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 | ERR1957967_R1.good.fq | 1,553,024 | 338,669,060 | 100.0% | 218.1 bases | 240 bases | 99.6% |
errors | ERR1957967_R2.good.fq | 1,553,022 | 317,685,185 | 100.0% | 204.6 bases | 240 bases | 98.4% |
total | 3,106,046 | 656,354,245 | 100.0% | 211.3 bases | 240 bases | 99.0% |
seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
---|---|---|---|---|---|---|---|
coverage | distribution | NC_000913 | 4,641,652 | 133.2 | 6.4 | 95.5% | Escherichia coli str. K-12 substr. MG1655, complete genome. |
coverage | distribution | BN000925 | 60,096 | 503.9 | 13.5 | 4.5% | 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 | 4573 |
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 | 186 |
Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.019 |
reference sequence | pr(no read start) |
---|---|
NC_000913 | 0.80272 |
BN000925 | 0.55965 |
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 | 15:12:01 08 Dec 2020 | 15:16:10 08 Dec 2020 | 4 minutes 9 seconds |
Read alignment to reference genome | 15:16:11 08 Dec 2020 | 15:48:41 08 Dec 2020 | 32 minutes 30 seconds |
Preprocessing alignments for candidate junction identification | 15:48:41 08 Dec 2020 | 15:52:15 08 Dec 2020 | 3 minutes 34 seconds |
Preliminary analysis of coverage distribution | 15:52:15 08 Dec 2020 | 16:02:59 08 Dec 2020 | 10 minutes 44 seconds |
Identifying junction candidates | 16:02:59 08 Dec 2020 | 16:03:06 08 Dec 2020 | 7 seconds |
Re-alignment to junction candidates | 16:03:06 08 Dec 2020 | 16:12:13 08 Dec 2020 | 9 minutes 7 seconds |
Resolving best read alignments | 16:12:13 08 Dec 2020 | 16:16:48 08 Dec 2020 | 4 minutes 35 seconds |
Creating BAM files | 16:16:48 08 Dec 2020 | 16:26:36 08 Dec 2020 | 9 minutes 48 seconds |
Tabulating error counts | 16:26:36 08 Dec 2020 | 16:29:52 08 Dec 2020 | 3 minutes 16 seconds |
Re-calibrating base error rates | 16:29:52 08 Dec 2020 | 16:29:57 08 Dec 2020 | 5 seconds |
Examining read alignment evidence | 16:29:57 08 Dec 2020 | 17:09:59 08 Dec 2020 | 40 minutes 2 seconds |
Polymorphism statistics | 17:09:59 08 Dec 2020 | 17:10:00 08 Dec 2020 | 1 second |
Output | 17:10:00 08 Dec 2020 | 17:11:17 08 Dec 2020 | 1 minute 17 seconds |
Total | 1 hour 59 minutes 15 seconds |