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 | GlyB_D15_I1_S2103_L001_R1_001.good.fq | 1,240,830 | 183,922,826 | 100.0% | 148.2 bases | 149 bases | 97.7% |
errors | GlyB_D15_I1_S2103_L001_R2_001.good.fq | 1,240,830 | 183,922,826 | 100.0% | 148.2 bases | 149 bases | 92.2% |
total | 2,481,660 | 367,845,652 | 100.0% | 148.2 bases | 149 bases | 95.0% |
seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
---|---|---|---|---|---|---|---|
coverage | distribution | NC_000913 | 4,641,653 | 74.9 | 1.8 | 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 | 17705 |
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 | 582 |
Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.038 |
reference sequence | pr(no read start) |
---|---|
NC_000913 | 0.80420 |
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 | 2.3.4.3 |
R | 3.5.1 |
step | start | end | elapsed |
---|---|---|---|
Read and reference sequence file input | 03:40:52 30 Oct 2018 | 03:41:26 30 Oct 2018 | 34 seconds |
Read alignment to reference genome | 03:41:26 30 Oct 2018 | 03:47:37 30 Oct 2018 | 6 minutes 11 seconds |
Preprocessing alignments for candidate junction identification | 03:47:37 30 Oct 2018 | 03:48:07 30 Oct 2018 | 30 seconds |
Preliminary analysis of coverage distribution | 03:48:07 30 Oct 2018 | 03:49:42 30 Oct 2018 | 1 minute 35 seconds |
Identifying junction candidates | 03:49:42 30 Oct 2018 | 03:49:44 30 Oct 2018 | 2 seconds |
Re-alignment to junction candidates | 03:49:44 30 Oct 2018 | 03:51:10 30 Oct 2018 | 1 minute 26 seconds |
Resolving best read alignments | 03:51:10 30 Oct 2018 | 03:51:59 30 Oct 2018 | 49 seconds |
Creating BAM files | 03:51:59 30 Oct 2018 | 03:53:28 30 Oct 2018 | 1 minute 29 seconds |
Tabulating error counts | 03:53:28 30 Oct 2018 | 03:53:56 30 Oct 2018 | 28 seconds |
Re-calibrating base error rates | 03:53:56 30 Oct 2018 | 03:53:57 30 Oct 2018 | 1 second |
Examining read alignment evidence | 03:53:57 30 Oct 2018 | 03:59:32 30 Oct 2018 | 5 minutes 35 seconds |
Polymorphism statistics | 03:59:32 30 Oct 2018 | 03:59:32 30 Oct 2018 | 0 seconds |
Output | 03:59:32 30 Oct 2018 | 03:59:43 30 Oct 2018 | 11 seconds |
Total | 18 minutes 51 seconds |