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 | SRR6462912_R1.good.fq | 888,046 | 71,581,072 | 100.0% | 80.6 bases | 81 bases | 98.2% |
errors | SRR6462912_R2.good.fq | 888,046 | 71,583,703 | 100.0% | 80.6 bases | 81 bases | 98.2% |
total | 1,776,092 | 143,164,775 | 100.0% | 80.6 bases | 81 bases | 98.2% |
seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
---|---|---|---|---|---|---|---|
coverage | distribution | NC_000913 | 4,641,652 | 31.3 | 2.6 | 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 | 2015 |
Coverage evenness (position-hash) score of junction candidates | ≥ 2 | ≥ 4 |
Test this many junction candidates (n). May be smaller if not enough passed the coverage evenness threshold | 100 ≤ n ≤ 5000 | 8 |
Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.000 |
reference sequence | pr(no read start) |
---|---|
NC_000913 | 0.83697 |
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 | 04:08:22 11 Nov 2020 | 04:09:43 11 Nov 2020 | 1 minute 21 seconds |
Read alignment to reference genome | 04:09:44 11 Nov 2020 | 04:16:26 11 Nov 2020 | 6 minutes 42 seconds |
Preprocessing alignments for candidate junction identification | 04:16:26 11 Nov 2020 | 04:17:33 11 Nov 2020 | 1 minute 7 seconds |
Preliminary analysis of coverage distribution | 04:17:33 11 Nov 2020 | 04:18:47 11 Nov 2020 | 1 minute 14 seconds |
Identifying junction candidates | 04:18:47 11 Nov 2020 | 04:18:48 11 Nov 2020 | 1 second |
Re-alignment to junction candidates | 04:18:48 11 Nov 2020 | 04:20:30 11 Nov 2020 | 1 minute 42 seconds |
Resolving best read alignments | 04:20:30 11 Nov 2020 | 04:21:59 11 Nov 2020 | 1 minute 29 seconds |
Creating BAM files | 04:21:59 11 Nov 2020 | 04:23:02 11 Nov 2020 | 1 minute 3 seconds |
Tabulating error counts | 04:23:02 11 Nov 2020 | 04:23:42 11 Nov 2020 | 40 seconds |
Re-calibrating base error rates | 04:23:42 11 Nov 2020 | 04:23:46 11 Nov 2020 | 4 seconds |
Examining read alignment evidence | 04:23:46 11 Nov 2020 | 04:33:12 11 Nov 2020 | 9 minutes 26 seconds |
Polymorphism statistics | 04:33:12 11 Nov 2020 | 04:33:13 11 Nov 2020 | 1 second |
Output | 04:33:13 11 Nov 2020 | 04:33:39 11 Nov 2020 | 26 seconds |
Total | 25 minutes 16 seconds |