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_25_S364_L002_R1_001.good.fq | 1,286,864 | 175,620,100 | 100.0% | 136.5 bases | 150 bases | 95.2% |
errors | Pputida_HGL_25_S364_L002_R2_001.good.fq | 1,286,864 | 175,620,100 | 100.0% | 136.5 bases | 150 bases | 93.2% |
total | 2,573,728 | 351,240,200 | 100.0% | 136.5 bases | 150 bases | 94.2% |
seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
---|---|---|---|---|---|---|---|
coverage | distribution | NC_002947 | 6,181,929 | 53.4 | 2.4 | 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 | 35472 |
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 | 561 |
Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.028 |
reference sequence | pr(no read start) |
---|---|
NC_002947 | 0.83399 |
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 | 21:02:56 26 Mar 2020 | 21:03:36 26 Mar 2020 | 40 seconds |
Read alignment to reference genome | 21:03:36 26 Mar 2020 | 21:09:37 26 Mar 2020 | 6 minutes 1 second |
Preprocessing alignments for candidate junction identification | 21:09:37 26 Mar 2020 | 21:10:12 26 Mar 2020 | 35 seconds |
Preliminary analysis of coverage distribution | 21:10:12 26 Mar 2020 | 21:11:39 26 Mar 2020 | 1 minute 27 seconds |
Identifying junction candidates | 21:11:39 26 Mar 2020 | 21:15:34 26 Mar 2020 | 3 minutes 55 seconds |
Re-alignment to junction candidates | 21:15:34 26 Mar 2020 | 21:17:05 26 Mar 2020 | 1 minute 31 seconds |
Resolving best read alignments | 21:17:05 26 Mar 2020 | 21:18:08 26 Mar 2020 | 1 minute 3 seconds |
Creating BAM files | 21:18:08 26 Mar 2020 | 21:19:25 26 Mar 2020 | 1 minute 17 seconds |
Tabulating error counts | 21:19:25 26 Mar 2020 | 21:19:52 26 Mar 2020 | 27 seconds |
Re-calibrating base error rates | 21:19:52 26 Mar 2020 | 21:19:55 26 Mar 2020 | 3 seconds |
Examining read alignment evidence | 21:19:55 26 Mar 2020 | 21:35:20 26 Mar 2020 | 15 minutes 25 seconds |
Polymorphism statistics | 21:35:20 26 Mar 2020 | 21:35:22 26 Mar 2020 | 2 seconds |
Output | 21:35:22 26 Mar 2020 | 21:37:14 26 Mar 2020 | 1 minute 52 seconds |
Total | 34 minutes 18 seconds |