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 | SRR3480973_pass_R1.good.fq | 1,303,081 | 324,539,714 | 100.0% | 249.1 bases | 250 bases | 99.5% |
errors | SRR3480973_pass_R2.good.fq | 1,303,081 | 324,539,714 | 100.0% | 249.1 bases | 250 bases | 94.6% |
total | 2,606,162 | 649,079,428 | 100.0% | 249.1 bases | 250 bases | 97.1% |
seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
---|---|---|---|---|---|---|---|
coverage | distribution | NC_007779 | 4,646,332 | 139.1 | 2.4 | 100.0% | Escherichia coli str. K-12 substr. W3110, complete sequence. |
total | 4,646,332 | 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 | 48955 |
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 | 122 |
Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.013 |
reference sequence | pr(no read start) |
---|---|
NC_007779 | 0.77195 |
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 | 22:58:49 14 Feb 2020 | 22:59:27 14 Feb 2020 | 38 seconds |
Read alignment to reference genome | 22:59:27 14 Feb 2020 | 23:08:50 14 Feb 2020 | 9 minutes 23 seconds |
Preprocessing alignments for candidate junction identification | 23:08:50 14 Feb 2020 | 23:09:34 14 Feb 2020 | 44 seconds |
Preliminary analysis of coverage distribution | 23:09:34 14 Feb 2020 | 23:11:48 14 Feb 2020 | 2 minutes 14 seconds |
Identifying junction candidates | 23:11:48 14 Feb 2020 | 23:11:53 14 Feb 2020 | 5 seconds |
Re-alignment to junction candidates | 23:11:53 14 Feb 2020 | 23:14:04 14 Feb 2020 | 2 minutes 11 seconds |
Resolving best read alignments | 23:14:04 14 Feb 2020 | 23:15:15 14 Feb 2020 | 1 minute 11 seconds |
Creating BAM files | 23:15:15 14 Feb 2020 | 23:17:12 14 Feb 2020 | 1 minute 57 seconds |
Tabulating error counts | 23:17:12 14 Feb 2020 | 23:18:00 14 Feb 2020 | 48 seconds |
Re-calibrating base error rates | 23:18:00 14 Feb 2020 | 23:18:01 14 Feb 2020 | 1 second |
Examining read alignment evidence | 23:18:01 14 Feb 2020 | 23:27:11 14 Feb 2020 | 9 minutes 10 seconds |
Polymorphism statistics | 23:27:11 14 Feb 2020 | 23:27:11 14 Feb 2020 | 0 seconds |
Output | 23:27:11 14 Feb 2020 | 23:27:43 14 Feb 2020 | 32 seconds |
Total | 28 minutes 54 seconds |