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 | SNFR_7_67_0_S2346_L001_R1_001.good.fq | 815,207 | 114,944,187 | 100.0% | 141.0 bases | 141 bases | 98.6% |
total | 815,207 | 114,944,187 | 100.0% | 141.0 bases | 141 bases | 98.6% |
seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
---|---|---|---|---|---|---|---|
coverage | distribution | USA300TCH1516_ALE | 2,872,915 | 38.2 | 2.3 | 98.3% | Staphylococcus species strain strain. |
coverage | distribution | CP000731 | 27,041 | NA | NA | 0.0% | Staphylococcus aureus subsp. aureus USA300_TCH1516 plasmid |
coverage | distribution | NC_012417 | 3,125 | 659.0 | 11.1 | 1.7% | 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.
Insufficient coverage Reference sequence counted as entirely deleted due to low coverage. Try either the -t,--targeted-sequencing
or the -c,--contig-reference
option if you want mutations called for these reference sequences.
option | limit | actual |
---|---|---|
Number of alignment pairs examined for constructing junction candidates | ≤ 100000 | 1814 |
Coverage evenness (position-hash) score of junction candidates | ≥ 2 | ≥ 2 |
Test this many junction candidates (n). May be smaller if not enough passed the coverage evenness threshold | 100 ≤ n ≤ 5000 | 12 |
Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.001 |
reference sequence | pr(no read start) |
---|---|
USA300TCH1516_ALE | 0.90420 |
CP000731 | 0.99913 |
NC_012417 | 0.30533 |
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 | 01:18:27 26 May 2019 | 01:18:39 26 May 2019 | 12 seconds |
Read alignment to reference genome | 01:18:39 26 May 2019 | 01:20:34 26 May 2019 | 1 minute 55 seconds |
Preprocessing alignments for candidate junction identification | 01:20:34 26 May 2019 | 01:20:44 26 May 2019 | 10 seconds |
Preliminary analysis of coverage distribution | 01:20:44 26 May 2019 | 01:21:11 26 May 2019 | 27 seconds |
Identifying junction candidates | 01:21:11 26 May 2019 | 01:21:11 26 May 2019 | 0 seconds |
Re-alignment to junction candidates | 01:21:11 26 May 2019 | 01:21:35 26 May 2019 | 24 seconds |
Resolving best read alignments | 01:21:35 26 May 2019 | 01:21:50 26 May 2019 | 15 seconds |
Creating BAM files | 01:21:50 26 May 2019 | 01:22:12 26 May 2019 | 22 seconds |
Tabulating error counts | 01:22:12 26 May 2019 | 01:22:20 26 May 2019 | 8 seconds |
Re-calibrating base error rates | 01:22:20 26 May 2019 | 01:22:22 26 May 2019 | 2 seconds |
Examining read alignment evidence | 01:22:22 26 May 2019 | 01:28:36 26 May 2019 | 6 minutes 14 seconds |
Polymorphism statistics | 01:28:36 26 May 2019 | 01:28:36 26 May 2019 | 0 seconds |
Output | 01:28:36 26 May 2019 | 01:28:40 26 May 2019 | 4 seconds |
Total | 10 minutes 13 seconds |