breseq version 0.33.1 revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
read file | reads | bases | passed filters | average | longest | mapped | |
---|---|---|---|---|---|---|---|
errors | Plate-3-BOP-1000-RPE-END-4_S68_L001_R1_001.good.fq | 390,784 | 54,993,977 | 100.0% | 140.7 bases | 148 bases | 98.6% |
errors | Plate-3-BOP-1000-RPE-END-4_S68_L001_R2_001.good.fq | 390,784 | 55,015,288 | 100.0% | 140.8 bases | 148 bases | 97.5% |
errors | Plate-3-BOP-1000-RPE-END-4_S68_L002_R1_001.good.fq | 364,325 | 51,342,254 | 100.0% | 140.9 bases | 148 bases | 98.6% |
errors | Plate-3-BOP-1000-RPE-END-4_S68_L002_R2_001.good.fq | 364,325 | 51,367,903 | 100.0% | 141.0 bases | 148 bases | 97.1% |
errors | Plate-3-BOP-1000-RPE-END-4_S68_L003_R1_001.good.fq | 378,215 | 53,191,548 | 100.0% | 140.6 bases | 148 bases | 98.5% |
errors | Plate-3-BOP-1000-RPE-END-4_S68_L003_R2_001.good.fq | 378,215 | 53,215,955 | 100.0% | 140.7 bases | 148 bases | 97.2% |
errors | Plate-3-BOP-1000-RPE-END-4_S68_L004_R1_001.good.fq | 384,279 | 54,019,963 | 100.0% | 140.6 bases | 148 bases | 98.6% |
errors | Plate-3-BOP-1000-RPE-END-4_S68_L004_R2_001.good.fq | 384,279 | 54,048,004 | 100.0% | 140.6 bases | 148 bases | 97.3% |
total | 3,035,206 | 427,194,892 | 100.0% | 140.7 bases | 148 bases | 97.9% |
seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
---|---|---|---|---|---|---|---|
coverage | distribution | NC_000913 | 4,641,652 | 78.5 | 3.6 | 100.0% | Escherichia coli str. K-12 substr. MG1655, complete genome. |
total | 4,641,652 | 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 | 26954 |
Coverage evenness (position-hash) score of junction candidates | ≥ 2 | ≥ 3 |
Test this many junction candidates (n). May be smaller if not enough passed the coverage evenness threshold | 100 ≤ n ≤ 5000 | 35 |
Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.002 |
reference sequence | pr(no read start) |
---|---|
NC_000913 | 0.76373 |
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 |
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 | 22:08:57 12 Sep 2020 | 22:09:44 12 Sep 2020 | 47 seconds |
Read alignment to reference genome | 22:09:44 12 Sep 2020 | 22:15:33 12 Sep 2020 | 5 minutes 49 seconds |
Preprocessing alignments for candidate junction identification | 22:15:33 12 Sep 2020 | 22:16:19 12 Sep 2020 | 46 seconds |
Preliminary analysis of coverage distribution | 22:16:19 12 Sep 2020 | 22:18:05 12 Sep 2020 | 1 minute 46 seconds |
Identifying junction candidates | 22:18:05 12 Sep 2020 | 22:18:37 12 Sep 2020 | 32 seconds |
Re-alignment to junction candidates | 22:18:37 12 Sep 2020 | 22:20:21 12 Sep 2020 | 1 minute 44 seconds |
Resolving best read alignments | 22:20:21 12 Sep 2020 | 22:21:33 12 Sep 2020 | 1 minute 12 seconds |
Creating BAM files | 22:21:33 12 Sep 2020 | 22:23:11 12 Sep 2020 | 1 minute 38 seconds |
Tabulating error counts | 22:23:11 12 Sep 2020 | 22:23:44 12 Sep 2020 | 33 seconds |
Re-calibrating base error rates | 22:23:44 12 Sep 2020 | 22:23:46 12 Sep 2020 | 2 seconds |
Examining read alignment evidence | 22:23:46 12 Sep 2020 | 22:53:04 12 Sep 2020 | 29 minutes 18 seconds |
Polymorphism statistics | 22:53:04 12 Sep 2020 | 22:53:04 12 Sep 2020 | 0 seconds |
Output | 22:53:04 12 Sep 2020 | 22:53:26 12 Sep 2020 | 22 seconds |
Total | 44 minutes 29 seconds |