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 | Pputida_HGL_14_S354_L002_R1_001.good.fq | 2,244,918 | 299,087,821 | 100.0% | 133.2 bases | 150 bases | 95.0% |
errors | Pputida_HGL_14_S354_L002_R2_001.good.fq | 2,244,918 | 299,087,821 | 100.0% | 133.2 bases | 150 bases | 93.3% |
total | 4,489,836 | 598,175,642 | 100.0% | 133.2 bases | 150 bases | 94.1% |
seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
---|---|---|---|---|---|---|---|
coverage | distribution | NC_002947 | 6,181,929 | 91.2 | 3.3 | 100.0% | Pseudomonas putida KT2440 chromosome, complete genome. |
total | 6,181,929 | 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 | 61691 |
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 | 1177 |
Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.059 |
reference sequence | pr(no read start) |
---|---|
NC_002947 | 0.73902 |
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 | 01:37:22 20 Aug 2019 | 01:38:23 20 Aug 2019 | 1 minute 1 second |
Read alignment to reference genome | 01:38:23 20 Aug 2019 | 01:48:15 20 Aug 2019 | 9 minutes 52 seconds |
Preprocessing alignments for candidate junction identification | 01:48:15 20 Aug 2019 | 01:49:24 20 Aug 2019 | 1 minute 9 seconds |
Preliminary analysis of coverage distribution | 01:49:24 20 Aug 2019 | 01:51:48 20 Aug 2019 | 2 minutes 24 seconds |
Identifying junction candidates | 01:51:48 20 Aug 2019 | 02:11:32 20 Aug 2019 | 19 minutes 44 seconds |
Re-alignment to junction candidates | 02:11:32 20 Aug 2019 | 02:14:09 20 Aug 2019 | 2 minutes 37 seconds |
Resolving best read alignments | 02:14:09 20 Aug 2019 | 02:15:56 20 Aug 2019 | 1 minute 47 seconds |
Creating BAM files | 02:15:56 20 Aug 2019 | 02:18:01 20 Aug 2019 | 2 minutes 5 seconds |
Tabulating error counts | 02:18:01 20 Aug 2019 | 02:18:45 20 Aug 2019 | 44 seconds |
Re-calibrating base error rates | 02:18:45 20 Aug 2019 | 02:18:46 20 Aug 2019 | 1 second |
Examining read alignment evidence | 02:18:46 20 Aug 2019 | 02:27:18 20 Aug 2019 | 8 minutes 32 seconds |
Polymorphism statistics | 02:27:18 20 Aug 2019 | 02:27:19 20 Aug 2019 | 1 second |
Output | 02:27:19 20 Aug 2019 | 02:27:59 20 Aug 2019 | 40 seconds |
Total | 50 minutes 37 seconds |