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_96_S282_L002_R1_001.good.fq | 706,361 | 99,901,749 | 100.0% | 141.4 bases | 150 bases | 94.4% |
errors | Pputida_HGL_96_S282_L002_R2_001.good.fq | 706,361 | 99,901,749 | 100.0% | 141.4 bases | 150 bases | 92.1% |
total | 1,412,722 | 199,803,498 | 100.0% | 141.4 bases | 150 bases | 93.3% |
seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
---|---|---|---|---|---|---|---|
coverage | distribution | NC_002947 | 6,181,929 | 30.2 | 2.3 | 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 | 29403 |
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 | 249 |
Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.013 |
reference sequence | pr(no read start) |
---|---|
NC_002947 | 0.90464 |
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 | 12:07:16 22 Aug 2019 | 12:07:37 22 Aug 2019 | 21 seconds |
Read alignment to reference genome | 12:07:37 22 Aug 2019 | 12:10:51 22 Aug 2019 | 3 minutes 14 seconds |
Preprocessing alignments for candidate junction identification | 12:10:51 22 Aug 2019 | 12:11:08 22 Aug 2019 | 17 seconds |
Preliminary analysis of coverage distribution | 12:11:08 22 Aug 2019 | 12:11:46 22 Aug 2019 | 38 seconds |
Identifying junction candidates | 12:11:46 22 Aug 2019 | 12:13:44 22 Aug 2019 | 1 minute 58 seconds |
Re-alignment to junction candidates | 12:13:44 22 Aug 2019 | 12:14:25 22 Aug 2019 | 41 seconds |
Resolving best read alignments | 12:14:25 22 Aug 2019 | 12:15:03 22 Aug 2019 | 38 seconds |
Creating BAM files | 12:15:03 22 Aug 2019 | 12:15:39 22 Aug 2019 | 36 seconds |
Tabulating error counts | 12:15:39 22 Aug 2019 | 12:15:53 22 Aug 2019 | 14 seconds |
Re-calibrating base error rates | 12:15:53 22 Aug 2019 | 12:15:54 22 Aug 2019 | 1 second |
Examining read alignment evidence | 12:15:54 22 Aug 2019 | 12:18:57 22 Aug 2019 | 3 minutes 3 seconds |
Polymorphism statistics | 12:18:57 22 Aug 2019 | 12:18:58 22 Aug 2019 | 1 second |
Output | 12:18:58 22 Aug 2019 | 12:19:09 22 Aug 2019 | 11 seconds |
Total | 11 minutes 53 seconds |