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 | ALE-81_S81_L001_R1_001.good.fq | 270,576 | 38,840,067 | 100.0% | 143.5 bases | 147 bases | 97.4% |
errors | ALE-81_S81_L001_R2_001.good.fq | 270,576 | 38,788,572 | 100.0% | 143.4 bases | 147 bases | 97.0% |
errors | ALE-81_S81_L002_R1_001.good.fq | 269,690 | 38,671,275 | 100.0% | 143.4 bases | 147 bases | 98.9% |
errors | ALE-81_S81_L002_R2_001.good.fq | 269,690 | 38,638,338 | 100.0% | 143.3 bases | 147 bases | 97.2% |
errors | ALE-81_S81_L003_R1_001.good.fq | 271,163 | 38,853,335 | 100.0% | 143.3 bases | 147 bases | 98.9% |
errors | ALE-81_S81_L003_R2_001.good.fq | 271,163 | 38,811,047 | 100.0% | 143.1 bases | 147 bases | 98.1% |
errors | ALE-81_S81_L004_R1_001.good.fq | 252,779 | 36,208,576 | 100.0% | 143.2 bases | 147 bases | 98.8% |
errors | ALE-81_S81_L004_R2_001.good.fq | 252,779 | 36,177,656 | 100.0% | 143.1 bases | 147 bases | 96.7% |
total | 2,128,416 | 304,988,866 | 100.0% | 143.3 bases | 147 bases | 97.9% |
seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
---|---|---|---|---|---|---|---|
coverage | distribution | NC_002947 | 6,181,873 | 61.1 | 30.3 | 100.0% | Pseudomonas putida KT2440 chromosome, complete genome. |
total | 6,181,873 | 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 | 8685 |
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 | 1148 |
Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.056 |
reference sequence | pr(no read start) |
---|---|
NC_002947 | 0.86138 |
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 | 14:00:03 18 Feb 2020 | 14:00:36 18 Feb 2020 | 33 seconds |
Read alignment to reference genome | 14:00:36 18 Feb 2020 | 14:05:07 18 Feb 2020 | 4 minutes 31 seconds |
Preprocessing alignments for candidate junction identification | 14:05:07 18 Feb 2020 | 14:05:36 18 Feb 2020 | 29 seconds |
Preliminary analysis of coverage distribution | 14:05:36 18 Feb 2020 | 14:06:45 18 Feb 2020 | 1 minute 9 seconds |
Identifying junction candidates | 14:06:45 18 Feb 2020 | 14:06:55 18 Feb 2020 | 10 seconds |
Re-alignment to junction candidates | 14:06:55 18 Feb 2020 | 14:08:38 18 Feb 2020 | 1 minute 43 seconds |
Resolving best read alignments | 14:08:38 18 Feb 2020 | 14:09:24 18 Feb 2020 | 46 seconds |
Creating BAM files | 14:09:24 18 Feb 2020 | 14:10:26 18 Feb 2020 | 1 minute 2 seconds |
Tabulating error counts | 14:10:26 18 Feb 2020 | 14:10:49 18 Feb 2020 | 23 seconds |
Re-calibrating base error rates | 14:10:49 18 Feb 2020 | 14:10:52 18 Feb 2020 | 3 seconds |
Examining read alignment evidence | 14:10:52 18 Feb 2020 | 14:15:36 18 Feb 2020 | 4 minutes 44 seconds |
Polymorphism statistics | 14:15:36 18 Feb 2020 | 14:15:37 18 Feb 2020 | 1 second |
Output | 14:15:37 18 Feb 2020 | 14:16:32 18 Feb 2020 | 55 seconds |
Total | 16 minutes 29 seconds |