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breseq version 0.26.1
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
read file | reads | bases | passed filters | average | longest | mapped | |
---|---|---|---|---|---|---|---|
errors | 433WJAAXX_6_1_pf_REL8595M | 20,616,201 | 721,567,035 | 100.0% | 35.0 bases | 35 bases | 96.4% |
total | 20,616,201 | 721,567,035 | 100.0% | 35.0 bases | 35 bases | 96.4% |
seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
---|---|---|---|---|---|---|---|
coverage | distribution | REL606 | 4,629,812 | 156.6 | 8.4 | 100.0% | Escherichia coli strain REL606. |
total | 4,629,812 | 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 | 100000 |
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 | 888 |
Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.014 |
reference sequence | pr(no read start) |
---|---|
REL606 | 0.21582 |
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 |
Polymorphism E-value cutoff | 2 |
Polymorphism frequency cutoff | OFF |
Polymorphism minimum coverage each strand | 2 |
Polymorphism bias cutoff | 0.001 |
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 | ≥2 bases |
step | start | end | elapsed |
---|---|---|---|
Read and reference sequence file input | 09:49:41 26 Jul 2015 | 09:52:08 26 Jul 2015 | 2 minutes 27 seconds |
Read alignment to reference genome | 09:52:08 26 Jul 2015 | 12:50:32 26 Jul 2015 | 2 hours 58 minutes 24 seconds |
Preprocessing alignments for candidate junction identification | 12:50:32 26 Jul 2015 | 13:01:09 26 Jul 2015 | 10 minutes 37 seconds |
Preliminary analysis of coverage distribution | 13:01:09 26 Jul 2015 | 13:07:26 26 Jul 2015 | 6 minutes 17 seconds |
Identifying junction candidates | 13:07:26 26 Jul 2015 | 13:07:38 26 Jul 2015 | 12 seconds |
Re-alignment to junction candidates | 13:07:38 26 Jul 2015 | 13:12:22 26 Jul 2015 | 4 minutes 44 seconds |
Resolving alignments with junction candidates | 13:12:22 26 Jul 2015 | 13:24:15 26 Jul 2015 | 11 minutes 53 seconds |
Creating BAM files | 13:24:15 26 Jul 2015 | 13:30:16 26 Jul 2015 | 6 minutes 1 second |
Tabulating error counts | 13:30:16 26 Jul 2015 | 13:32:03 26 Jul 2015 | 1 minute 47 seconds |
Re-calibrating base error rates | 13:32:03 26 Jul 2015 | 13:32:04 26 Jul 2015 | 1 second |
Examining read alignment evidence | 13:32:04 26 Jul 2015 | 14:26:23 26 Jul 2015 | 54 minutes 19 seconds |
Polymorphism statistics | 14:26:23 26 Jul 2015 | 14:26:58 26 Jul 2015 | 35 seconds |
Output | 14:26:58 26 Jul 2015 | 14:29:44 26 Jul 2015 | 2 minutes 46 seconds |
Total | 4 hours 40 minutes 3 seconds |