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 | SvNSRound2_24_26_S103_L002_R1_001.good.fq | 1,007,896 | 145,250,780 | 100.0% | 144.1 bases | 149 bases | 94.9% |
errors | SvNSRound2_24_26_S103_L002_R2_001.good.fq | 1,007,896 | 145,250,780 | 100.0% | 144.1 bases | 149 bases | 84.7% |
total | 2,015,792 | 290,501,560 | 100.0% | 144.1 bases | 149 bases | 89.8% |
seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
---|---|---|---|---|---|---|---|
coverage | distribution | NC_000913_3_bme_pgi | 4,641,653 | 55.9 | 1.7 | 100.0% | Escherichia coli str. K-12 substr. MG1655, B. melitensis pgi gene, complete genome. |
total | 4,641,653 | 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 | 13957 |
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 | 122 |
Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.008 |
reference sequence | pr(no read start) |
---|---|
NC_000913_3_bme_pgi | 0.84665 |
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 | 18:07:19 19 Dec 2020 | 18:09:06 19 Dec 2020 | 1 minute 47 seconds |
Read alignment to reference genome | 18:09:07 19 Dec 2020 | 18:27:24 19 Dec 2020 | 18 minutes 17 seconds |
Preprocessing alignments for candidate junction identification | 18:27:24 19 Dec 2020 | 18:28:44 19 Dec 2020 | 1 minute 20 seconds |
Preliminary analysis of coverage distribution | 18:28:44 19 Dec 2020 | 18:32:17 19 Dec 2020 | 3 minutes 33 seconds |
Identifying junction candidates | 18:32:17 19 Dec 2020 | 18:32:57 19 Dec 2020 | 40 seconds |
Re-alignment to junction candidates | 18:32:57 19 Dec 2020 | 18:36:36 19 Dec 2020 | 3 minutes 39 seconds |
Resolving best read alignments | 18:36:36 19 Dec 2020 | 18:38:38 19 Dec 2020 | 2 minutes 2 seconds |
Creating BAM files | 18:38:38 19 Dec 2020 | 18:42:18 19 Dec 2020 | 3 minutes 40 seconds |
Tabulating error counts | 18:42:18 19 Dec 2020 | 18:43:31 19 Dec 2020 | 1 minute 13 seconds |
Re-calibrating base error rates | 18:43:31 19 Dec 2020 | 18:43:34 19 Dec 2020 | 3 seconds |
Examining read alignment evidence | 18:43:34 19 Dec 2020 | 19:00:22 19 Dec 2020 | 16 minutes 48 seconds |
Polymorphism statistics | 19:00:22 19 Dec 2020 | 19:00:23 19 Dec 2020 | 1 second |
Output | 19:00:23 19 Dec 2020 | 19:00:48 19 Dec 2020 | 25 seconds |
Total | 53 minutes 28 seconds |