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 | SRR19973057_R1.good.fq | 5,205,379 | 775,434,576 | 100.0% | 149.0 bases | 149 bases | 96.6% |
errors | SRR19973057_R2.good.fq | 5,205,379 | 775,434,576 | 100.0% | 149.0 bases | 149 bases | 96.5% |
total | 10,410,758 | 1,550,869,152 | 100.0% | 149.0 bases | 149 bases | 96.6% |
seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
---|---|---|---|---|---|---|---|
coverage | distribution | CP009273 | 4,631,469 | 320.1 | 3.2 | 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 | 25403 |
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 | 107 |
Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.007 |
reference sequence | pr(no read start) |
---|---|
CP009273 | 0.48025 |
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 | 09:45:13 24 Jan 2023 | 09:47:50 24 Jan 2023 | 2 minutes 37 seconds |
Read alignment to reference genome | 09:47:50 24 Jan 2023 | 10:07:12 24 Jan 2023 | 19 minutes 22 seconds |
Preprocessing alignments for candidate junction identification | 10:07:12 24 Jan 2023 | 10:09:27 24 Jan 2023 | 2 minutes 15 seconds |
Preliminary analysis of coverage distribution | 10:09:27 24 Jan 2023 | 10:13:39 24 Jan 2023 | 4 minutes 12 seconds |
Identifying junction candidates | 10:13:39 24 Jan 2023 | 10:13:42 24 Jan 2023 | 3 seconds |
Re-alignment to junction candidates | 10:13:42 24 Jan 2023 | 10:18:55 24 Jan 2023 | 5 minutes 13 seconds |
Resolving best read alignments | 10:18:55 24 Jan 2023 | 10:22:28 24 Jan 2023 | 3 minutes 33 seconds |
Creating BAM files | 10:22:28 24 Jan 2023 | 10:26:15 24 Jan 2023 | 3 minutes 47 seconds |
Tabulating error counts | 10:26:15 24 Jan 2023 | 10:28:29 24 Jan 2023 | 2 minutes 14 seconds |
Re-calibrating base error rates | 10:28:29 24 Jan 2023 | 10:28:30 24 Jan 2023 | 1 second |
Examining read alignment evidence | 10:28:30 24 Jan 2023 | 12:11:46 24 Jan 2023 | 1 hour 43 minutes 16 seconds |
Polymorphism statistics | 12:11:46 24 Jan 2023 | 12:11:50 24 Jan 2023 | 4 seconds |
Output | 12:11:50 24 Jan 2023 | 12:13:11 24 Jan 2023 | 1 minute 21 seconds |
Total | 2 hours 27 minutes 58 seconds |