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-1-BOP-27-RPE-END-1_S37_L001_R1_001.good.fq | 775,166 | 106,704,616 | 100.0% | 137.7 bases | 149 bases | 97.1% |
errors | Plate-1-BOP-27-RPE-END-1_S37_L001_R2_001.good.fq | 775,166 | 106,130,561 | 100.0% | 136.9 bases | 149 bases | 97.9% |
errors | Plate-1-BOP-27-RPE-END-1_S37_L002_R1_001.good.fq | 705,053 | 97,109,732 | 100.0% | 137.7 bases | 149 bases | 97.2% |
errors | Plate-1-BOP-27-RPE-END-1_S37_L002_R2_001.good.fq | 705,053 | 96,621,524 | 100.0% | 137.0 bases | 149 bases | 97.7% |
errors | Plate-1-BOP-27-RPE-END-1_S37_L003_R1_001.good.fq | 750,566 | 103,242,327 | 100.0% | 137.6 bases | 149 bases | 97.0% |
errors | Plate-1-BOP-27-RPE-END-1_S37_L003_R2_001.good.fq | 750,566 | 102,703,047 | 100.0% | 136.8 bases | 149 bases | 97.7% |
errors | Plate-1-BOP-27-RPE-END-1_S37_L004_R1_001.good.fq | 775,002 | 106,637,694 | 100.0% | 137.6 bases | 149 bases | 97.3% |
errors | Plate-1-BOP-27-RPE-END-1_S37_L004_R2_001.good.fq | 775,002 | 106,130,821 | 100.0% | 136.9 bases | 149 bases | 97.7% |
total | 6,011,574 | 825,280,322 | 100.0% | 137.3 bases | 149 bases | 97.4% |
seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
---|---|---|---|---|---|---|---|
coverage | distribution | NC_000913 | 4,641,652 | 171.6 | 4.8 | 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 | 31011 |
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 | 169 |
Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.011 |
reference sequence | pr(no read start) |
---|---|
NC_000913 | 0.59237 |
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 | ≤ 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 | 08:36:03 11 Sep 2020 | 08:37:32 11 Sep 2020 | 1 minute 29 seconds |
Read alignment to reference genome | 08:37:33 11 Sep 2020 | 08:48:38 11 Sep 2020 | 11 minutes 5 seconds |
Preprocessing alignments for candidate junction identification | 08:48:38 11 Sep 2020 | 08:50:08 11 Sep 2020 | 1 minute 30 seconds |
Preliminary analysis of coverage distribution | 08:50:08 11 Sep 2020 | 08:53:29 11 Sep 2020 | 3 minutes 21 seconds |
Identifying junction candidates | 08:53:29 11 Sep 2020 | 08:54:33 11 Sep 2020 | 1 minute 4 seconds |
Re-alignment to junction candidates | 08:54:33 11 Sep 2020 | 08:58:03 11 Sep 2020 | 3 minutes 30 seconds |
Resolving best read alignments | 08:58:03 11 Sep 2020 | 09:00:24 11 Sep 2020 | 2 minutes 21 seconds |
Creating BAM files | 09:00:24 11 Sep 2020 | 09:03:27 11 Sep 2020 | 3 minutes 3 seconds |
Tabulating error counts | 09:03:27 11 Sep 2020 | 09:04:31 11 Sep 2020 | 1 minute 4 seconds |
Re-calibrating base error rates | 09:04:31 11 Sep 2020 | 09:04:34 11 Sep 2020 | 3 seconds |
Examining read alignment evidence | 09:04:34 11 Sep 2020 | 09:17:01 11 Sep 2020 | 12 minutes 27 seconds |
Polymorphism statistics | 09:17:01 11 Sep 2020 | 09:17:02 11 Sep 2020 | 1 second |
Output | 09:17:02 11 Sep 2020 | 09:17:28 11 Sep 2020 | 26 seconds |
Total | 41 minutes 24 seconds |