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 | ERR1957961_R1.good.fq | 1,320,283 | 296,290,450 | 100.0% | 224.4 bases | 240 bases | 99.6% |
errors | ERR1957961_R2.good.fq | 1,320,280 | 275,293,108 | 100.0% | 208.5 bases | 240 bases | 98.1% |
total | 2,640,563 | 571,583,558 | 100.0% | 216.5 bases | 240 bases | 98.9% |
seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
---|---|---|---|---|---|---|---|
coverage | distribution | NC_000913 | 4,641,652 | 121.8 | 5.6 | 100.0% | Escherichia coli str. K-12 substr. MG1655, complete genome. |
total | 4,641,652 | 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 | 8314 |
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 | 125 |
Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.013 |
reference sequence | pr(no read start) |
---|---|
NC_000913 | 0.81919 |
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 | 15:07:56 08 Dec 2020 | 15:11:15 08 Dec 2020 | 3 minutes 19 seconds |
Read alignment to reference genome | 15:11:16 08 Dec 2020 | 15:42:18 08 Dec 2020 | 31 minutes 2 seconds |
Preprocessing alignments for candidate junction identification | 15:42:18 08 Dec 2020 | 15:45:13 08 Dec 2020 | 2 minutes 55 seconds |
Preliminary analysis of coverage distribution | 15:45:13 08 Dec 2020 | 15:54:41 08 Dec 2020 | 9 minutes 28 seconds |
Identifying junction candidates | 15:54:41 08 Dec 2020 | 15:54:51 08 Dec 2020 | 10 seconds |
Re-alignment to junction candidates | 15:54:51 08 Dec 2020 | 16:02:50 08 Dec 2020 | 7 minutes 59 seconds |
Resolving best read alignments | 16:02:50 08 Dec 2020 | 16:06:39 08 Dec 2020 | 3 minutes 49 seconds |
Creating BAM files | 16:06:39 08 Dec 2020 | 16:15:08 08 Dec 2020 | 8 minutes 29 seconds |
Tabulating error counts | 16:15:08 08 Dec 2020 | 16:17:56 08 Dec 2020 | 2 minutes 48 seconds |
Re-calibrating base error rates | 16:17:56 08 Dec 2020 | 16:18:00 08 Dec 2020 | 4 seconds |
Examining read alignment evidence | 16:18:00 08 Dec 2020 | 16:52:57 08 Dec 2020 | 34 minutes 57 seconds |
Polymorphism statistics | 16:52:57 08 Dec 2020 | 16:52:57 08 Dec 2020 | 0 seconds |
Output | 16:52:57 08 Dec 2020 | 16:53:56 08 Dec 2020 | 59 seconds |
Total | 1 hour 45 minutes 59 seconds |