breseq version 0.35.4 revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
read file | reads | bases | passed filters | average | longest | mapped | |
---|---|---|---|---|---|---|---|
errors | JADR40_R1_A5_F60_I1_R1_S52_L001_R1_001.good.fq | 574,872 | 72,976,554 | 100.0% | 126.9 bases | 139 bases | 96.0% |
errors | JADR40_R1_A5_F60_I1_R1_S52_L001_R2_001.good.fq | 574,872 | 72,979,385 | 100.0% | 126.9 bases | 139 bases | 92.7% |
errors | JADR40_R1_A5_F60_I1_R1_S52_L002_R1_001.good.fq | 580,350 | 73,779,727 | 100.0% | 127.1 bases | 139 bases | 96.7% |
errors | JADR40_R1_A5_F60_I1_R1_S52_L002_R2_001.good.fq | 580,350 | 73,783,486 | 100.0% | 127.1 bases | 139 bases | 94.4% |
errors | JADR40_R1_A5_F60_I1_R1_S52_L003_R1_001.good.fq | 579,006 | 73,497,666 | 100.0% | 126.9 bases | 139 bases | 96.6% |
errors | JADR40_R1_A5_F60_I1_R1_S52_L003_R2_001.good.fq | 579,006 | 73,499,921 | 100.0% | 126.9 bases | 139 bases | 94.4% |
errors | JADR40_R1_A5_F60_I1_R1_S52_L004_R1_001.good.fq | 577,663 | 73,126,303 | 100.0% | 126.6 bases | 139 bases | 97.1% |
errors | JADR40_R1_A5_F60_I1_R1_S52_L004_R2_001.good.fq | 577,663 | 73,127,856 | 100.0% | 126.6 bases | 139 bases | 95.5% |
total | 4,623,782 | 586,770,898 | 100.0% | 126.9 bases | 139 bases | 95.4% |
seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
---|---|---|---|---|---|---|---|
coverage | distribution | BS168_reference_genome | 4,215,606 | 130.8 | 8.8 | 99.9% | Bacillus subtilis subsp. subtilis str. 168 complete genome. |
coverage | distribution | Exported | 6,538 | 75.7 | 5.2 | 0.1% | natural circular DNA |
total | 4,222,144 | 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 | 1014 |
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 | 94 |
Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.006 |
reference sequence | pr(no read start) |
---|---|
BS168_reference_genome | 0.76087 |
Exported | 0.83841 |
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 |
Minimum probablilty assigned that no mapped read will start at a given position and strand for junction prediction | 0.1 |
Junction allow suboptimal matches | FALSE |
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 | 2.2.6 |
R | 3.4.4 |
step | start | end | elapsed |
---|---|---|---|
Read and reference sequence file input | 10:21:34 04 Jun 2021 | 10:22:50 04 Jun 2021 | 1 minute 16 seconds |
Read alignment to reference genome | 10:22:51 04 Jun 2021 | 10:33:04 04 Jun 2021 | 10 minutes 13 seconds |
Preprocessing alignments for candidate junction identification | 10:33:04 04 Jun 2021 | 10:34:10 04 Jun 2021 | 1 minute 6 seconds |
Preliminary analysis of coverage distribution | 10:34:10 04 Jun 2021 | 10:36:49 04 Jun 2021 | 2 minutes 39 seconds |
Identifying junction candidates | 10:36:49 04 Jun 2021 | 10:36:49 04 Jun 2021 | 0 seconds |
Re-alignment to junction candidates | 10:36:49 04 Jun 2021 | 10:39:09 04 Jun 2021 | 2 minutes 20 seconds |
Resolving best read alignments | 10:39:09 04 Jun 2021 | 10:40:32 04 Jun 2021 | 1 minute 23 seconds |
Creating BAM files | 10:40:32 04 Jun 2021 | 10:42:54 04 Jun 2021 | 2 minutes 22 seconds |
Tabulating error counts | 10:42:54 04 Jun 2021 | 10:43:44 04 Jun 2021 | 50 seconds |
Re-calibrating base error rates | 10:43:44 04 Jun 2021 | 10:43:48 04 Jun 2021 | 4 seconds |
Examining read alignment evidence | 10:43:48 04 Jun 2021 | 10:54:24 04 Jun 2021 | 10 minutes 36 seconds |
Polymorphism statistics | 10:54:24 04 Jun 2021 | 10:54:24 04 Jun 2021 | 0 seconds |
Output | 10:54:24 04 Jun 2021 | 10:54:39 04 Jun 2021 | 15 seconds |
Total | 33 minutes 4 seconds |