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_1_52_0_S2417_L001_R1_001.good.fq | 1,064,668 | 150,091,694 | 100.0% | 141.0 bases | 141 bases | 98.6% |
errors | SNFR_1_52_0_S2417_L001_R2_001.good.fq | 1,064,668 | 150,091,694 | 100.0% | 141.0 bases | 141 bases | 93.8% |
total | 2,129,336 | 300,183,388 | 100.0% | 141.0 bases | 141 bases | 96.2% |
seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
---|---|---|---|---|---|---|---|
coverage | distribution | USA300TCH1516_ALE | 2,872,915 | 94.7 | 2.6 | 95.3% | Staphylococcus species strain strain. |
coverage | distribution | CP000731 | 27,041 | 317.8 | 5.3 | 3.0% | Staphylococcus aureus subsp. aureus USA300_TCH1516 plasmid |
coverage | distribution | NC_012417 | 3,125 | 1690.0 | 7.6 | 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.
option | limit | actual |
---|---|---|
Number of alignment pairs examined for constructing junction candidates | ≤ 100000 | 3571 |
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 | 25 |
Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.003 |
reference sequence | pr(no read start) |
---|---|
USA300TCH1516_ALE | 0.77342 |
CP000731 | 0.46670 |
NC_012417 | 0.11265 |
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 | 20:53:42 25 May 2019 | 20:54:12 25 May 2019 | 30 seconds |
Read alignment to reference genome | 20:54:12 25 May 2019 | 20:59:31 25 May 2019 | 5 minutes 19 seconds |
Preprocessing alignments for candidate junction identification | 20:59:31 25 May 2019 | 21:00:01 25 May 2019 | 30 seconds |
Preliminary analysis of coverage distribution | 21:00:01 25 May 2019 | 21:01:11 25 May 2019 | 1 minute 10 seconds |
Identifying junction candidates | 21:01:11 25 May 2019 | 21:01:11 25 May 2019 | 0 seconds |
Re-alignment to junction candidates | 21:01:11 25 May 2019 | 21:02:18 25 May 2019 | 1 minute 7 seconds |
Resolving best read alignments | 21:02:18 25 May 2019 | 21:03:02 25 May 2019 | 44 seconds |
Creating BAM files | 21:03:02 25 May 2019 | 21:04:02 25 May 2019 | 1 minute 0 seconds |
Tabulating error counts | 21:04:02 25 May 2019 | 21:04:24 25 May 2019 | 22 seconds |
Re-calibrating base error rates | 21:04:24 25 May 2019 | 21:04:26 25 May 2019 | 2 seconds |
Examining read alignment evidence | 21:04:26 25 May 2019 | 21:34:07 25 May 2019 | 29 minutes 41 seconds |
Polymorphism statistics | 21:34:07 25 May 2019 | 21:34:07 25 May 2019 | 0 seconds |
Output | 21:34:07 25 May 2019 | 21:34:15 25 May 2019 | 8 seconds |
Total | 40 minutes 33 seconds |