprocessing alignments for candidate junction identification | 12:42:52 24 Mar 2023 | 12:44:55 24 Mar 2023 | 2 minutes 3 seconds |
Preliminary analysis of coverage distribution | 12:44:55 24 Mar 2023 | 12:51:07 24 Mar 2023 | 6 minutes 12 seconds |
Identifying junction candidates | 12:51:07 24 Mar 2023 | 12:51:34 24 Mar 2023 | 27 seconds |
Re-alignment to junction candidates | 12:51:34 24 Mar 2023 | 12:56:38 24 Mar 2023 | 5 minutes 4 seconds |
Resolving best read alignments | 12:56:38 24 Mar 2023 | 12:59:57 24 Mar 2023 | 3 minutes 19 seconds |
Creating BAM files | 12:59:57 24 Mar 2023 | 13:05:41 24 Mar 2023 | 5 minutes 44 seconds |
Tabulating error counts | 13:05:41 24 Mar 2023 | 13:07:49 24 Mar 2023 | 2 minutes 8 seconds |
Re-calibrating base error rates | 13:07:49 24 Mar 2023 | 13:07:50 24 Mar 2023 | 1 second |
Examining read alignment evidence | 13:07:50 24 Mar 2023 | 13:31:42 24 Mar 2023 | 23 minutes 52 seconds |
Polymorphism statistics | 13:31:42 24 Mar 2023 | 13:31:43 24 Mar 2023 | 1 second |
Output | 13:31:43 24 Mar 2023 | 13:32:17 24 Mar 2023 | 34 seconds |
Total | 1 hour 10 minutes 47 seconds |