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 | PAL050_S49_L007_R1_001.good.fq | 3,635,323 | 330,241,654 | 100.0% | 90.8 bases | 91 bases | 96.4% |
errors | PAL050_S49_L007_R2_001.good.fq | 3,635,323 | 330,241,654 | 100.0% | 90.8 bases | 91 bases | 96.4% |
total | 7,270,646 | 660,483,308 | 100.0% | 90.8 bases | 91 bases | 96.4% |
seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
---|---|---|---|---|---|---|---|
coverage | distribution | USA300TCH1516_ALE | 2,872,915 | 208.1 | 5.4 | 95.8% | Staphylococcus species strain strain. |
coverage | distribution | CP000731 | 27,041 | 982.9 | 48.1 | 4.0% | Staphylococcus aureus subsp. aureus USA300_TCH1516 plasmid |
coverage | distribution | NC_012417 | 3,125 | 317.9 | 3.3 | 0.2% | Staphylococcus aureus subsp. aureus USA300_TCH1516 plasmid |
total | 2,903,081 | 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 | 100044 |
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 | 1450 |
Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.095 |
reference sequence | pr(no read start) |
---|---|
USA300TCH1516_ALE | 0.42495 |
CP000731 | 0.07727 |
NC_012417 | 0.31498 |
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 | 04:29:20 25 May 2019 | 04:30:43 25 May 2019 | 1 minute 23 seconds |
Read alignment to reference genome | 04:30:43 25 May 2019 | 04:40:39 25 May 2019 | 9 minutes 56 seconds |
Preprocessing alignments for candidate junction identification | 04:40:39 25 May 2019 | 04:42:00 25 May 2019 | 1 minute 21 seconds |
Preliminary analysis of coverage distribution | 04:42:00 25 May 2019 | 04:44:15 25 May 2019 | 2 minutes 15 seconds |
Identifying junction candidates | 04:44:15 25 May 2019 | 04:48:03 25 May 2019 | 3 minutes 48 seconds |
Re-alignment to junction candidates | 04:48:03 25 May 2019 | 04:51:33 25 May 2019 | 3 minutes 30 seconds |
Resolving best read alignments | 04:51:33 25 May 2019 | 04:53:45 25 May 2019 | 2 minutes 12 seconds |
Creating BAM files | 04:53:45 25 May 2019 | 04:55:45 25 May 2019 | 2 minutes 0 seconds |
Tabulating error counts | 04:55:45 25 May 2019 | 04:56:38 25 May 2019 | 53 seconds |
Re-calibrating base error rates | 04:56:38 25 May 2019 | 04:56:40 25 May 2019 | 2 seconds |
Examining read alignment evidence | 04:56:40 25 May 2019 | 05:05:48 25 May 2019 | 9 minutes 8 seconds |
Polymorphism statistics | 05:05:48 25 May 2019 | 05:05:49 25 May 2019 | 1 second |
Output | 05:05:49 25 May 2019 | 05:06:46 25 May 2019 | 57 seconds |
Total | 37 minutes 26 seconds |