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_6_S329_L002_R1_001.good.fq | 3,775,502 | 499,209,824 | 100.0% | 132.2 bases | 150 bases | 93.3% |
errors | Pputida_HGL_6_S329_L002_R2_001.good.fq | 3,775,502 | 499,209,824 | 100.0% | 132.2 bases | 150 bases | 91.6% |
total | 7,551,004 | 998,419,648 | 100.0% | 132.2 bases | 150 bases | 92.5% |
seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
---|---|---|---|---|---|---|---|
coverage | distribution | NC_002947 | 6,181,929 | 148.6 | 5.2 | 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 | 100011 |
Coverage evenness (position-hash) score of junction candidates | ≥ 2 | ≥ 4 |
Test this many junction candidates (n). May be smaller if not enough passed the coverage evenness threshold | 100 ≤ n ≤ 5000 | 986 |
Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.049 |
reference sequence | pr(no read start) |
---|---|
NC_002947 | 0.62375 |
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 | 05:04:37 20 Aug 2019 | 05:06:17 20 Aug 2019 | 1 minute 40 seconds |
Read alignment to reference genome | 05:06:18 20 Aug 2019 | 05:22:32 20 Aug 2019 | 16 minutes 14 seconds |
Preprocessing alignments for candidate junction identification | 05:22:32 20 Aug 2019 | 05:24:18 20 Aug 2019 | 1 minute 46 seconds |
Preliminary analysis of coverage distribution | 05:24:18 20 Aug 2019 | 05:27:53 20 Aug 2019 | 3 minutes 35 seconds |
Identifying junction candidates | 05:27:53 20 Aug 2019 | 05:30:18 20 Aug 2019 | 2 minutes 25 seconds |
Re-alignment to junction candidates | 05:30:18 20 Aug 2019 | 05:34:35 20 Aug 2019 | 4 minutes 17 seconds |
Resolving best read alignments | 05:34:35 20 Aug 2019 | 05:37:25 20 Aug 2019 | 2 minutes 50 seconds |
Creating BAM files | 05:37:25 20 Aug 2019 | 05:40:43 20 Aug 2019 | 3 minutes 18 seconds |
Tabulating error counts | 05:40:43 20 Aug 2019 | 05:41:58 20 Aug 2019 | 1 minute 15 seconds |
Re-calibrating base error rates | 05:41:59 20 Aug 2019 | 05:42:00 20 Aug 2019 | 1 second |
Examining read alignment evidence | 05:42:00 20 Aug 2019 | 05:56:02 20 Aug 2019 | 14 minutes 2 seconds |
Polymorphism statistics | 05:56:02 20 Aug 2019 | 05:56:03 20 Aug 2019 | 1 second |
Output | 05:56:03 20 Aug 2019 | 05:56:51 20 Aug 2019 | 48 seconds |
Total | 52 minutes 12 seconds |