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 | SRR13523665_R1.good.fq | 409,820 | 75,398,774 | 100.0% | 184.0 bases | 275 bases | 93.9% |
errors | SRR13523665_R2.good.fq | 409,819 | 91,138,345 | 100.0% | 222.4 bases | 275 bases | 41.1% |
total | 819,639 | 166,537,119 | 100.0% | 203.2 bases | 275 bases | 67.5% |
seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
---|---|---|---|---|---|---|---|
coverage | distribution | NC_000913 | 4,641,652 | 21.1 | 3.0 | 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 | 536 |
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 | 39 |
Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.005 |
reference sequence | pr(no read start) |
---|---|
NC_000913 | 0.95491 |
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 | 09:07:52 01 Feb 2023 | 09:08:12 01 Feb 2023 | 20 seconds |
Read alignment to reference genome | 09:08:12 01 Feb 2023 | 09:14:23 01 Feb 2023 | 6 minutes 11 seconds |
Preprocessing alignments for candidate junction identification | 09:14:23 01 Feb 2023 | 09:14:39 01 Feb 2023 | 16 seconds |
Preliminary analysis of coverage distribution | 09:14:39 01 Feb 2023 | 09:15:13 01 Feb 2023 | 34 seconds |
Identifying junction candidates | 09:15:13 01 Feb 2023 | 09:15:14 01 Feb 2023 | 1 second |
Re-alignment to junction candidates | 09:15:14 01 Feb 2023 | 09:16:09 01 Feb 2023 | 55 seconds |
Resolving best read alignments | 09:16:09 01 Feb 2023 | 09:16:32 01 Feb 2023 | 23 seconds |
Creating BAM files | 09:16:32 01 Feb 2023 | 09:17:01 01 Feb 2023 | 29 seconds |
Tabulating error counts | 09:17:01 01 Feb 2023 | 09:17:16 01 Feb 2023 | 15 seconds |
Re-calibrating base error rates | 09:17:16 01 Feb 2023 | 09:17:18 01 Feb 2023 | 2 seconds |
Examining read alignment evidence | 09:17:18 01 Feb 2023 | 09:26:54 01 Feb 2023 | 9 minutes 36 seconds |
Polymorphism statistics | 09:26:54 01 Feb 2023 | 09:26:55 01 Feb 2023 | 1 second |
Output | 09:26:55 01 Feb 2023 | 09:28:01 01 Feb 2023 | 1 minute 6 seconds |
Total | 20 minutes 9 seconds |