breseq version 0.33.2 revision caddc01d3be9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
read file | reads | bases | passed filters | average | longest | mapped | |
---|---|---|---|---|---|---|---|
errors | Pputida_HGL_52_S184_L001_R1_001.good.fq | 1,146,500 | 157,906,133 | 100.0% | 137.7 bases | 150 bases | 94.3% |
errors | Pputida_HGL_52_S184_L001_R2_001.good.fq | 1,146,500 | 157,906,133 | 100.0% | 137.7 bases | 150 bases | 91.8% |
total | 2,293,000 | 315,812,266 | 100.0% | 137.7 bases | 150 bases | 93.0% |
seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
---|---|---|---|---|---|---|---|
coverage | distribution | NC_002947 | 6,181,929 | 47.5 | 2.6 | 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 | 33923 |
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 | 456 |
Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.023 |
reference sequence | pr(no read start) |
---|---|
NC_002947 | 0.85461 |
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 | 21:42:03 20 Aug 2019 | 21:43:01 20 Aug 2019 | 58 seconds |
Read alignment to reference genome | 21:43:02 20 Aug 2019 | 21:51:37 20 Aug 2019 | 8 minutes 35 seconds |
Preprocessing alignments for candidate junction identification | 21:51:37 20 Aug 2019 | 21:52:27 20 Aug 2019 | 50 seconds |
Preliminary analysis of coverage distribution | 21:52:27 20 Aug 2019 | 21:53:52 20 Aug 2019 | 1 minute 25 seconds |
Identifying junction candidates | 21:53:52 20 Aug 2019 | 21:59:23 20 Aug 2019 | 5 minutes 31 seconds |
Re-alignment to junction candidates | 21:59:23 20 Aug 2019 | 22:01:38 20 Aug 2019 | 2 minutes 15 seconds |
Resolving best read alignments | 22:01:38 20 Aug 2019 | 22:02:52 20 Aug 2019 | 1 minute 14 seconds |
Creating BAM files | 22:02:52 20 Aug 2019 | 22:04:19 20 Aug 2019 | 1 minute 27 seconds |
Tabulating error counts | 22:04:19 20 Aug 2019 | 22:05:02 20 Aug 2019 | 43 seconds |
Re-calibrating base error rates | 22:05:02 20 Aug 2019 | 22:05:04 20 Aug 2019 | 2 seconds |
Examining read alignment evidence | 22:05:04 20 Aug 2019 | 22:14:21 20 Aug 2019 | 9 minutes 17 seconds |
Polymorphism statistics | 22:14:21 20 Aug 2019 | 22:14:22 20 Aug 2019 | 1 second |
Output | 22:14:22 20 Aug 2019 | 22:14:51 20 Aug 2019 | 29 seconds |
Total | 32 minutes 47 seconds |