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 | SRR19973059_R1.good.fq | 5,537,848 | 830,532,089 | 100.0% | 150.0 bases | 150 bases | 93.7% |
errors | SRR19973059_R2.good.fq | 5,537,848 | 830,532,089 | 100.0% | 150.0 bases | 150 bases | 93.6% |
total | 11,075,696 | 1,661,064,178 | 100.0% | 150.0 bases | 150 bases | 93.7% |
seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
---|---|---|---|---|---|---|---|
coverage | distribution | CP009273 | 4,631,469 | 331.7 | 5.9 | 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 | 41630 |
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 | 117 |
Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.008 |
reference sequence | pr(no read start) |
---|---|
CP009273 | 0.47734 |
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 | 09:49:21 24 Jan 2023 | 09:52:06 24 Jan 2023 | 2 minutes 45 seconds |
Read alignment to reference genome | 09:52:06 24 Jan 2023 | 10:14:06 24 Jan 2023 | 22 minutes 0 seconds |
Preprocessing alignments for candidate junction identification | 10:14:06 24 Jan 2023 | 10:16:25 24 Jan 2023 | 2 minutes 19 seconds |
Preliminary analysis of coverage distribution | 10:16:25 24 Jan 2023 | 10:21:00 24 Jan 2023 | 4 minutes 35 seconds |
Identifying junction candidates | 10:21:00 24 Jan 2023 | 10:21:03 24 Jan 2023 | 3 seconds |
Re-alignment to junction candidates | 10:21:03 24 Jan 2023 | 10:27:03 24 Jan 2023 | 6 minutes 0 seconds |
Resolving best read alignments | 10:27:03 24 Jan 2023 | 10:30:57 24 Jan 2023 | 3 minutes 54 seconds |
Creating BAM files | 10:30:57 24 Jan 2023 | 10:34:56 24 Jan 2023 | 3 minutes 59 seconds |
Tabulating error counts | 10:34:56 24 Jan 2023 | 10:37:23 24 Jan 2023 | 2 minutes 27 seconds |
Re-calibrating base error rates | 10:37:23 24 Jan 2023 | 10:37:25 24 Jan 2023 | 2 seconds |
Examining read alignment evidence | 10:37:25 24 Jan 2023 | 12:30:28 24 Jan 2023 | 1 hour 53 minutes 3 seconds |
Polymorphism statistics | 12:30:28 24 Jan 2023 | 12:30:32 24 Jan 2023 | 4 seconds |
Output | 12:30:32 24 Jan 2023 | 12:31:07 24 Jan 2023 | 35 seconds |
Total | 2 hours 41 minutes 46 seconds |