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 | SRR19973085_R1.good.fq | 4,683,142 | 697,635,466 | 100.0% | 149.0 bases | 149 bases | 95.7% |
errors | SRR19973085_R2.good.fq | 4,683,142 | 697,635,466 | 100.0% | 149.0 bases | 149 bases | 95.6% |
total | 9,366,284 | 1,395,270,932 | 100.0% | 149.0 bases | 149 bases | 95.7% |
seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
---|---|---|---|---|---|---|---|
coverage | distribution | CP009273 | 4,631,469 | 285.0 | 3.1 | 100.0% | Escherichia coli BW25113, 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 | 28179 |
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 | 66 |
Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.004 |
reference sequence | pr(no read start) |
---|---|
CP009273 | 0.51055 |
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 | 09:42:51 24 Jan 2023 | 09:45:13 24 Jan 2023 | 2 minutes 22 seconds |
Read alignment to reference genome | 09:45:13 24 Jan 2023 | 10:02:50 24 Jan 2023 | 17 minutes 37 seconds |
Preprocessing alignments for candidate junction identification | 10:02:50 24 Jan 2023 | 10:04:50 24 Jan 2023 | 2 minutes 0 seconds |
Preliminary analysis of coverage distribution | 10:04:50 24 Jan 2023 | 10:08:40 24 Jan 2023 | 3 minutes 50 seconds |
Identifying junction candidates | 10:08:40 24 Jan 2023 | 10:08:42 24 Jan 2023 | 2 seconds |
Re-alignment to junction candidates | 10:08:42 24 Jan 2023 | 10:13:24 24 Jan 2023 | 4 minutes 42 seconds |
Resolving best read alignments | 10:13:24 24 Jan 2023 | 10:16:39 24 Jan 2023 | 3 minutes 15 seconds |
Creating BAM files | 10:16:39 24 Jan 2023 | 10:20:03 24 Jan 2023 | 3 minutes 24 seconds |
Tabulating error counts | 10:20:03 24 Jan 2023 | 10:22:02 24 Jan 2023 | 1 minute 59 seconds |
Re-calibrating base error rates | 10:22:02 24 Jan 2023 | 10:22:03 24 Jan 2023 | 1 second |
Examining read alignment evidence | 10:22:03 24 Jan 2023 | 11:50:01 24 Jan 2023 | 1 hour 27 minutes 58 seconds |
Polymorphism statistics | 11:50:01 24 Jan 2023 | 11:50:05 24 Jan 2023 | 4 seconds |
Output | 11:50:05 24 Jan 2023 | 11:51:03 24 Jan 2023 | 58 seconds |
Total | 2 hours 8 minutes 12 seconds |