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 | SRR064643_R1.good.fq | 4,872,745 | 369,606,257 | 100.0% | 75.9 bases | 76 bases | 87.8% |
errors | SRR064643_R2.good.fq | 4,872,746 | 369,606,333 | 100.0% | 75.9 bases | 76 bases | 83.5% |
total | 9,745,491 | 739,212,590 | 100.0% | 75.9 bases | 76 bases | 85.7% |
seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
---|---|---|---|---|---|---|---|
coverage | distribution | NC_000913 | 4,639,221 | 132.7 | 6.5 | 100.0% | Escherichia coli K12, complete genome. |
total | 4,639,221 | 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 | 13990 |
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 | 603 |
Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.021 |
reference sequence | pr(no read start) |
---|---|
NC_000913 | 0.48367 |
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 | 18:40:39 13 May 2019 | 18:42:13 13 May 2019 | 1 minute 34 seconds |
Read alignment to reference genome | 18:42:13 13 May 2019 | 19:00:11 13 May 2019 | 17 minutes 58 seconds |
Preprocessing alignments for candidate junction identification | 19:00:11 13 May 2019 | 19:01:46 13 May 2019 | 1 minute 35 seconds |
Preliminary analysis of coverage distribution | 19:01:46 13 May 2019 | 19:04:16 13 May 2019 | 2 minutes 30 seconds |
Identifying junction candidates | 19:04:16 13 May 2019 | 19:04:33 13 May 2019 | 17 seconds |
Re-alignment to junction candidates | 19:04:33 13 May 2019 | 19:08:31 13 May 2019 | 3 minutes 58 seconds |
Resolving best read alignments | 19:08:31 13 May 2019 | 19:11:05 13 May 2019 | 2 minutes 34 seconds |
Creating BAM files | 19:11:05 13 May 2019 | 19:13:19 13 May 2019 | 2 minutes 14 seconds |
Tabulating error counts | 19:13:19 13 May 2019 | 19:14:15 13 May 2019 | 56 seconds |
Re-calibrating base error rates | 19:14:15 13 May 2019 | 19:14:16 13 May 2019 | 1 second |
Examining read alignment evidence | 19:14:16 13 May 2019 | 19:24:01 13 May 2019 | 9 minutes 45 seconds |
Polymorphism statistics | 19:24:01 13 May 2019 | 19:24:03 13 May 2019 | 2 seconds |
Output | 19:24:03 13 May 2019 | 19:24:42 13 May 2019 | 39 seconds |
Total | 44 minutes 3 seconds |