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_15_S336_L002_R1_001.good.fq | 565,026 | 78,456,373 | 100.0% | 138.9 bases | 150 bases | 95.8% |
errors | Pputida_HGL_15_S336_L002_R2_001.good.fq | 565,026 | 78,456,373 | 100.0% | 138.9 bases | 150 bases | 93.4% |
total | 1,130,052 | 156,912,746 | 100.0% | 138.9 bases | 150 bases | 94.6% |
seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
---|---|---|---|---|---|---|---|
coverage | distribution | NC_002947 | 6,181,929 | 24.2 | 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 | 11456 |
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 | 48 |
Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.002 |
reference sequence | pr(no read start) |
---|---|
NC_002947 | 0.92144 |
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 | 14:13:04 06 Apr 2020 | 14:13:23 06 Apr 2020 | 19 seconds |
Read alignment to reference genome | 14:13:24 06 Apr 2020 | 14:16:07 06 Apr 2020 | 2 minutes 43 seconds |
Preprocessing alignments for candidate junction identification | 14:16:07 06 Apr 2020 | 14:16:22 06 Apr 2020 | 15 seconds |
Preliminary analysis of coverage distribution | 14:16:22 06 Apr 2020 | 14:16:57 06 Apr 2020 | 35 seconds |
Identifying junction candidates | 14:16:57 06 Apr 2020 | 14:17:03 06 Apr 2020 | 6 seconds |
Re-alignment to junction candidates | 14:17:03 06 Apr 2020 | 14:17:34 06 Apr 2020 | 31 seconds |
Resolving best read alignments | 14:17:34 06 Apr 2020 | 14:18:00 06 Apr 2020 | 26 seconds |
Creating BAM files | 14:18:00 06 Apr 2020 | 14:18:32 06 Apr 2020 | 32 seconds |
Tabulating error counts | 14:18:32 06 Apr 2020 | 14:18:44 06 Apr 2020 | 12 seconds |
Re-calibrating base error rates | 14:18:44 06 Apr 2020 | 14:18:45 06 Apr 2020 | 1 second |
Examining read alignment evidence | 14:18:45 06 Apr 2020 | 14:24:30 06 Apr 2020 | 5 minutes 45 seconds |
Polymorphism statistics | 14:24:30 06 Apr 2020 | 14:24:30 06 Apr 2020 | 0 seconds |
Output | 14:24:30 06 Apr 2020 | 14:24:55 06 Apr 2020 | 25 seconds |
Total | 11 minutes 50 seconds |