breseq version 0.32.1 revision 5f2cb669173e
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
read file | reads | bases | passed filters | average | longest | mapped | |
---|---|---|---|---|---|---|---|
errors | SNFR_19_57_0_S2386_L001_R1_001.good.fq | 400,081 | 56,374,613 | 100.0% | 140.9 bases | 141 bases | 95.2% |
errors | SNFR_19_57_0_S2386_L001_R2_001.good.fq | 400,081 | 56,374,613 | 100.0% | 140.9 bases | 141 bases | 90.7% |
total | 800,162 | 112,749,226 | 100.0% | 140.9 bases | 141 bases | 93.0% |
seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
---|---|---|---|---|---|---|---|
coverage | distribution | CP000730 | 2,872,915 | 36.1 | 2.1 | 100.0% | Staphylococcus aureus subsp. aureus USA300_TCH1516, complete |
total | 2,872,915 | 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 | 923 |
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 | 13 |
Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.001 |
reference sequence | pr(no read start) |
---|---|
CP000730 | 0.89989 |
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 |
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 | OFF |
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 | 0.025 |
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 | 2.3.4.1 |
R | 3.5.0 |
step | start | end | elapsed |
---|---|---|---|
Read and reference sequence file input | 17:25:05 22 Jun 2018 | 17:25:36 22 Jun 2018 | 31 seconds |
Read alignment to reference genome | 17:25:36 22 Jun 2018 | 17:27:14 22 Jun 2018 | 1 minute 38 seconds |
Preprocessing alignments for candidate junction identification | 17:27:14 22 Jun 2018 | 17:27:34 22 Jun 2018 | 20 seconds |
Preliminary analysis of coverage distribution | 17:27:34 22 Jun 2018 | 17:28:05 22 Jun 2018 | 31 seconds |
Identifying junction candidates | 17:28:05 22 Jun 2018 | 17:28:05 22 Jun 2018 | 0 seconds |
Re-alignment to junction candidates | 17:28:05 22 Jun 2018 | 17:28:27 22 Jun 2018 | 22 seconds |
Resolving best read alignments | 17:28:27 22 Jun 2018 | 17:29:01 22 Jun 2018 | 34 seconds |
Creating BAM files | 17:29:01 22 Jun 2018 | 17:29:26 22 Jun 2018 | 25 seconds |
Tabulating error counts | 17:29:26 22 Jun 2018 | 17:29:37 22 Jun 2018 | 11 seconds |
Re-calibrating base error rates | 17:29:37 22 Jun 2018 | 17:29:38 22 Jun 2018 | 1 second |
Examining read alignment evidence | 17:29:38 22 Jun 2018 | 17:36:35 22 Jun 2018 | 6 minutes 57 seconds |
Polymorphism statistics | 17:36:35 22 Jun 2018 | 17:36:37 22 Jun 2018 | 2 seconds |
Output | 17:36:37 22 Jun 2018 | 17:36:44 22 Jun 2018 | 7 seconds |
Total | 11 minutes 39 seconds |