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-62_S62_L001_R1_001.good.fq | 448,199 | 63,099,748 | 100.0% | 140.8 bases | 149 bases | 95.8% |
errors | ALE-62_S62_L001_R2_001.good.fq | 448,199 | 62,878,357 | 100.0% | 140.3 bases | 149 bases | 96.2% |
errors | ALE-62_S62_L002_R1_001.good.fq | 440,966 | 61,951,724 | 100.0% | 140.5 bases | 149 bases | 97.3% |
errors | ALE-62_S62_L002_R2_001.good.fq | 440,966 | 61,797,491 | 100.0% | 140.1 bases | 149 bases | 96.8% |
errors | ALE-62_S62_L003_R1_001.good.fq | 459,162 | 64,468,316 | 100.0% | 140.4 bases | 149 bases | 97.2% |
errors | ALE-62_S62_L003_R2_001.good.fq | 459,162 | 64,281,991 | 100.0% | 140.0 bases | 149 bases | 97.4% |
errors | ALE-62_S62_L004_R1_001.good.fq | 423,182 | 59,388,328 | 100.0% | 140.3 bases | 149 bases | 97.2% |
errors | ALE-62_S62_L004_R2_001.good.fq | 423,182 | 59,245,448 | 100.0% | 140.0 bases | 149 bases | 96.5% |
total | 3,543,018 | 497,111,403 | 100.0% | 140.3 bases | 149 bases | 96.8% |
seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
---|---|---|---|---|---|---|---|
coverage | distribution | NC_002947 | 6,181,873 | 78.2 | 2.1 | 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 | 39611 |
Coverage evenness (position-hash) score of junction candidates | ≥ 2 | ≥ 3 |
Test this many junction candidates (n). May be smaller if not enough passed the coverage evenness threshold | 100 ≤ n ≤ 5000 | 131 |
Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.007 |
reference sequence | pr(no read start) |
---|---|
NC_002947 | 0.77752 |
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 | 18:31:01 17 Feb 2020 | 18:31:54 17 Feb 2020 | 53 seconds |
Read alignment to reference genome | 18:31:54 17 Feb 2020 | 18:39:35 17 Feb 2020 | 7 minutes 41 seconds |
Preprocessing alignments for candidate junction identification | 18:39:35 17 Feb 2020 | 18:40:29 17 Feb 2020 | 54 seconds |
Preliminary analysis of coverage distribution | 18:40:29 17 Feb 2020 | 18:42:36 17 Feb 2020 | 2 minutes 7 seconds |
Identifying junction candidates | 18:42:36 17 Feb 2020 | 18:44:56 17 Feb 2020 | 2 minutes 20 seconds |
Re-alignment to junction candidates | 18:44:56 17 Feb 2020 | 18:47:14 17 Feb 2020 | 2 minutes 18 seconds |
Resolving best read alignments | 18:47:14 17 Feb 2020 | 18:48:32 17 Feb 2020 | 1 minute 18 seconds |
Creating BAM files | 18:48:32 17 Feb 2020 | 18:50:28 17 Feb 2020 | 1 minute 56 seconds |
Tabulating error counts | 18:50:28 17 Feb 2020 | 18:51:09 17 Feb 2020 | 41 seconds |
Re-calibrating base error rates | 18:51:09 17 Feb 2020 | 18:51:11 17 Feb 2020 | 2 seconds |
Examining read alignment evidence | 18:51:11 17 Feb 2020 | 18:58:51 17 Feb 2020 | 7 minutes 40 seconds |
Polymorphism statistics | 18:58:51 17 Feb 2020 | 18:58:51 17 Feb 2020 | 0 seconds |
Output | 18:58:51 17 Feb 2020 | 18:59:15 17 Feb 2020 | 24 seconds |
Total | 28 minutes 14 seconds |