breseq version 0.35.4 revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
read file | reads | bases | passed filters | average | longest | mapped | |
---|---|---|---|---|---|---|---|
errors | SRR6462916_R1.good.fq | 956,244 | 77,076,814 | 100.0% | 80.6 bases | 81 bases | 98.2% |
errors | SRR6462916_R2.good.fq | 956,244 | 77,080,059 | 100.0% | 80.6 bases | 81 bases | 98.2% |
total | 1,912,488 | 154,156,873 | 100.0% | 80.6 bases | 81 bases | 98.2% |
seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
---|---|---|---|---|---|---|---|
coverage | distribution | NC_000913 | 4,641,652 | 34.8 | 4.8 | 100.0% | Escherichia coli str. K-12 substr. MG1655, complete genome. |
total | 4,641,652 | 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 | 2530 |
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 | 11 |
Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.000 |
reference sequence | pr(no read start) |
---|---|
NC_000913 | 0.82703 |
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 |
Minimum probablilty assigned that no mapped read will start at a given position and strand for junction prediction | 0.1 |
Junction allow suboptimal matches | FALSE |
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 | 04:08:39 11 Nov 2020 | 04:10:02 11 Nov 2020 | 1 minute 23 seconds |
Read alignment to reference genome | 04:10:03 11 Nov 2020 | 04:17:06 11 Nov 2020 | 7 minutes 3 seconds |
Preprocessing alignments for candidate junction identification | 04:17:06 11 Nov 2020 | 04:18:16 11 Nov 2020 | 1 minute 10 seconds |
Preliminary analysis of coverage distribution | 04:18:16 11 Nov 2020 | 04:19:43 11 Nov 2020 | 1 minute 27 seconds |
Identifying junction candidates | 04:19:43 11 Nov 2020 | 04:19:43 11 Nov 2020 | 0 seconds |
Re-alignment to junction candidates | 04:19:43 11 Nov 2020 | 04:21:33 11 Nov 2020 | 1 minute 50 seconds |
Resolving best read alignments | 04:21:33 11 Nov 2020 | 04:23:05 11 Nov 2020 | 1 minute 32 seconds |
Creating BAM files | 04:23:05 11 Nov 2020 | 04:24:11 11 Nov 2020 | 1 minute 6 seconds |
Tabulating error counts | 04:24:11 11 Nov 2020 | 04:24:54 11 Nov 2020 | 43 seconds |
Re-calibrating base error rates | 04:24:54 11 Nov 2020 | 04:24:57 11 Nov 2020 | 3 seconds |
Examining read alignment evidence | 04:24:57 11 Nov 2020 | 04:34:37 11 Nov 2020 | 9 minutes 40 seconds |
Polymorphism statistics | 04:34:37 11 Nov 2020 | 04:34:38 11 Nov 2020 | 1 second |
Output | 04:34:38 11 Nov 2020 | 04:36:01 11 Nov 2020 | 1 minute 23 seconds |
Total | 27 minutes 21 seconds |