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 | SNFM_19_74_1_S210_S1993_L006_R1_001.good.fq | 790,941 | 105,857,728 | 100.0% | 133.8 bases | 141 bases | 94.7% |
errors | SNFM_19_74_1_S210_S1993_L006_R2_001.good.fq | 790,941 | 105,857,728 | 100.0% | 133.8 bases | 141 bases | 93.5% |
errors | SNFM_19_74_1_S210_S1993_L008_R1_001.good.fq | 348,645 | 46,448,554 | 100.0% | 133.2 bases | 141 bases | 94.5% |
errors | SNFM_19_74_1_S210_S1993_L008_R2_001.good.fq | 348,645 | 46,448,554 | 100.0% | 133.2 bases | 141 bases | 92.3% |
total | 2,279,172 | 304,612,564 | 100.0% | 133.7 bases | 141 bases | 93.9% |
seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
---|---|---|---|---|---|---|---|
coverage | distribution | USA300TCH1516_ALE | 2,872,915 | 98.0 | 3.3 | 96.9% | 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 | 3257.0 | 215.3 | 3.1% | 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 | 80655 |
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 | 201 |
Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.020 |
reference sequence | pr(no read start) |
---|---|
USA300TCH1516_ALE | 0.73015 |
CP000731 | 0.99474 |
NC_012417 | 0.04665 |
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 | 08:54:22 24 May 2019 | 08:54:54 24 May 2019 | 32 seconds |
Read alignment to reference genome | 08:54:54 24 May 2019 | 09:00:05 24 May 2019 | 5 minutes 11 seconds |
Preprocessing alignments for candidate junction identification | 09:00:05 24 May 2019 | 09:00:39 24 May 2019 | 34 seconds |
Preliminary analysis of coverage distribution | 09:00:39 24 May 2019 | 09:01:35 24 May 2019 | 56 seconds |
Identifying junction candidates | 09:01:35 24 May 2019 | 09:02:56 24 May 2019 | 1 minute 21 seconds |
Re-alignment to junction candidates | 09:02:56 24 May 2019 | 09:04:24 24 May 2019 | 1 minute 28 seconds |
Resolving best read alignments | 09:04:24 24 May 2019 | 09:05:14 24 May 2019 | 50 seconds |
Creating BAM files | 09:05:14 24 May 2019 | 09:06:01 24 May 2019 | 47 seconds |
Tabulating error counts | 09:06:01 24 May 2019 | 09:06:25 24 May 2019 | 24 seconds |
Re-calibrating base error rates | 09:06:25 24 May 2019 | 09:06:27 24 May 2019 | 2 seconds |
Examining read alignment evidence | 09:06:27 24 May 2019 | 09:10:58 24 May 2019 | 4 minutes 31 seconds |
Polymorphism statistics | 09:10:58 24 May 2019 | 09:10:59 24 May 2019 | 1 second |
Output | 09:10:59 24 May 2019 | 09:11:10 24 May 2019 | 11 seconds |
Total | 16 minutes 48 seconds |