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_5_S227_L002_R1_001.good.fq | 446,467 | 62,108,208 | 100.0% | 139.1 bases | 150 bases | 88.6% |
errors | Pputida_HGL_5_S227_L002_R2_001.good.fq | 446,467 | 62,108,208 | 100.0% | 139.1 bases | 150 bases | 86.5% |
total | 892,934 | 124,216,416 | 100.0% | 139.1 bases | 150 bases | 87.5% |
seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
---|---|---|---|---|---|---|---|
coverage | distribution | NC_002947 | 6,181,929 | 17.9 | 2.8 | 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 | 16237 |
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 | 100 |
Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.005 |
reference sequence | pr(no read start) |
---|---|
NC_002947 | 0.94140 |
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 | 00:12:14 07 Apr 2020 | 00:12:30 07 Apr 2020 | 16 seconds |
Read alignment to reference genome | 00:12:31 07 Apr 2020 | 00:14:54 07 Apr 2020 | 2 minutes 23 seconds |
Preprocessing alignments for candidate junction identification | 00:14:54 07 Apr 2020 | 00:15:05 07 Apr 2020 | 11 seconds |
Preliminary analysis of coverage distribution | 00:15:05 07 Apr 2020 | 00:15:32 07 Apr 2020 | 27 seconds |
Identifying junction candidates | 00:15:32 07 Apr 2020 | 00:15:39 07 Apr 2020 | 7 seconds |
Re-alignment to junction candidates | 00:15:39 07 Apr 2020 | 00:16:08 07 Apr 2020 | 29 seconds |
Resolving best read alignments | 00:16:08 07 Apr 2020 | 00:16:26 07 Apr 2020 | 18 seconds |
Creating BAM files | 00:16:26 07 Apr 2020 | 00:16:49 07 Apr 2020 | 23 seconds |
Tabulating error counts | 00:16:49 07 Apr 2020 | 00:16:58 07 Apr 2020 | 9 seconds |
Re-calibrating base error rates | 00:16:58 07 Apr 2020 | 00:16:59 07 Apr 2020 | 1 second |
Examining read alignment evidence | 00:16:59 07 Apr 2020 | 00:20:47 07 Apr 2020 | 3 minutes 48 seconds |
Polymorphism statistics | 00:20:47 07 Apr 2020 | 00:20:48 07 Apr 2020 | 1 second |
Output | 00:20:48 07 Apr 2020 | 00:21:25 07 Apr 2020 | 37 seconds |
Total | 9 minutes 10 seconds |