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_R2_A2_F60_I1_R1_S81_L001_R1_001.good.fq | 405,653 | 51,124,017 | 100.0% | 126.0 bases | 139 bases | 95.6% |
errors | JADR33_R2_A2_F60_I1_R1_S81_L001_R2_001.good.fq | 405,653 | 51,126,123 | 100.0% | 126.0 bases | 139 bases | 92.6% |
errors | JADR33_R2_A2_F60_I1_R1_S81_L002_R1_001.good.fq | 400,331 | 50,470,285 | 100.0% | 126.1 bases | 139 bases | 96.4% |
errors | JADR33_R2_A2_F60_I1_R1_S81_L002_R2_001.good.fq | 400,331 | 50,472,911 | 100.0% | 126.1 bases | 139 bases | 94.3% |
errors | JADR33_R2_A2_F60_I1_R1_S81_L003_R1_001.good.fq | 412,061 | 51,961,869 | 100.0% | 126.1 bases | 139 bases | 96.3% |
errors | JADR33_R2_A2_F60_I1_R1_S81_L003_R2_001.good.fq | 412,061 | 51,965,033 | 100.0% | 126.1 bases | 139 bases | 94.2% |
errors | JADR33_R2_A2_F60_I1_R1_S81_L004_R1_001.good.fq | 399,367 | 50,116,101 | 100.0% | 125.5 bases | 139 bases | 96.8% |
errors | JADR33_R2_A2_F60_I1_R1_S81_L004_R2_001.good.fq | 399,367 | 50,117,928 | 100.0% | 125.5 bases | 139 bases | 95.3% |
total | 3,234,824 | 407,354,267 | 100.0% | 125.9 bases | 139 bases | 95.2% |
seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
---|---|---|---|---|---|---|---|
coverage | distribution | BS168_reference_genome | 4,215,606 | 82.7 | 6.2 | 92.0% | Bacillus subtilis subsp. subtilis str. 168 complete genome. |
coverage | distribution | pSIJ663_pHT315_araE_xy | 11,568 | 5227.8 | 290.8 | 8.0% | . |
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 | 10284 |
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 | 72 |
Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.005 |
reference sequence | pr(no read start) |
---|---|
BS168_reference_genome | 0.81711 |
pSIJ663_pHT315_araE_xy | 0.47439 |
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 | 10:17:43 04 Jun 2021 | 10:18:37 04 Jun 2021 | 54 seconds |
Read alignment to reference genome | 10:18:37 04 Jun 2021 | 10:25:28 04 Jun 2021 | 6 minutes 51 seconds |
Preprocessing alignments for candidate junction identification | 10:25:28 04 Jun 2021 | 10:26:13 04 Jun 2021 | 45 seconds |
Preliminary analysis of coverage distribution | 10:26:13 04 Jun 2021 | 10:28:04 04 Jun 2021 | 1 minute 51 seconds |
Identifying junction candidates | 10:28:04 04 Jun 2021 | 10:28:05 04 Jun 2021 | 1 second |
Re-alignment to junction candidates | 10:28:05 04 Jun 2021 | 10:29:48 04 Jun 2021 | 1 minute 43 seconds |
Resolving best read alignments | 10:29:48 04 Jun 2021 | 10:30:50 04 Jun 2021 | 1 minute 2 seconds |
Creating BAM files | 10:30:50 04 Jun 2021 | 10:32:31 04 Jun 2021 | 1 minute 41 seconds |
Tabulating error counts | 10:32:31 04 Jun 2021 | 10:33:07 04 Jun 2021 | 36 seconds |
Re-calibrating base error rates | 10:33:07 04 Jun 2021 | 10:33:10 04 Jun 2021 | 3 seconds |
Examining read alignment evidence | 10:33:10 04 Jun 2021 | 10:40:39 04 Jun 2021 | 7 minutes 29 seconds |
Polymorphism statistics | 10:40:39 04 Jun 2021 | 10:40:40 04 Jun 2021 | 1 second |
Output | 10:40:40 04 Jun 2021 | 10:40:59 04 Jun 2021 | 19 seconds |
Total | 23 minutes 16 seconds |