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 | ERR1957972_R1.good.fq | 1,257,202 | 284,067,921 | 100.0% | 226.0 bases | 240 bases | 99.4% |
errors | ERR1957972_R2.good.fq | 1,257,194 | 257,351,549 | 100.0% | 204.7 bases | 240 bases | 97.0% |
total | 2,514,396 | 541,419,470 | 100.0% | 215.3 bases | 240 bases | 98.2% |
seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
---|---|---|---|---|---|---|---|
coverage | distribution | NC_000913 | 4,641,652 | 107.2 | 5.3 | 93.9% | Escherichia coli str. K-12 substr. MG1655, complete genome. |
coverage | distribution | BN000925 | 60,096 | 565.6 | 15.7 | 6.1% | TPA_exp: Birmingham IncP-alpha plasmid, complete sequence, isolate |
total | 4,701,748 | 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 | 3167 |
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 | 102 |
Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.011 |
reference sequence | pr(no read start) |
---|---|
NC_000913 | 0.83520 |
BN000925 | 0.54393 |
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 | 15:02:52 08 Dec 2020 | 15:05:30 08 Dec 2020 | 2 minutes 38 seconds |
Read alignment to reference genome | 15:05:31 08 Dec 2020 | 15:33:35 08 Dec 2020 | 28 minutes 4 seconds |
Preprocessing alignments for candidate junction identification | 15:33:35 08 Dec 2020 | 15:35:51 08 Dec 2020 | 2 minutes 16 seconds |
Preliminary analysis of coverage distribution | 15:35:51 08 Dec 2020 | 15:42:53 08 Dec 2020 | 7 minutes 2 seconds |
Identifying junction candidates | 15:42:53 08 Dec 2020 | 15:42:57 08 Dec 2020 | 4 seconds |
Re-alignment to junction candidates | 15:42:57 08 Dec 2020 | 15:51:16 08 Dec 2020 | 8 minutes 19 seconds |
Resolving best read alignments | 15:51:16 08 Dec 2020 | 15:54:09 08 Dec 2020 | 2 minutes 53 seconds |
Creating BAM files | 15:54:09 08 Dec 2020 | 16:00:29 08 Dec 2020 | 6 minutes 20 seconds |
Tabulating error counts | 16:00:29 08 Dec 2020 | 16:02:53 08 Dec 2020 | 2 minutes 24 seconds |
Re-calibrating base error rates | 16:02:53 08 Dec 2020 | 16:02:57 08 Dec 2020 | 4 seconds |
Examining read alignment evidence | 16:02:57 08 Dec 2020 | 16:30:19 08 Dec 2020 | 27 minutes 22 seconds |
Polymorphism statistics | 16:30:19 08 Dec 2020 | 16:30:20 08 Dec 2020 | 1 second |
Output | 16:30:20 08 Dec 2020 | 16:31:19 08 Dec 2020 | 59 seconds |
Total | 1 hour 28 minutes 26 seconds |