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 | AA_PAL031_S31_R1_001.good.fq | 1,572,100 | 233,794,929 | 100.0% | 148.7 bases | 149 bases | 98.3% |
errors | AA_PAL031_S31_R2_001.good.fq | 1,572,100 | 233,794,929 | 100.0% | 148.7 bases | 149 bases | 96.2% |
total | 3,144,200 | 467,589,858 | 100.0% | 148.7 bases | 149 bases | 97.2% |
seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
---|---|---|---|---|---|---|---|
coverage | distribution | NC_000913 | 4,641,652 | 96.9 | 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 | 17588 |
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 | 570 |
Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.037 |
reference sequence | pr(no read start) |
---|---|
NC_000913 | 0.75417 |
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 | ≤ 0 |
Number of bases that at least one read must overlap each uniquely aligned side of a predicted junction | ≥ 6 |
option | value |
---|---|
Mode | Full Polymorphism |
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 | 2 |
Polymorphism frequency cutoff | 0.05 |
Polymorphism minimum variant coverage each strand | 2 |
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 | ≥3 bases |
Skip base substitutions when they create a homopolymer flanked on each side by | ≥5 bases |
program | version |
---|---|
bowtie2 | 2.2.6 |
R | 3.4.4 |
step | start | end | elapsed |
---|---|---|---|
Read and reference sequence file input | 20:31:30 15 Apr 2021 | 20:32:28 15 Apr 2021 | 58 seconds |
Read alignment to reference genome | 20:32:29 15 Apr 2021 | 20:41:16 15 Apr 2021 | 8 minutes 47 seconds |
Preprocessing alignments for candidate junction identification | 20:41:16 15 Apr 2021 | 20:41:55 15 Apr 2021 | 39 seconds |
Preliminary analysis of coverage distribution | 20:41:55 15 Apr 2021 | 20:44:35 15 Apr 2021 | 2 minutes 40 seconds |
Identifying junction candidates | 20:44:35 15 Apr 2021 | 20:44:41 15 Apr 2021 | 6 seconds |
Re-alignment to junction candidates | 20:44:41 15 Apr 2021 | 20:46:46 15 Apr 2021 | 2 minutes 5 seconds |
Resolving best read alignments | 20:46:46 15 Apr 2021 | 20:47:42 15 Apr 2021 | 56 seconds |
Creating BAM files | 20:47:42 15 Apr 2021 | 20:50:14 15 Apr 2021 | 2 minutes 32 seconds |
Tabulating error counts | 20:50:14 15 Apr 2021 | 20:50:55 15 Apr 2021 | 41 seconds |
Re-calibrating base error rates | 20:50:55 15 Apr 2021 | 20:50:56 15 Apr 2021 | 1 second |
Examining read alignment evidence | 20:50:56 15 Apr 2021 | 21:51:34 15 Apr 2021 | 1 hour 38 seconds |
Polymorphism statistics | 21:51:34 15 Apr 2021 | 21:51:35 15 Apr 2021 | 1 second |
Output | 21:51:35 15 Apr 2021 | 21:52:09 15 Apr 2021 | 34 seconds |
Total | 1 hour 20 minutes 38 seconds |