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 | JADR46_R1.good.fq | 3,998,926 | 599,794,994 | 100.0% | 150.0 bases | 150 bases | 99.4% |
errors | JADR46_R2.good.fq | 3,998,926 | 599,794,994 | 100.0% | 150.0 bases | 150 bases | 99.1% |
total | 7,997,852 | 1,199,589,988 | 100.0% | 150.0 bases | 150 bases | 99.2% |
seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
---|---|---|---|---|---|---|---|
coverage | distribution | CP006881 | 4,033,459 | 280.4 | 9.6 | 93.5% | Bacillus subtilis PY79, complete genome. |
coverage | distribution | Exported | 6,538 | 13093.4 | 487.4 | 6.5% | natural circular DNA |
total | 4,039,997 | 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 | 25106 |
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 | 0.005 |
reference sequence | pr(no read start) |
---|---|
CP006881 | 0.43585 |
Exported | 0.02883 |
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 | 11:42:20 20 Jan 2021 | 11:44:44 20 Jan 2021 | 2 minutes 24 seconds |
Read alignment to reference genome | 11:44:44 20 Jan 2021 | 12:03:44 20 Jan 2021 | 19 minutes 0 seconds |
Preprocessing alignments for candidate junction identification | 12:03:45 20 Jan 2021 | 12:05:35 20 Jan 2021 | 1 minute 50 seconds |
Preliminary analysis of coverage distribution | 12:05:35 20 Jan 2021 | 12:12:09 20 Jan 2021 | 6 minutes 34 seconds |
Identifying junction candidates | 12:12:09 20 Jan 2021 | 12:12:10 20 Jan 2021 | 1 second |
Re-alignment to junction candidates | 12:12:10 20 Jan 2021 | 12:17:03 20 Jan 2021 | 4 minutes 53 seconds |
Resolving best read alignments | 12:17:03 20 Jan 2021 | 12:19:41 20 Jan 2021 | 2 minutes 38 seconds |
Creating BAM files | 12:19:41 20 Jan 2021 | 12:25:46 20 Jan 2021 | 6 minutes 5 seconds |
Tabulating error counts | 12:25:46 20 Jan 2021 | 12:27:39 20 Jan 2021 | 1 minute 53 seconds |
Re-calibrating base error rates | 12:27:39 20 Jan 2021 | 12:27:41 20 Jan 2021 | 2 seconds |
Examining read alignment evidence | 12:27:41 20 Jan 2021 | 12:50:33 20 Jan 2021 | 22 minutes 52 seconds |
Polymorphism statistics | 12:50:33 20 Jan 2021 | 12:50:34 20 Jan 2021 | 1 second |
Output | 12:50:34 20 Jan 2021 | 12:51:33 20 Jan 2021 | 59 seconds |
Total | 1 hour 9 minutes 12 seconds |