breseq version 0.33.1 revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
read file | reads | bases | passed filters | average | longest | mapped | |
---|---|---|---|---|---|---|---|
errors | DRR075740_R1.good.fq | 3,329,300 | 768,428,667 | 100.0% | 230.8 bases | 289 bases | 99.1% |
errors | DRR075740_R2.good.fq | 3,329,300 | 770,033,627 | 100.0% | 231.3 bases | 289 bases | 95.8% |
total | 6,658,600 | 1,538,462,294 | 100.0% | 231.0 bases | 289 bases | 97.5% |
seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
---|---|---|---|---|---|---|---|
coverage | distribution | CP042583 | 3,977,116 | 385.2 | 7.5 | 100.0% | Escherichia coli str. K-12 substr. MDS42 strain SynAC chromosome, |
total | 3,977,116 | 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 | 22386 |
Coverage evenness (position-hash) score of junction candidates | ≥ 2 | ≥ 3 |
Test this many junction candidates (n). May be smaller if not enough passed the coverage evenness threshold | 100 ≤ n ≤ 5000 | 80 |
Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.012 |
reference sequence | pr(no read start) |
---|---|
CP042583 | 0.65852 |
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 | ≤ 3 |
Number of bases that at least one read must overlap each uniquely aligned side of a predicted junction | ≥ 1 |
option | value |
---|---|
Mode | Consensus/Mixed Base |
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 | 10 |
Polymorphism frequency cutoff | 0.2 |
Polymorphism minimum variant coverage each strand | OFF |
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 | OFF |
Skip base substitutions when they create a homopolymer flanked on each side by | OFF |
program | version |
---|---|
bowtie2 | 2.2.6 |
R | 3.4.4 |
step | start | end | elapsed |
---|---|---|---|
Read and reference sequence file input | 07:44:00 07 Mar 2020 | 07:46:00 07 Mar 2020 | 2 minutes 0 seconds |
Read alignment to reference genome | 07:46:00 07 Mar 2020 | 08:10:00 07 Mar 2020 | 24 minutes 0 seconds |
Preprocessing alignments for candidate junction identification | 08:10:00 07 Mar 2020 | 08:12:02 07 Mar 2020 | 2 minutes 2 seconds |
Preliminary analysis of coverage distribution | 08:12:02 07 Mar 2020 | 08:16:22 07 Mar 2020 | 4 minutes 20 seconds |
Identifying junction candidates | 08:16:22 07 Mar 2020 | 08:18:34 07 Mar 2020 | 2 minutes 12 seconds |
Re-alignment to junction candidates | 08:18:34 07 Mar 2020 | 08:23:16 07 Mar 2020 | 4 minutes 42 seconds |
Resolving best read alignments | 08:23:16 07 Mar 2020 | 08:26:43 07 Mar 2020 | 3 minutes 27 seconds |
Creating BAM files | 08:26:43 07 Mar 2020 | 08:30:18 07 Mar 2020 | 3 minutes 35 seconds |
Tabulating error counts | 08:30:18 07 Mar 2020 | 08:32:50 07 Mar 2020 | 2 minutes 32 seconds |
Re-calibrating base error rates | 08:32:50 07 Mar 2020 | 08:32:51 07 Mar 2020 | 1 second |
Examining read alignment evidence | 08:32:51 07 Mar 2020 | 08:59:15 07 Mar 2020 | 26 minutes 24 seconds |
Polymorphism statistics | 08:59:15 07 Mar 2020 | 08:59:24 07 Mar 2020 | 9 seconds |
Output | 08:59:24 07 Mar 2020 | 09:13:47 07 Mar 2020 | 14 minutes 23 seconds |
Total | 1 hour 29 minutes 47 seconds |