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 | SRR14920172_R1.good.fq | 9,873,579 | 1,362,016,304 | 100.0% | 137.9 bases | 140 bases | 99.2% |
errors | SRR14920172_R2.good.fq | 9,873,579 | 1,362,016,304 | 100.0% | 137.9 bases | 140 bases | 96.8% |
total | 19,747,158 | 2,724,032,608 | 100.0% | 137.9 bases | 140 bases | 98.0% |
seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
---|---|---|---|---|---|---|---|
coverage | distribution | NZ_CP025268 | 4,643,559 | 586.6 | 22.0 | 100.0% | Escherichia coli str. K-12 substr. MG1655 strain K-12 chromosome, |
total | 4,643,559 | 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 | 23794 |
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 | 534 |
Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.034 |
reference sequence | pr(no read start) |
---|---|
NZ_CP025268 | 0.52777 |
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 | 23:16:26 03 Mar 2023 | 23:21:44 03 Mar 2023 | 5 minutes 18 seconds |
Read alignment to reference genome | 23:21:44 03 Mar 2023 | 00:03:30 04 Mar 2023 | 41 minutes 46 seconds |
Preprocessing alignments for candidate junction identification | 00:03:30 04 Mar 2023 | 00:08:39 04 Mar 2023 | 5 minutes 9 seconds |
Preliminary analysis of coverage distribution | 00:08:39 04 Mar 2023 | 00:18:08 04 Mar 2023 | 9 minutes 29 seconds |
Identifying junction candidates | 00:18:08 04 Mar 2023 | 00:20:37 04 Mar 2023 | 2 minutes 29 seconds |
Re-alignment to junction candidates | 00:20:37 04 Mar 2023 | 00:32:23 04 Mar 2023 | 11 minutes 46 seconds |
Resolving best read alignments | 00:32:23 04 Mar 2023 | 00:39:05 04 Mar 2023 | 6 minutes 42 seconds |
Creating BAM files | 00:39:05 04 Mar 2023 | 00:47:07 04 Mar 2023 | 8 minutes 2 seconds |
Tabulating error counts | 00:47:07 04 Mar 2023 | 00:50:56 04 Mar 2023 | 3 minutes 49 seconds |
Re-calibrating base error rates | 00:50:56 04 Mar 2023 | 00:50:57 04 Mar 2023 | 1 second |
Examining read alignment evidence | 00:50:57 04 Mar 2023 | 01:40:19 04 Mar 2023 | 49 minutes 22 seconds |
Polymorphism statistics | 01:40:19 04 Mar 2023 | 01:40:20 04 Mar 2023 | 1 second |
Output | 01:40:20 04 Mar 2023 | 01:42:24 04 Mar 2023 | 2 minutes 4 seconds |
Total | 2 hours 25 minutes 58 seconds |