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 | JADR49_R4_A16_F57_I0_R1_S92_L001_R1_001.good.fq | 403,854 | 50,850,097 | 100.0% | 125.9 bases | 139 bases | 95.4% |
errors | JADR49_R4_A16_F57_I0_R1_S92_L001_R2_001.good.fq | 403,854 | 50,850,945 | 100.0% | 125.9 bases | 139 bases | 92.3% |
errors | JADR49_R4_A16_F57_I0_R1_S92_L002_R1_001.good.fq | 401,081 | 50,528,792 | 100.0% | 126.0 bases | 139 bases | 96.2% |
errors | JADR49_R4_A16_F57_I0_R1_S92_L002_R2_001.good.fq | 401,081 | 50,529,950 | 100.0% | 126.0 bases | 139 bases | 94.0% |
errors | JADR49_R4_A16_F57_I0_R1_S92_L003_R1_001.good.fq | 404,805 | 50,905,239 | 100.0% | 125.8 bases | 139 bases | 96.2% |
errors | JADR49_R4_A16_F57_I0_R1_S92_L003_R2_001.good.fq | 404,805 | 50,904,962 | 100.0% | 125.8 bases | 139 bases | 94.2% |
errors | JADR49_R4_A16_F57_I0_R1_S92_L004_R1_001.good.fq | 401,104 | 50,246,678 | 100.0% | 125.3 bases | 139 bases | 96.8% |
errors | JADR49_R4_A16_F57_I0_R1_S92_L004_R2_001.good.fq | 401,104 | 50,246,818 | 100.0% | 125.3 bases | 139 bases | 95.3% |
total | 3,221,688 | 405,063,481 | 100.0% | 125.7 bases | 139 bases | 95.0% |
seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
---|---|---|---|---|---|---|---|
coverage | distribution | CP006881 | 4,033,459 | 68.5 | 5.9 | 75.2% | Bacillus subtilis PY79, complete genome. |
coverage | distribution | pSIJ663_pHT315_araE_xy | 11,568 | 16182.5 | 1003.4 | 24.8% | . |
total | 4,045,027 | 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 | 29350 |
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 | 68 |
Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.005 |
reference sequence | pr(no read start) |
---|---|
CP006881 | 0.83926 |
pSIJ663_pHT315_araE_xy | 0.42373 |
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 | 10:17:11 04 Jun 2021 | 10:18:04 04 Jun 2021 | 53 seconds |
Read alignment to reference genome | 10:18:04 04 Jun 2021 | 10:24:42 04 Jun 2021 | 6 minutes 38 seconds |
Preprocessing alignments for candidate junction identification | 10:24:42 04 Jun 2021 | 10:25:25 04 Jun 2021 | 43 seconds |
Preliminary analysis of coverage distribution | 10:25:25 04 Jun 2021 | 10:27:19 04 Jun 2021 | 1 minute 54 seconds |
Identifying junction candidates | 10:27:19 04 Jun 2021 | 10:27:21 04 Jun 2021 | 2 seconds |
Re-alignment to junction candidates | 10:27:21 04 Jun 2021 | 10:29:40 04 Jun 2021 | 2 minutes 19 seconds |
Resolving best read alignments | 10:29:40 04 Jun 2021 | 10:30:42 04 Jun 2021 | 1 minute 2 seconds |
Creating BAM files | 10:30:42 04 Jun 2021 | 10:32:24 04 Jun 2021 | 1 minute 42 seconds |
Tabulating error counts | 10:32:24 04 Jun 2021 | 10:33:10 04 Jun 2021 | 46 seconds |
Re-calibrating base error rates | 10:33:10 04 Jun 2021 | 10:33:14 04 Jun 2021 | 4 seconds |
Examining read alignment evidence | 10:33:14 04 Jun 2021 | 11:13:35 04 Jun 2021 | 40 minutes 21 seconds |
Polymorphism statistics | 11:13:35 04 Jun 2021 | 11:13:38 04 Jun 2021 | 3 seconds |
Output | 11:13:38 04 Jun 2021 | 11:14:45 04 Jun 2021 | 1 minute 7 seconds |
Total | 57 minutes 34 seconds |