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 | PAL052_S51_L007_R1_001.good.fq | 3,105,743 | 282,488,085 | 100.0% | 91.0 bases | 91 bases | 97.8% |
errors | PAL052_S51_L007_R2_001.good.fq | 3,105,743 | 282,488,085 | 100.0% | 91.0 bases | 91 bases | 97.5% |
total | 6,211,486 | 564,976,170 | 100.0% | 91.0 bases | 91 bases | 97.6% |
seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
---|---|---|---|---|---|---|---|
coverage | distribution | USA300TCH1516_ALE | 2,872,915 | 177.5 | 3.0 | 92.9% | Staphylococcus species strain strain. |
coverage | distribution | CP000731 | 27,041 | 528.5 | 9.9 | 2.5% | Staphylococcus aureus subsp. aureus USA300_TCH1516 plasmid |
coverage | distribution | NC_012417 | 3,125 | 8302.8 | 38.1 | 4.6% | 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 | 90516 |
Coverage evenness (position-hash) score of junction candidates | ≥ 2 | ≥ 5 |
Test this many junction candidates (n). May be smaller if not enough passed the coverage evenness threshold | 100 ≤ n ≤ 5000 | 946 |
Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.062 |
reference sequence | pr(no read start) |
---|---|
USA300TCH1516_ALE | 0.47124 |
CP000731 | 0.17534 |
NC_012417 | 0.02995 |
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 | 02:37:07 26 May 2019 | 02:38:20 26 May 2019 | 1 minute 13 seconds |
Read alignment to reference genome | 02:38:20 26 May 2019 | 02:46:31 26 May 2019 | 8 minutes 11 seconds |
Preprocessing alignments for candidate junction identification | 02:46:31 26 May 2019 | 02:47:39 26 May 2019 | 1 minute 8 seconds |
Preliminary analysis of coverage distribution | 02:47:39 26 May 2019 | 02:49:42 26 May 2019 | 2 minutes 3 seconds |
Identifying junction candidates | 02:49:42 26 May 2019 | 02:50:51 26 May 2019 | 1 minute 9 seconds |
Re-alignment to junction candidates | 02:50:51 26 May 2019 | 02:54:10 26 May 2019 | 3 minutes 19 seconds |
Resolving best read alignments | 02:54:10 26 May 2019 | 02:56:07 26 May 2019 | 1 minute 57 seconds |
Creating BAM files | 02:56:07 26 May 2019 | 02:57:55 26 May 2019 | 1 minute 48 seconds |
Tabulating error counts | 02:57:55 26 May 2019 | 02:58:42 26 May 2019 | 47 seconds |
Re-calibrating base error rates | 02:58:42 26 May 2019 | 02:58:43 26 May 2019 | 1 second |
Examining read alignment evidence | 02:58:43 26 May 2019 | 03:06:40 26 May 2019 | 7 minutes 57 seconds |
Polymorphism statistics | 03:06:40 26 May 2019 | 03:06:41 26 May 2019 | 1 second |
Output | 03:06:41 26 May 2019 | 03:07:23 26 May 2019 | 42 seconds |
Total | 30 minutes 16 seconds |