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 | SRR5762422_R1.good.fq | 37,171,703 | 2,507,712,646 | 100.0% | 67.5 bases | 68 bases | 98.7% |
total | 37,171,703 | 2,507,712,646 | 100.0% | 67.5 bases | 68 bases | 98.7% |
seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
---|---|---|---|---|---|---|---|
coverage | distribution | CP009273 | 4,631,469 | 520.7 | 32.4 | 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 | 43223 |
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 | 2477 |
Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.077 |
reference sequence | pr(no read start) |
---|---|
CP009273 | 0.48589 |
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 | 11:26:22 03 May 2021 | 11:34:41 03 May 2021 | 8 minutes 19 seconds |
Read alignment to reference genome | 11:34:41 03 May 2021 | 12:16:40 03 May 2021 | 41 minutes 59 seconds |
Preprocessing alignments for candidate junction identification | 12:16:40 03 May 2021 | 12:23:28 03 May 2021 | 6 minutes 48 seconds |
Preliminary analysis of coverage distribution | 12:23:28 03 May 2021 | 12:34:47 03 May 2021 | 11 minutes 19 seconds |
Identifying junction candidates | 12:34:47 03 May 2021 | 12:36:33 03 May 2021 | 1 minute 46 seconds |
Re-alignment to junction candidates | 12:36:33 03 May 2021 | 12:49:49 03 May 2021 | 13 minutes 16 seconds |
Resolving best read alignments | 12:49:49 03 May 2021 | 12:59:41 03 May 2021 | 9 minutes 52 seconds |
Creating BAM files | 12:59:41 03 May 2021 | 13:09:58 03 May 2021 | 10 minutes 17 seconds |
Tabulating error counts | 13:09:58 03 May 2021 | 13:13:38 03 May 2021 | 3 minutes 40 seconds |
Re-calibrating base error rates | 13:13:38 03 May 2021 | 13:13:39 03 May 2021 | 1 second |
Examining read alignment evidence | 13:13:39 03 May 2021 | 18:26:10 03 May 2021 | 5 hours 12 minutes 31 seconds |
Polymorphism statistics | 18:26:10 03 May 2021 | 18:26:11 03 May 2021 | 1 second |
Output | 18:26:11 03 May 2021 | 18:28:32 03 May 2021 | 2 minutes 21 seconds |
Total | 7 hours 2 minutes 10 seconds |