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 | SRR12717907_R1.good.fq | 3,172,619 | 462,533,881 | 100.0% | 145.8 bases | 149 bases | 97.2% |
errors | SRR12717907_R2.good.fq | 3,172,619 | 470,789,258 | 100.0% | 148.4 bases | 149 bases | 96.7% |
total | 6,345,238 | 933,323,139 | 100.0% | 147.1 bases | 149 bases | 96.9% |
seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
---|---|---|---|---|---|---|---|
coverage | distribution | NC_000913 | 4,641,652 | 192.4 | 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 | 96282 |
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 | 1305 |
Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.084 |
reference sequence | pr(no read start) |
---|---|
NC_000913 | 0.54507 |
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 | 20:23:31 01 Feb 2021 | 20:29:27 01 Feb 2021 | 5 minutes 56 seconds |
Read alignment to reference genome | 20:29:28 01 Feb 2021 | 21:15:00 01 Feb 2021 | 45 minutes 32 seconds |
Preprocessing alignments for candidate junction identification | 21:15:02 01 Feb 2021 | 21:20:42 01 Feb 2021 | 5 minutes 40 seconds |
Preliminary analysis of coverage distribution | 21:20:42 01 Feb 2021 | 21:32:04 01 Feb 2021 | 11 minutes 22 seconds |
Identifying junction candidates | 21:32:04 01 Feb 2021 | 21:32:35 01 Feb 2021 | 31 seconds |
Re-alignment to junction candidates | 21:32:35 01 Feb 2021 | 21:47:41 01 Feb 2021 | 15 minutes 6 seconds |
Resolving best read alignments | 21:47:41 01 Feb 2021 | 21:55:51 01 Feb 2021 | 8 minutes 10 seconds |
Creating BAM files | 21:55:51 01 Feb 2021 | 22:05:59 01 Feb 2021 | 10 minutes 8 seconds |
Tabulating error counts | 22:05:59 01 Feb 2021 | 22:10:34 01 Feb 2021 | 4 minutes 35 seconds |
Re-calibrating base error rates | 22:10:34 01 Feb 2021 | 22:10:37 01 Feb 2021 | 3 seconds |
Examining read alignment evidence | 22:10:37 01 Feb 2021 | 23:02:27 01 Feb 2021 | 51 minutes 50 seconds |
Polymorphism statistics | 23:02:27 01 Feb 2021 | 23:02:29 01 Feb 2021 | 2 seconds |
Output | 23:02:29 01 Feb 2021 | 23:03:36 01 Feb 2021 | 1 minute 7 seconds |
Total | 2 hours 40 minutes 2 seconds |