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 | ERR1351681_R1.good.fq | 3,346,467 | 337,915,537 | 100.0% | 101.0 bases | 101 bases | 99.4% |
errors | ERR1351681_R2.good.fq | 3,346,467 | 337,915,537 | 100.0% | 101.0 bases | 101 bases | 99.0% |
total | 6,692,934 | 675,831,074 | 100.0% | 101.0 bases | 101 bases | 99.2% |
seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
---|---|---|---|---|---|---|---|
coverage | distribution | CP009273 | 4,631,469 | 138.0 | 2.2 | 96.0% | Escherichia coli BW25113, complete genome. |
coverage | distribution | KX077536 | 8,187 | 3704.3 | 43.9 | 4.0% | Vector pCBB, complete sequence. |
total | 4,639,656 | 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 | 8017 |
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 | 57 |
Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.003 |
reference sequence | pr(no read start) |
---|---|
CP009273 | 0.52290 |
KX077536 | 0.00563 |
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 | 12:34:12 30 Mar 2021 | 12:35:59 30 Mar 2021 | 1 minute 47 seconds |
Read alignment to reference genome | 12:36:00 30 Mar 2021 | 12:46:56 30 Mar 2021 | 10 minutes 56 seconds |
Preprocessing alignments for candidate junction identification | 12:46:56 30 Mar 2021 | 12:48:16 30 Mar 2021 | 1 minute 20 seconds |
Preliminary analysis of coverage distribution | 12:48:16 30 Mar 2021 | 12:51:58 30 Mar 2021 | 3 minutes 42 seconds |
Identifying junction candidates | 12:51:58 30 Mar 2021 | 12:51:59 30 Mar 2021 | 1 second |
Re-alignment to junction candidates | 12:51:59 30 Mar 2021 | 12:54:49 30 Mar 2021 | 2 minutes 50 seconds |
Resolving best read alignments | 12:54:49 30 Mar 2021 | 12:56:38 30 Mar 2021 | 1 minute 49 seconds |
Creating BAM files | 12:56:38 30 Mar 2021 | 12:59:58 30 Mar 2021 | 3 minutes 20 seconds |
Tabulating error counts | 12:59:58 30 Mar 2021 | 13:01:02 30 Mar 2021 | 1 minute 4 seconds |
Re-calibrating base error rates | 13:01:02 30 Mar 2021 | 13:01:04 30 Mar 2021 | 2 seconds |
Examining read alignment evidence | 13:01:04 30 Mar 2021 | 13:12:24 30 Mar 2021 | 11 minutes 20 seconds |
Polymorphism statistics | 13:12:24 30 Mar 2021 | 13:12:24 30 Mar 2021 | 0 seconds |
Output | 13:12:24 30 Mar 2021 | 13:12:47 30 Mar 2021 | 23 seconds |
Total | 38 minutes 34 seconds |