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 | SRR5762420_R1.good.fq | 34,537,528 | 2,330,332,916 | 100.0% | 67.5 bases | 68 bases | 98.9% |
total | 34,537,528 | 2,330,332,916 | 100.0% | 67.5 bases | 68 bases | 98.9% |
seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
---|---|---|---|---|---|---|---|
coverage | distribution | CP009273 | 4,631,469 | 491.6 | 33.9 | 100.0% | Escherichia coli BW25113, complete genome. |
total | 4,631,469 | 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 | 35891 |
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 | 1975 |
Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.061 |
reference sequence | pr(no read start) |
---|---|
CP009273 | 0.49689 |
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 | ≤ 0 |
Number of bases that at least one read must overlap each uniquely aligned side of a predicted junction | ≥ 6 |
option | value |
---|---|
Mode | Full Polymorphism |
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 | 2 |
Polymorphism frequency cutoff | 0.05 |
Polymorphism minimum variant coverage each strand | 2 |
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 | ≥3 bases |
Skip base substitutions when they create a homopolymer flanked on each side by | ≥5 bases |
program | version |
---|---|
bowtie2 | 2.2.6 |
R | 3.4.4 |
step | start | end | elapsed |
---|---|---|---|
Read and reference sequence file input | 11:24:21 03 May 2021 | 11:31:58 03 May 2021 | 7 minutes 37 seconds |
Read alignment to reference genome | 11:31:58 03 May 2021 | 12:09:46 03 May 2021 | 37 minutes 48 seconds |
Preprocessing alignments for candidate junction identification | 12:09:46 03 May 2021 | 12:16:07 03 May 2021 | 6 minutes 21 seconds |
Preliminary analysis of coverage distribution | 12:16:07 03 May 2021 | 12:26:34 03 May 2021 | 10 minutes 27 seconds |
Identifying junction candidates | 12:26:34 03 May 2021 | 12:27:39 03 May 2021 | 1 minute 5 seconds |
Re-alignment to junction candidates | 12:27:39 03 May 2021 | 12:38:21 03 May 2021 | 10 minutes 42 seconds |
Resolving best read alignments | 12:38:21 03 May 2021 | 12:47:24 03 May 2021 | 9 minutes 3 seconds |
Creating BAM files | 12:47:24 03 May 2021 | 12:56:55 03 May 2021 | 9 minutes 31 seconds |
Tabulating error counts | 12:56:55 03 May 2021 | 13:00:19 03 May 2021 | 3 minutes 24 seconds |
Re-calibrating base error rates | 13:00:19 03 May 2021 | 13:00:19 03 May 2021 | 0 seconds |
Examining read alignment evidence | 13:00:19 03 May 2021 | 17:36:31 03 May 2021 | 4 hours 36 minutes 12 seconds |
Polymorphism statistics | 17:36:31 03 May 2021 | 17:36:32 03 May 2021 | 1 second |
Output | 17:36:32 03 May 2021 | 17:38:27 03 May 2021 | 1 minute 55 seconds |
Total | 6 hours 14 minutes 6 seconds |