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 | ERR2001777.good.fq | 8,624,996 | 427,864,388 | 100.0% | 49.6 bases | 50 bases | 98.0% |
total | 8,624,996 | 427,864,388 | 100.0% | 49.6 bases | 50 bases | 98.0% |
seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
---|---|---|---|---|---|---|---|
coverage | distribution | NC_000913 | 4,641,652 | 117.0 | 2.6 | 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 | 5136 |
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 | 136 |
Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.003 |
reference sequence | pr(no read start) |
---|---|
NC_000913 | 0.52624 |
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 | 2.3.4.1 |
R | 3.4.4 |
step | start | end | elapsed |
---|---|---|---|
Read and reference sequence file input | 18:57:13 01 Apr 2019 | 18:58:28 01 Apr 2019 | 1 minute 15 seconds |
Read alignment to reference genome | 18:58:28 01 Apr 2019 | 19:31:31 01 Apr 2019 | 33 minutes 3 seconds |
Preprocessing alignments for candidate junction identification | 19:31:31 01 Apr 2019 | 19:32:51 01 Apr 2019 | 1 minute 20 seconds |
Preliminary analysis of coverage distribution | 19:32:51 01 Apr 2019 | 19:35:22 01 Apr 2019 | 2 minutes 31 seconds |
Identifying junction candidates | 19:35:22 01 Apr 2019 | 19:35:23 01 Apr 2019 | 1 second |
Re-alignment to junction candidates | 19:35:23 01 Apr 2019 | 19:37:52 01 Apr 2019 | 2 minutes 29 seconds |
Resolving best read alignments | 19:37:52 01 Apr 2019 | 19:39:51 01 Apr 2019 | 1 minute 59 seconds |
Creating BAM files | 19:39:51 01 Apr 2019 | 19:42:08 01 Apr 2019 | 2 minutes 17 seconds |
Tabulating error counts | 19:42:08 01 Apr 2019 | 19:42:45 01 Apr 2019 | 37 seconds |
Re-calibrating base error rates | 19:42:45 01 Apr 2019 | 19:42:46 01 Apr 2019 | 1 second |
Examining read alignment evidence | 19:42:46 01 Apr 2019 | 19:48:45 01 Apr 2019 | 5 minutes 59 seconds |
Polymorphism statistics | 19:48:45 01 Apr 2019 | 19:48:45 01 Apr 2019 | 0 seconds |
Output | 19:48:45 01 Apr 2019 | 19:49:29 01 Apr 2019 | 44 seconds |
Total | 52 minutes 16 seconds |