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_3_67_1_S178_S2001_L006_R1_001.good.fq | 643,150 | 87,132,786 | 100.0% | 135.5 bases | 141 bases | 96.0% |
errors | SNFR_3_67_1_S178_S2001_L006_R2_001.good.fq | 643,150 | 87,132,786 | 100.0% | 135.5 bases | 141 bases | 95.2% |
errors | SNFR_3_67_1_S178_S2001_L008_R1_001.good.fq | 280,765 | 37,906,019 | 100.0% | 135.0 bases | 141 bases | 95.9% |
errors | SNFR_3_67_1_S178_S2001_L008_R2_001.good.fq | 280,765 | 37,906,019 | 100.0% | 135.0 bases | 141 bases | 94.1% |
total | 1,847,830 | 250,077,610 | 100.0% | 135.3 bases | 141 bases | 95.4% |
seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
---|---|---|---|---|---|---|---|
coverage | distribution | USA300TCH1516_ALE | 2,872,915 | 88.5 | 14.8 | 96.0% | Staphylococcus species strain strain. |
coverage | distribution | CP000731 | 27,041 | 171.3 | 45.8 | 2.5% | Staphylococcus aureus subsp. aureus USA300_TCH1516 plasmid |
coverage | distribution | NC_012417 | 3,125 | 308.7 | 5.7 | 1.5% | 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 | 37341 |
Coverage evenness (position-hash) score of junction candidates | ≥ 2 | ≥ 3 |
Test this many junction candidates (n). May be smaller if not enough passed the coverage evenness threshold | 100 ≤ n ≤ 5000 | 129 |
Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.013 |
reference sequence | pr(no read start) |
---|---|
USA300TCH1516_ALE | 0.77634 |
CP000731 | 0.56353 |
NC_012417 | 0.16582 |
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 | 08:59:15 25 May 2019 | 08:59:41 25 May 2019 | 26 seconds |
Read alignment to reference genome | 08:59:41 25 May 2019 | 09:03:43 25 May 2019 | 4 minutes 2 seconds |
Preprocessing alignments for candidate junction identification | 09:03:43 25 May 2019 | 09:04:05 25 May 2019 | 22 seconds |
Preliminary analysis of coverage distribution | 09:04:05 25 May 2019 | 09:04:50 25 May 2019 | 45 seconds |
Identifying junction candidates | 09:04:50 25 May 2019 | 09:05:25 25 May 2019 | 35 seconds |
Re-alignment to junction candidates | 09:05:25 25 May 2019 | 09:06:27 25 May 2019 | 1 minute 2 seconds |
Resolving best read alignments | 09:06:27 25 May 2019 | 09:07:08 25 May 2019 | 41 seconds |
Creating BAM files | 09:07:08 25 May 2019 | 09:07:47 25 May 2019 | 39 seconds |
Tabulating error counts | 09:07:47 25 May 2019 | 09:08:06 25 May 2019 | 19 seconds |
Re-calibrating base error rates | 09:08:06 25 May 2019 | 09:08:08 25 May 2019 | 2 seconds |
Examining read alignment evidence | 09:08:08 25 May 2019 | 09:11:46 25 May 2019 | 3 minutes 38 seconds |
Polymorphism statistics | 09:11:46 25 May 2019 | 09:11:46 25 May 2019 | 0 seconds |
Output | 09:11:46 25 May 2019 | 09:11:55 25 May 2019 | 9 seconds |
Total | 12 minutes 40 seconds |