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 | DRR075742_R1.good.fq | 2,001,254 | 533,258,828 | 100.0% | 266.5 bases | 289 bases | 99.4% |
errors | DRR075742_R2.good.fq | 2,001,254 | 533,787,576 | 100.0% | 266.7 bases | 289 bases | 94.6% |
total | 4,002,508 | 1,067,046,404 | 100.0% | 266.6 bases | 289 bases | 97.0% |
seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
---|---|---|---|---|---|---|---|
coverage | distribution | AP012306 | 3,976,195 | 250.8 | 5.5 | 100.0% | Escherichia coli str. K-12 substr. MDS42 DNA, complete genome. |
total | 3,976,195 | 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 | 13195 |
Coverage evenness (position-hash) score of junction candidates | ≥ 2 | ≥ 3 |
Test this many junction candidates (n). May be smaller if not enough passed the coverage evenness threshold | 100 ≤ n ≤ 5000 | 36 |
Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.005 |
reference sequence | pr(no read start) |
---|---|
AP012306 | 0.74988 |
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 | 10:38:52 09 Feb 2023 | 10:40:03 09 Feb 2023 | 1 minute 11 seconds |
Read alignment to reference genome | 10:40:03 09 Feb 2023 | 10:56:32 09 Feb 2023 | 16 minutes 29 seconds |
Preprocessing alignments for candidate junction identification | 10:56:32 09 Feb 2023 | 10:57:40 09 Feb 2023 | 1 minute 8 seconds |
Preliminary analysis of coverage distribution | 10:57:40 09 Feb 2023 | 11:01:10 09 Feb 2023 | 3 minutes 30 seconds |
Identifying junction candidates | 11:01:10 09 Feb 2023 | 11:01:30 09 Feb 2023 | 20 seconds |
Re-alignment to junction candidates | 11:01:30 09 Feb 2023 | 11:04:46 09 Feb 2023 | 3 minutes 16 seconds |
Resolving best read alignments | 11:04:46 09 Feb 2023 | 11:06:18 09 Feb 2023 | 1 minute 32 seconds |
Creating BAM files | 11:06:18 09 Feb 2023 | 11:09:14 09 Feb 2023 | 2 minutes 56 seconds |
Tabulating error counts | 11:09:14 09 Feb 2023 | 11:10:57 09 Feb 2023 | 1 minute 43 seconds |
Re-calibrating base error rates | 11:10:57 09 Feb 2023 | 11:10:58 09 Feb 2023 | 1 second |
Examining read alignment evidence | 11:10:58 09 Feb 2023 | 11:31:17 09 Feb 2023 | 20 minutes 19 seconds |
Polymorphism statistics | 11:31:17 09 Feb 2023 | 11:31:17 09 Feb 2023 | 0 seconds |
Output | 11:31:17 09 Feb 2023 | 11:31:36 09 Feb 2023 | 19 seconds |
Total | 52 minutes 44 seconds |