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 | JADR33_R4_A4_F59_I0_R1_S67_L001_R1_001.good.fq | 426,538 | 54,234,623 | 100.0% | 127.2 bases | 139 bases | 95.9% |
errors | JADR33_R4_A4_F59_I0_R1_S67_L001_R2_001.good.fq | 426,538 | 54,235,609 | 100.0% | 127.2 bases | 139 bases | 92.9% |
errors | JADR33_R4_A4_F59_I0_R1_S67_L002_R1_001.good.fq | 427,814 | 54,466,265 | 100.0% | 127.3 bases | 139 bases | 96.7% |
errors | JADR33_R4_A4_F59_I0_R1_S67_L002_R2_001.good.fq | 427,814 | 54,466,116 | 100.0% | 127.3 bases | 139 bases | 94.7% |
errors | JADR33_R4_A4_F59_I0_R1_S67_L003_R1_001.good.fq | 429,245 | 54,599,771 | 100.0% | 127.2 bases | 139 bases | 96.6% |
errors | JADR33_R4_A4_F59_I0_R1_S67_L003_R2_001.good.fq | 429,245 | 54,600,238 | 100.0% | 127.2 bases | 139 bases | 94.6% |
errors | JADR33_R4_A4_F59_I0_R1_S67_L004_R1_001.good.fq | 424,045 | 53,749,207 | 100.0% | 126.8 bases | 139 bases | 97.2% |
errors | JADR33_R4_A4_F59_I0_R1_S67_L004_R2_001.good.fq | 424,045 | 53,749,497 | 100.0% | 126.8 bases | 139 bases | 95.7% |
total | 3,415,284 | 434,101,326 | 100.0% | 127.1 bases | 139 bases | 95.5% |
seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
---|---|---|---|---|---|---|---|
coverage | distribution | BS168_reference_genome | 4,215,606 | 70.0 | 5.4 | 75.2% | Bacillus subtilis subsp. subtilis str. 168 complete genome. |
coverage | distribution | pSIJ663_pHT315_araE_xy | 11,568 | 17251.2 | 902.2 | 24.8% | . |
total | 4,227,174 | 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 | 32327 |
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 | 83 |
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 | 0.83709 |
pSIJ663_pHT315_araE_xy | 0.41923 |
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 | ≤ 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 | 2.2.6 |
R | 3.4.4 |
step | start | end | elapsed |
---|---|---|---|
Read and reference sequence file input | 10:17:40 04 Jun 2021 | 10:18:38 04 Jun 2021 | 58 seconds |
Read alignment to reference genome | 10:18:38 04 Jun 2021 | 10:25:39 04 Jun 2021 | 7 minutes 1 second |
Preprocessing alignments for candidate junction identification | 10:25:39 04 Jun 2021 | 10:26:26 04 Jun 2021 | 47 seconds |
Preliminary analysis of coverage distribution | 10:26:26 04 Jun 2021 | 10:28:27 04 Jun 2021 | 2 minutes 1 second |
Identifying junction candidates | 10:28:27 04 Jun 2021 | 10:28:29 04 Jun 2021 | 2 seconds |
Re-alignment to junction candidates | 10:28:29 04 Jun 2021 | 10:30:58 04 Jun 2021 | 2 minutes 29 seconds |
Resolving best read alignments | 10:30:58 04 Jun 2021 | 10:32:06 04 Jun 2021 | 1 minute 8 seconds |
Creating BAM files | 10:32:06 04 Jun 2021 | 10:33:56 04 Jun 2021 | 1 minute 50 seconds |
Tabulating error counts | 10:33:56 04 Jun 2021 | 10:34:38 04 Jun 2021 | 42 seconds |
Re-calibrating base error rates | 10:34:38 04 Jun 2021 | 10:34:41 04 Jun 2021 | 3 seconds |
Examining read alignment evidence | 10:34:41 04 Jun 2021 | 11:17:42 04 Jun 2021 | 43 minutes 1 second |
Polymorphism statistics | 11:17:42 04 Jun 2021 | 11:17:45 04 Jun 2021 | 3 seconds |
Output | 11:17:45 04 Jun 2021 | 11:18:28 04 Jun 2021 | 43 seconds |
Total | 1 hour 48 seconds |