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 | PAL28_S28_L007_R1_001.good.fq | 5,657,745 | 514,607,319 | 100.0% | 91.0 bases | 91 bases | 98.4% |
errors | PAL28_S28_L007_R2_001.good.fq | 5,657,745 | 514,607,319 | 100.0% | 91.0 bases | 91 bases | 97.4% |
total | 11,315,490 | 1,029,214,638 | 100.0% | 91.0 bases | 91 bases | 97.9% |
seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
---|---|---|---|---|---|---|---|
coverage | distribution | USA300TCH1516_ALE | 2,872,915 | 326.9 | 4.1 | 93.9% | Staphylococcus species strain strain. |
coverage | distribution | CP000731 | 27,041 | 1309.7 | 10.0 | 3.4% | Staphylococcus aureus subsp. aureus USA300_TCH1516 plasmid |
coverage | distribution | NC_012417 | 3,125 | 10155.8 | 73.9 | 2.7% | 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 | 64473 |
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 | 598 |
Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.039 |
reference sequence | pr(no read start) |
---|---|
USA300TCH1516_ALE | 0.28092 |
CP000731 | 0.04415 |
NC_012417 | 0.03140 |
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 | 11:51:31 23 May 2019 | 11:53:41 23 May 2019 | 2 minutes 10 seconds |
Read alignment to reference genome | 11:53:41 23 May 2019 | 12:08:23 23 May 2019 | 14 minutes 42 seconds |
Preprocessing alignments for candidate junction identification | 12:08:23 23 May 2019 | 12:10:29 23 May 2019 | 2 minutes 6 seconds |
Preliminary analysis of coverage distribution | 12:10:29 23 May 2019 | 12:14:11 23 May 2019 | 3 minutes 42 seconds |
Identifying junction candidates | 12:14:11 23 May 2019 | 12:15:09 23 May 2019 | 58 seconds |
Re-alignment to junction candidates | 12:15:09 23 May 2019 | 12:19:56 23 May 2019 | 4 minutes 47 seconds |
Resolving best read alignments | 12:19:56 23 May 2019 | 12:23:40 23 May 2019 | 3 minutes 44 seconds |
Creating BAM files | 12:23:40 23 May 2019 | 12:27:02 23 May 2019 | 3 minutes 22 seconds |
Tabulating error counts | 12:27:02 23 May 2019 | 12:28:34 23 May 2019 | 1 minute 32 seconds |
Re-calibrating base error rates | 12:28:34 23 May 2019 | 12:28:37 23 May 2019 | 3 seconds |
Examining read alignment evidence | 12:28:37 23 May 2019 | 13:52:07 23 May 2019 | 1 hour 23 minutes 30 seconds |
Polymorphism statistics | 13:52:07 23 May 2019 | 13:52:09 23 May 2019 | 2 seconds |
Output | 13:52:09 23 May 2019 | 13:52:58 23 May 2019 | 49 seconds |
Total | 2 hours 1 minute 27 seconds |