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 | C13-Redo-Population-2-23_S11_L001_R1_001.good.fq | 1,213,402 | 298,657,378 | 100.0% | 246.1 bases | 281 bases | 98.2% |
errors | C13-Redo-Population-2-23_S11_L001_R2_001.good.fq | 1,213,402 | 301,184,537 | 100.0% | 248.2 bases | 281 bases | 89.1% |
total | 2,426,804 | 599,841,915 | 100.0% | 247.2 bases | 281 bases | 93.6% |
seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
---|---|---|---|---|---|---|---|
coverage | distribution | NC_000913 | 4,641,652 | 118.6 | 8.5 | 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 | 3075 |
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 | 478 |
Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.058 |
reference sequence | pr(no read start) |
---|---|
NC_000913 | 0.84430 |
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 | 2.3.4.1 |
R | 3.4.4 |
step | start | end | elapsed |
---|---|---|---|
Read and reference sequence file input | 01:53:39 16 May 2019 | 01:54:17 16 May 2019 | 38 seconds |
Read alignment to reference genome | 01:54:17 16 May 2019 | 02:07:16 16 May 2019 | 12 minutes 59 seconds |
Preprocessing alignments for candidate junction identification | 02:07:16 16 May 2019 | 02:07:55 16 May 2019 | 39 seconds |
Preliminary analysis of coverage distribution | 02:07:55 16 May 2019 | 02:10:13 16 May 2019 | 2 minutes 18 seconds |
Identifying junction candidates | 02:10:13 16 May 2019 | 02:10:17 16 May 2019 | 4 seconds |
Re-alignment to junction candidates | 02:10:17 16 May 2019 | 02:13:31 16 May 2019 | 3 minutes 14 seconds |
Resolving best read alignments | 02:13:31 16 May 2019 | 02:14:42 16 May 2019 | 1 minute 11 seconds |
Creating BAM files | 02:14:42 16 May 2019 | 02:16:45 16 May 2019 | 2 minutes 3 seconds |
Tabulating error counts | 02:16:45 16 May 2019 | 02:17:38 16 May 2019 | 53 seconds |
Re-calibrating base error rates | 02:17:38 16 May 2019 | 02:17:39 16 May 2019 | 1 second |
Examining read alignment evidence | 02:17:39 16 May 2019 | 03:20:33 16 May 2019 | 1 hour 2 minutes 54 seconds |
Polymorphism statistics | 03:20:33 16 May 2019 | 03:20:34 16 May 2019 | 1 second |
Output | 03:20:34 16 May 2019 | 03:20:47 16 May 2019 | 13 seconds |
Total | 1 hour 27 minutes 8 seconds |