breseq version 0.32.0 revision 6ff6de7d1b87
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
read file | reads | bases | passed filters | average | longest | mapped | |
---|---|---|---|---|---|---|---|
errors | Evo04sdhCadhBEvo03EP_S22_L001_R1_001.good.fq | 769,465 | 209,264,854 | 100.0% | 272.0 bases | 289 bases | 99.8% |
errors | Evo04sdhCadhBEvo03EP_S22_L001_R2_001.good.fq | 769,465 | 209,328,254 | 100.0% | 272.0 bases | 289 bases | 98.2% |
total | 1,538,930 | 418,593,108 | 100.0% | 272.0 bases | 289 bases | 99.0% |
seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
---|---|---|---|---|---|---|---|
coverage | distribution | NC_000913 | 4,641,653 | 93.1 | 3.7 | 100.0% | Escherichia coli str. K-12 sbstr. MG1655, complete genome. Live strain from Systems Biology Research Group |
total | 4,641,653 | 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 | 2624 |
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 | 163 |
Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.021 |
reference sequence | pr(no read start) |
---|---|
NC_000913 | 0.88591 |
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 | 2.2.8 |
R | 3.3.1 |
step | start | end | elapsed |
---|---|---|---|
Read and reference sequence file input | 01:59:04 18 Mar 2018 | 01:59:28 18 Mar 2018 | 24 seconds |
Read alignment to reference genome | 01:59:28 18 Mar 2018 | 02:01:24 18 Mar 2018 | 1 minute 56 seconds |
Preprocessing alignments for candidate junction identification | 02:01:24 18 Mar 2018 | 02:01:52 18 Mar 2018 | 28 seconds |
Preliminary analysis of coverage distribution | 02:01:52 18 Mar 2018 | 02:02:50 18 Mar 2018 | 58 seconds |
Identifying junction candidates | 02:02:50 18 Mar 2018 | 02:02:53 18 Mar 2018 | 3 seconds |
Re-alignment to junction candidates | 02:02:53 18 Mar 2018 | 02:03:14 18 Mar 2018 | 21 seconds |
Resolving best read alignments | 02:03:14 18 Mar 2018 | 02:04:02 18 Mar 2018 | 48 seconds |
Creating BAM files | 02:04:02 18 Mar 2018 | 02:04:48 18 Mar 2018 | 46 seconds |
Tabulating error counts | 02:04:48 18 Mar 2018 | 02:05:22 18 Mar 2018 | 34 seconds |
Re-calibrating base error rates | 02:05:22 18 Mar 2018 | 02:05:23 18 Mar 2018 | 1 second |
Examining read alignment evidence | 02:05:23 18 Mar 2018 | 02:36:04 18 Mar 2018 | 30 minutes 41 seconds |
Polymorphism statistics | 02:36:04 18 Mar 2018 | 02:36:04 18 Mar 2018 | 0 seconds |
Output | 02:36:04 18 Mar 2018 | 02:36:20 18 Mar 2018 | 16 seconds |
Total | 37 minutes 16 seconds |