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_95_S220_L002_R1_001.good.fq | 509,369 | 68,085,953 | 100.0% | 133.7 bases | 150 bases | 94.4% |
errors | Pputida_HGL_95_S220_L002_R2_001.good.fq | 509,369 | 68,085,953 | 100.0% | 133.7 bases | 150 bases | 92.3% |
total | 1,018,738 | 136,171,906 | 100.0% | 133.7 bases | 150 bases | 93.3% |
seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
---|---|---|---|---|---|---|---|
coverage | distribution | NC_002947 | 6,181,929 | 20.6 | 1.9 | 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 | 18260 |
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 | 97 |
Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.005 |
reference sequence | pr(no read start) |
---|---|
NC_002947 | 0.92937 |
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 | ≤ 0 |
Number of bases that at least one read must overlap each uniquely aligned side of a predicted junction | ≥ 6 |
option | value |
---|---|
Mode | Full Polymorphism |
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 | 2 |
Polymorphism frequency cutoff | 0.05 |
Polymorphism minimum variant coverage each strand | 2 |
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 | ≥3 bases |
Skip base substitutions when they create a homopolymer flanked on each side by | ≥5 bases |
program | version |
---|---|
bowtie2 | 2.3.4.1 |
R | 3.4.4 |
step | start | end | elapsed |
---|---|---|---|
Read and reference sequence file input | 12:34:38 22 Aug 2019 | 12:34:53 22 Aug 2019 | 15 seconds |
Read alignment to reference genome | 12:34:54 22 Aug 2019 | 12:37:07 22 Aug 2019 | 2 minutes 13 seconds |
Preprocessing alignments for candidate junction identification | 12:37:07 22 Aug 2019 | 12:37:19 22 Aug 2019 | 12 seconds |
Preliminary analysis of coverage distribution | 12:37:19 22 Aug 2019 | 12:37:47 22 Aug 2019 | 28 seconds |
Identifying junction candidates | 12:37:47 22 Aug 2019 | 12:38:05 22 Aug 2019 | 18 seconds |
Re-alignment to junction candidates | 12:38:05 22 Aug 2019 | 12:38:29 22 Aug 2019 | 24 seconds |
Resolving best read alignments | 12:38:29 22 Aug 2019 | 12:38:51 22 Aug 2019 | 22 seconds |
Creating BAM files | 12:38:51 22 Aug 2019 | 12:39:17 22 Aug 2019 | 26 seconds |
Tabulating error counts | 12:39:17 22 Aug 2019 | 12:39:26 22 Aug 2019 | 9 seconds |
Re-calibrating base error rates | 12:39:26 22 Aug 2019 | 12:39:27 22 Aug 2019 | 1 second |
Examining read alignment evidence | 12:39:27 22 Aug 2019 | 12:43:25 22 Aug 2019 | 3 minutes 58 seconds |
Polymorphism statistics | 12:43:25 22 Aug 2019 | 12:43:26 22 Aug 2019 | 1 second |
Output | 12:43:26 22 Aug 2019 | 12:43:53 22 Aug 2019 | 27 seconds |
Total | 9 minutes 14 seconds |