breseq version 0.25c
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
read file | reads | bases | passed filters | average | longest | mapped | |
---|---|---|---|---|---|---|---|
errors | 3_D6_GCCAAT_L001_R2_001 | 12,756,085 | 1,288,364,585 | 100.0% | 101.0 bases | 101 bases | 99.0% |
total | 12,756,085 | 1,288,364,585 | 100.0% | 101.0 bases | 101 bases | 99.0% |
seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
---|---|---|---|---|---|---|---|
coverage | distribution | NC_007779 | 4,646,332 | 273.3 | 1.9 | 100.0% | Escherichia coli str. K-12 substr. W3110, complete genome. |
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 | 100008 |
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 | 118 |
Total length of all junction candidates (factor times the reference genome length) | ≥ 0.1 | 0.005 |
reference sequence | pr(no read start) |
---|---|
NC_007779 | 0.30539 |
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 | 12:59:47 06 Mar 2015 | 13:01:28 06 Mar 2015 | 1 minute 41 seconds |
Read alignment to reference genome | 13:01:28 06 Mar 2015 | 13:07:35 06 Mar 2015 | 6 minutes 7 seconds |
Preprocessing alignments for candidate junction identification | 13:07:35 06 Mar 2015 | 13:11:28 06 Mar 2015 | 3 minutes 53 seconds |
Preliminary analysis of coverage distribution | 13:11:28 06 Mar 2015 | 13:19:54 06 Mar 2015 | 8 minutes 26 seconds |
Identifying junction candidates | 13:19:54 06 Mar 2015 | 13:19:59 06 Mar 2015 | 5 seconds |
Re-alignment to junction candidates | 13:19:59 06 Mar 2015 | 13:21:20 06 Mar 2015 | 1 minute 21 seconds |
Resolving alignments with junction candidates | 13:21:20 06 Mar 2015 | 13:26:37 06 Mar 2015 | 5 minutes 17 seconds |
Creating BAM files | 13:26:37 06 Mar 2015 | 13:34:16 06 Mar 2015 | 7 minutes 39 seconds |
Tabulating error counts | 13:34:16 06 Mar 2015 | 13:36:49 06 Mar 2015 | 2 minutes 33 seconds |
Re-calibrating base error rates | 13:36:49 06 Mar 2015 | 13:36:50 06 Mar 2015 | 1 second |
Examining read alignment evidence | 13:36:50 06 Mar 2015 | 14:41:55 06 Mar 2015 | 1 hour 5 minutes 5 seconds |
Polymorphism statistics | 14:41:55 06 Mar 2015 | 14:41:57 06 Mar 2015 | 2 seconds |
Output | 14:41:57 06 Mar 2015 | 14:43:23 06 Mar 2015 | 1 minute 26 seconds |
Total | 1 hour 43 minutes 36 seconds |