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_9_S376_L002_R1_001.good.fq | 1,532,032 | 211,336,153 | 100.0% | 137.9 bases | 150 bases | 94.7% |
errors | Pputida_HGL_9_S376_L002_R2_001.good.fq | 1,532,032 | 211,336,153 | 100.0% | 137.9 bases | 150 bases | 92.7% |
total | 3,064,064 | 422,672,306 | 100.0% | 137.9 bases | 150 bases | 93.7% |
seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
---|---|---|---|---|---|---|---|
coverage | distribution | NC_002947 | 6,181,929 | 64.3 | 2.9 | 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 | 50398 |
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 | 779 |
Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.039 |
reference sequence | pr(no read start) |
---|---|
NC_002947 | 0.81022 |
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 | 14:34:44 06 Apr 2020 | 14:35:32 06 Apr 2020 | 48 seconds |
Read alignment to reference genome | 14:35:32 06 Apr 2020 | 14:42:54 06 Apr 2020 | 7 minutes 22 seconds |
Preprocessing alignments for candidate junction identification | 14:42:54 06 Apr 2020 | 14:43:39 06 Apr 2020 | 45 seconds |
Preliminary analysis of coverage distribution | 14:43:39 06 Apr 2020 | 14:45:20 06 Apr 2020 | 1 minute 41 seconds |
Identifying junction candidates | 14:45:20 06 Apr 2020 | 14:55:08 06 Apr 2020 | 9 minutes 48 seconds |
Re-alignment to junction candidates | 14:55:08 06 Apr 2020 | 14:56:58 06 Apr 2020 | 1 minute 50 seconds |
Resolving best read alignments | 14:56:58 06 Apr 2020 | 14:58:21 06 Apr 2020 | 1 minute 23 seconds |
Creating BAM files | 14:58:21 06 Apr 2020 | 14:59:54 06 Apr 2020 | 1 minute 33 seconds |
Tabulating error counts | 14:59:54 06 Apr 2020 | 15:00:26 06 Apr 2020 | 32 seconds |
Re-calibrating base error rates | 15:00:26 06 Apr 2020 | 15:00:28 06 Apr 2020 | 2 seconds |
Examining read alignment evidence | 15:00:28 06 Apr 2020 | 15:07:03 06 Apr 2020 | 6 minutes 35 seconds |
Polymorphism statistics | 15:07:03 06 Apr 2020 | 15:07:03 06 Apr 2020 | 0 seconds |
Output | 15:07:03 06 Apr 2020 | 15:07:33 06 Apr 2020 | 30 seconds |
Total | 32 minutes 49 seconds |