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 | SRR5762427_R1.good.fq | 51,331,608 | 3,463,938,805 | 100.0% | 67.5 bases | 68 bases | 99.3% |
total | 51,331,608 | 3,463,938,805 | 100.0% | 67.5 bases | 68 bases | 99.3% |
seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
---|---|---|---|---|---|---|---|
coverage | distribution | CP009273 | 4,631,469 | 742.9 | 44.4 | 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 | 56300 |
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 | 2692 |
Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.084 |
reference sequence | pr(no read start) |
---|---|
CP009273 | 0.44358 |
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 | 11:35:07 03 May 2021 | 11:46:40 03 May 2021 | 11 minutes 33 seconds |
Read alignment to reference genome | 11:46:41 03 May 2021 | 12:44:05 03 May 2021 | 57 minutes 24 seconds |
Preprocessing alignments for candidate junction identification | 12:44:05 03 May 2021 | 12:54:57 03 May 2021 | 10 minutes 52 seconds |
Preliminary analysis of coverage distribution | 12:54:57 03 May 2021 | 13:10:46 03 May 2021 | 15 minutes 49 seconds |
Identifying junction candidates | 13:10:46 03 May 2021 | 13:13:16 03 May 2021 | 2 minutes 30 seconds |
Re-alignment to junction candidates | 13:13:16 03 May 2021 | 13:30:41 03 May 2021 | 17 minutes 25 seconds |
Resolving best read alignments | 13:30:41 03 May 2021 | 13:44:22 03 May 2021 | 13 minutes 41 seconds |
Creating BAM files | 13:44:22 03 May 2021 | 13:58:35 03 May 2021 | 14 minutes 13 seconds |
Tabulating error counts | 13:58:35 03 May 2021 | 14:03:40 03 May 2021 | 5 minutes 5 seconds |
Re-calibrating base error rates | 14:03:40 03 May 2021 | 14:03:41 03 May 2021 | 1 second |
Examining read alignment evidence | 14:03:41 03 May 2021 | 22:05:28 03 May 2021 | 8 hours 1 minute 47 seconds |
Polymorphism statistics | 22:05:28 03 May 2021 | 22:05:29 03 May 2021 | 1 second |
Output | 22:05:29 03 May 2021 | 22:08:40 03 May 2021 | 3 minutes 11 seconds |
Total | 10 hours 33 minutes 32 seconds |