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_R2_A6_F61_I0_R1_S79_L001_R1_001.good.fq | 427,046 | 54,206,902 | 100.0% | 126.9 bases | 139 bases | 96.2% |
errors | JADR40_R2_A6_F61_I0_R1_S79_L001_R2_001.good.fq | 427,046 | 54,209,473 | 100.0% | 126.9 bases | 139 bases | 93.3% |
errors | JADR40_R2_A6_F61_I0_R1_S79_L002_R1_001.good.fq | 431,252 | 54,783,904 | 100.0% | 127.0 bases | 139 bases | 96.9% |
errors | JADR40_R2_A6_F61_I0_R1_S79_L002_R2_001.good.fq | 431,252 | 54,786,405 | 100.0% | 127.0 bases | 139 bases | 94.9% |
errors | JADR40_R2_A6_F61_I0_R1_S79_L003_R1_001.good.fq | 430,877 | 54,677,805 | 100.0% | 126.9 bases | 139 bases | 96.8% |
errors | JADR40_R2_A6_F61_I0_R1_S79_L003_R2_001.good.fq | 430,877 | 54,679,903 | 100.0% | 126.9 bases | 139 bases | 94.9% |
errors | JADR40_R2_A6_F61_I0_R1_S79_L004_R1_001.good.fq | 429,791 | 54,366,240 | 100.0% | 126.5 bases | 139 bases | 97.3% |
errors | JADR40_R2_A6_F61_I0_R1_S79_L004_R2_001.good.fq | 429,791 | 54,368,915 | 100.0% | 126.5 bases | 139 bases | 95.9% |
total | 3,437,932 | 436,079,547 | 100.0% | 126.8 bases | 139 bases | 95.8% |
seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
---|---|---|---|---|---|---|---|
coverage | distribution | BS168_reference_genome | 4,215,606 | 80.6 | 5.7 | 83.2% | Bacillus subtilis subsp. subtilis str. 168 complete genome. |
coverage | distribution | Exported | 6,538 | 10916.4 | 394.6 | 16.8% | 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 | 15313 |
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 | 51 |
Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.003 |
reference sequence | pr(no read start) |
---|---|
BS168_reference_genome | 0.82131 |
Exported | 0.11410 |
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 | 10:19:01 04 Jun 2021 | 10:19:58 04 Jun 2021 | 57 seconds |
Read alignment to reference genome | 10:19:58 04 Jun 2021 | 10:27:39 04 Jun 2021 | 7 minutes 41 seconds |
Preprocessing alignments for candidate junction identification | 10:27:39 04 Jun 2021 | 10:28:26 04 Jun 2021 | 47 seconds |
Preliminary analysis of coverage distribution | 10:28:26 04 Jun 2021 | 10:30:27 04 Jun 2021 | 2 minutes 1 second |
Identifying junction candidates | 10:30:27 04 Jun 2021 | 10:30:28 04 Jun 2021 | 1 second |
Re-alignment to junction candidates | 10:30:28 04 Jun 2021 | 10:32:21 04 Jun 2021 | 1 minute 53 seconds |
Resolving best read alignments | 10:32:21 04 Jun 2021 | 10:33:25 04 Jun 2021 | 1 minute 4 seconds |
Creating BAM files | 10:33:25 04 Jun 2021 | 10:35:13 04 Jun 2021 | 1 minute 48 seconds |
Tabulating error counts | 10:35:13 04 Jun 2021 | 10:36:07 04 Jun 2021 | 54 seconds |
Re-calibrating base error rates | 10:36:07 04 Jun 2021 | 10:36:11 04 Jun 2021 | 4 seconds |
Examining read alignment evidence | 10:36:11 04 Jun 2021 | 11:16:48 04 Jun 2021 | 40 minutes 37 seconds |
Polymorphism statistics | 11:16:48 04 Jun 2021 | 11:16:50 04 Jun 2021 | 2 seconds |
Output | 11:16:50 04 Jun 2021 | 11:17:25 04 Jun 2021 | 35 seconds |
Total | 58 minutes 24 seconds |