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 | SRR14920200_R1.good.fq | 11,627,145 | 1,609,978,077 | 100.0% | 138.5 bases | 140 bases | 99.5% |
errors | SRR14920200_R2.good.fq | 11,627,144 | 1,609,977,937 | 100.0% | 138.5 bases | 140 bases | 95.7% |
total | 23,254,289 | 3,219,956,014 | 100.0% | 138.5 bases | 140 bases | 97.6% |
seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
---|---|---|---|---|---|---|---|
coverage | distribution | NZ_CP025268 | 4,643,559 | 676.6 | 23.4 | 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 | 41446 |
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 | 859 |
Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.054 |
reference sequence | pr(no read start) |
---|---|
NZ_CP025268 | 0.49057 |
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 | 23:28:42 05 Mar 2023 | 23:34:30 05 Mar 2023 | 5 minutes 48 seconds |
Read alignment to reference genome | 23:34:30 05 Mar 2023 | 00:24:34 06 Mar 2023 | 50 minutes 4 seconds |
Preprocessing alignments for candidate junction identification | 00:24:34 06 Mar 2023 | 00:31:01 06 Mar 2023 | 6 minutes 27 seconds |
Preliminary analysis of coverage distribution | 00:31:01 06 Mar 2023 | 00:42:10 06 Mar 2023 | 11 minutes 9 seconds |
Identifying junction candidates | 00:42:10 06 Mar 2023 | 00:48:22 06 Mar 2023 | 6 minutes 12 seconds |
Re-alignment to junction candidates | 00:48:22 06 Mar 2023 | 01:03:44 06 Mar 2023 | 15 minutes 22 seconds |
Resolving best read alignments | 01:03:44 06 Mar 2023 | 01:11:50 06 Mar 2023 | 8 minutes 6 seconds |
Creating BAM files | 01:11:50 06 Mar 2023 | 01:21:25 06 Mar 2023 | 9 minutes 35 seconds |
Tabulating error counts | 01:21:25 06 Mar 2023 | 01:25:59 06 Mar 2023 | 4 minutes 34 seconds |
Re-calibrating base error rates | 01:25:59 06 Mar 2023 | 01:26:00 06 Mar 2023 | 1 second |
Examining read alignment evidence | 01:26:00 06 Mar 2023 | 02:24:56 06 Mar 2023 | 58 minutes 56 seconds |
Polymorphism statistics | 02:24:56 06 Mar 2023 | 02:24:57 06 Mar 2023 | 1 second |
Output | 02:24:57 06 Mar 2023 | 02:27:31 06 Mar 2023 | 2 minutes 34 seconds |
Total | 2 hours 58 minutes 49 seconds |