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 | R2_Lane3_BC09_R1.good.fq | 1,166,558 | 88,590,249 | 100.0% | 75.9 bases | 76 bases | 97.9% |
errors | R2_Lane3_BC09_R2.good.fq | 1,166,557 | 88,590,173 | 100.0% | 75.9 bases | 76 bases | 95.0% |
total | 2,333,115 | 177,180,422 | 100.0% | 75.9 bases | 76 bases | 96.5% |
seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
---|---|---|---|---|---|---|---|
coverage | distribution | REL606 | 4,629,812 | 37.2 | 1.9 | 100.0% | Escherichia coli strain REL606. |
total | 4,629,812 | 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 | 3697 |
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 | 37 |
Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.001 |
reference sequence | pr(no read start) |
---|---|
REL606 | 0.79899 |
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 | 2.3.4.1 |
R | 3.4.4 |
step | start | end | elapsed |
---|---|---|---|
Read and reference sequence file input | 20:40:50 01 Feb 2019 | 20:41:14 01 Feb 2019 | 24 seconds |
Read alignment to reference genome | 20:41:15 01 Feb 2019 | 20:44:52 01 Feb 2019 | 3 minutes 37 seconds |
Preprocessing alignments for candidate junction identification | 20:44:52 01 Feb 2019 | 20:45:18 01 Feb 2019 | 26 seconds |
Preliminary analysis of coverage distribution | 20:45:18 01 Feb 2019 | 20:46:17 01 Feb 2019 | 59 seconds |
Identifying junction candidates | 20:46:17 01 Feb 2019 | 20:46:17 01 Feb 2019 | 0 seconds |
Re-alignment to junction candidates | 20:46:17 01 Feb 2019 | 20:47:07 01 Feb 2019 | 50 seconds |
Resolving best read alignments | 20:47:07 01 Feb 2019 | 20:47:49 01 Feb 2019 | 42 seconds |
Creating BAM files | 20:47:49 01 Feb 2019 | 20:48:43 01 Feb 2019 | 54 seconds |
Tabulating error counts | 20:48:43 01 Feb 2019 | 20:48:58 01 Feb 2019 | 15 seconds |
Re-calibrating base error rates | 20:48:58 01 Feb 2019 | 20:48:59 01 Feb 2019 | 1 second |
Examining read alignment evidence | 20:48:59 01 Feb 2019 | 20:51:37 01 Feb 2019 | 2 minutes 38 seconds |
Polymorphism statistics | 20:51:37 01 Feb 2019 | 20:51:37 01 Feb 2019 | 0 seconds |
Output | 20:51:37 01 Feb 2019 | 20:51:44 01 Feb 2019 | 7 seconds |
Total | 10 minutes 53 seconds |