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_21_0_S2337_L001_R1_001.good.fq | 1,110,776 | 156,584,172 | 100.0% | 141.0 bases | 141 bases | 98.1% |
errors | SNFR_3_21_0_S2337_L001_R2_001.good.fq | 1,110,776 | 156,584,172 | 100.0% | 141.0 bases | 141 bases | 93.4% |
total | 2,221,552 | 313,168,344 | 100.0% | 141.0 bases | 141 bases | 95.8% |
seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
---|---|---|---|---|---|---|---|
coverage | distribution | USA300TCH1516_ALE | 2,872,915 | 97.4 | 4.1 | 95.1% | Staphylococcus species strain strain. |
coverage | distribution | CP000731 | 27,041 | 370.1 | 4.7 | 3.3% | Staphylococcus aureus subsp. aureus USA300_TCH1516 plasmid |
coverage | distribution | NC_012417 | 3,125 | 1595.3 | 23.6 | 1.6% | 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 | 3684 |
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 | 73 |
Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.007 |
reference sequence | pr(no read start) |
---|---|
USA300TCH1516_ALE | 0.79622 |
CP000731 | 0.47862 |
NC_012417 | 0.14830 |
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 | 01:55:03 26 May 2019 | 01:55:34 26 May 2019 | 31 seconds |
Read alignment to reference genome | 01:55:34 26 May 2019 | 02:01:05 26 May 2019 | 5 minutes 31 seconds |
Preprocessing alignments for candidate junction identification | 02:01:05 26 May 2019 | 02:01:34 26 May 2019 | 29 seconds |
Preliminary analysis of coverage distribution | 02:01:34 26 May 2019 | 02:02:47 26 May 2019 | 1 minute 13 seconds |
Identifying junction candidates | 02:02:47 26 May 2019 | 02:02:48 26 May 2019 | 1 second |
Re-alignment to junction candidates | 02:02:48 26 May 2019 | 02:04:00 26 May 2019 | 1 minute 12 seconds |
Resolving best read alignments | 02:04:00 26 May 2019 | 02:04:45 26 May 2019 | 45 seconds |
Creating BAM files | 02:04:45 26 May 2019 | 02:05:48 26 May 2019 | 1 minute 3 seconds |
Tabulating error counts | 02:05:48 26 May 2019 | 02:06:11 26 May 2019 | 23 seconds |
Re-calibrating base error rates | 02:06:11 26 May 2019 | 02:06:13 26 May 2019 | 2 seconds |
Examining read alignment evidence | 02:06:13 26 May 2019 | 02:36:57 26 May 2019 | 30 minutes 44 seconds |
Polymorphism statistics | 02:36:57 26 May 2019 | 02:36:57 26 May 2019 | 0 seconds |
Output | 02:36:57 26 May 2019 | 02:37:06 26 May 2019 | 9 seconds |
Total | 42 minutes 3 seconds |