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 | CCK_gndEvo03EP_Isolate_1_S1629_L005_R1_001.good.fq | 730,598 | 104,344,433 | 100.0% | 142.8 bases | 143 bases | 95.3% |
errors | CCK_gndEvo03EP_Isolate_1_S1629_L005_R2_001.good.fq | 730,598 | 104,344,433 | 100.0% | 142.8 bases | 143 bases | 85.3% |
total | 1,461,196 | 208,688,866 | 100.0% | 142.8 bases | 143 bases | 90.3% |
seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
---|---|---|---|---|---|---|---|
coverage | distribution | NC_000913 | 4,641,652 | 40.3 | 1.6 | 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 | 5244 |
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 | 75 |
Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.005 |
reference sequence | pr(no read start) |
---|---|
NC_000913 | 0.88816 |
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 | 13:50:15 27 Feb 2020 | 13:50:38 27 Feb 2020 | 23 seconds |
Read alignment to reference genome | 13:50:38 27 Feb 2020 | 13:55:19 27 Feb 2020 | 4 minutes 41 seconds |
Preprocessing alignments for candidate junction identification | 13:55:19 27 Feb 2020 | 13:55:39 27 Feb 2020 | 20 seconds |
Preliminary analysis of coverage distribution | 13:55:39 27 Feb 2020 | 13:56:27 27 Feb 2020 | 48 seconds |
Identifying junction candidates | 13:56:27 27 Feb 2020 | 13:56:28 27 Feb 2020 | 1 second |
Re-alignment to junction candidates | 13:56:28 27 Feb 2020 | 13:57:34 27 Feb 2020 | 1 minute 6 seconds |
Resolving best read alignments | 13:57:34 27 Feb 2020 | 13:58:05 27 Feb 2020 | 31 seconds |
Creating BAM files | 13:58:05 27 Feb 2020 | 13:58:48 27 Feb 2020 | 43 seconds |
Tabulating error counts | 13:58:48 27 Feb 2020 | 13:59:02 27 Feb 2020 | 14 seconds |
Re-calibrating base error rates | 13:59:02 27 Feb 2020 | 13:59:03 27 Feb 2020 | 1 second |
Examining read alignment evidence | 13:59:03 27 Feb 2020 | 14:02:15 27 Feb 2020 | 3 minutes 12 seconds |
Polymorphism statistics | 14:02:15 27 Feb 2020 | 14:02:16 27 Feb 2020 | 1 second |
Output | 14:02:16 27 Feb 2020 | 14:02:27 27 Feb 2020 | 11 seconds |
Total | 12 minutes 12 seconds |