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 | SvNSRound4_18_5_S372_L002_R1_001.good.fq | 421,746 | 60,489,234 | 100.0% | 143.4 bases | 149 bases | 97.7% |
errors | SvNSRound4_18_5_S372_L002_R2_001.good.fq | 421,746 | 60,489,234 | 100.0% | 143.4 bases | 149 bases | 90.3% |
total | 843,492 | 120,978,468 | 100.0% | 143.4 bases | 149 bases | 94.0% |
seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
---|---|---|---|---|---|---|---|
coverage | distribution | NC_000913_3_pae_tpiA | 4,641,568 | 23.8 | 1.6 | 100.0% | Escherichia coli str. K-12 substr. MG1655, P. aerophilum tpiA gene, complete genome. |
total | 4,641,568 | 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 | 3804 |
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 | 373 |
Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.024 |
reference sequence | pr(no read start) |
---|---|
NC_000913_3_pae_tpiA | 0.92634 |
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 | 17:57:15 19 Dec 2020 | 17:58:01 19 Dec 2020 | 46 seconds |
Read alignment to reference genome | 17:58:02 19 Dec 2020 | 18:05:28 19 Dec 2020 | 7 minutes 26 seconds |
Preprocessing alignments for candidate junction identification | 18:05:28 19 Dec 2020 | 18:06:02 19 Dec 2020 | 34 seconds |
Preliminary analysis of coverage distribution | 18:06:02 19 Dec 2020 | 18:07:38 19 Dec 2020 | 1 minute 36 seconds |
Identifying junction candidates | 18:07:38 19 Dec 2020 | 18:07:40 19 Dec 2020 | 2 seconds |
Re-alignment to junction candidates | 18:07:40 19 Dec 2020 | 18:09:21 19 Dec 2020 | 1 minute 41 seconds |
Resolving best read alignments | 18:09:21 19 Dec 2020 | 18:10:10 19 Dec 2020 | 49 seconds |
Creating BAM files | 18:10:10 19 Dec 2020 | 18:11:35 19 Dec 2020 | 1 minute 25 seconds |
Tabulating error counts | 18:11:35 19 Dec 2020 | 18:12:07 19 Dec 2020 | 32 seconds |
Re-calibrating base error rates | 18:12:07 19 Dec 2020 | 18:12:10 19 Dec 2020 | 3 seconds |
Examining read alignment evidence | 18:12:10 19 Dec 2020 | 18:20:15 19 Dec 2020 | 8 minutes 5 seconds |
Polymorphism statistics | 18:20:15 19 Dec 2020 | 18:20:16 19 Dec 2020 | 1 second |
Output | 18:20:16 19 Dec 2020 | 18:20:39 19 Dec 2020 | 23 seconds |
Total | 23 minutes 23 seconds |