mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
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 | 2_D22_AGTCAA_L004_R2_001 | 14,577,868 | 1,472,364,668 | 100.0% | 101.0 bases | 101 bases | 98.0% |
| total | 14,577,868 | 1,472,364,668 | 100.0% | 101.0 bases | 101 bases | 98.0% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_007779 | 4,646,332 | 292.0 | 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 | 100017 |
| 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 | 141 |
| Total length of all junction candidates (factor times the reference genome length) | ≥ 0.1 | 0.006 |
| reference sequence | pr(no read start) |
|---|---|
| NC_007779 | 0.28314 |
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 | 13:11:03 05 Mar 2015 | 13:13:08 05 Mar 2015 | 2 minutes 5 seconds |
| Read alignment to reference genome | 13:13:08 05 Mar 2015 | 13:20:21 05 Mar 2015 | 7 minutes 13 seconds |
| Preprocessing alignments for candidate junction identification | 13:20:21 05 Mar 2015 | 13:24:49 05 Mar 2015 | 4 minutes 28 seconds |
| Preliminary analysis of coverage distribution | 13:24:49 05 Mar 2015 | 13:34:31 05 Mar 2015 | 9 minutes 42 seconds |
| Identifying junction candidates | 13:34:31 05 Mar 2015 | 13:34:36 05 Mar 2015 | 5 seconds |
| Re-alignment to junction candidates | 13:34:36 05 Mar 2015 | 13:36:10 05 Mar 2015 | 1 minute 34 seconds |
| Resolving alignments with junction candidates | 13:36:10 05 Mar 2015 | 13:42:14 05 Mar 2015 | 6 minutes 4 seconds |
| Creating BAM files | 13:42:14 05 Mar 2015 | 13:50:55 05 Mar 2015 | 8 minutes 41 seconds |
| Tabulating error counts | 13:50:55 05 Mar 2015 | 13:53:51 05 Mar 2015 | 2 minutes 56 seconds |
| Re-calibrating base error rates | 13:53:51 05 Mar 2015 | 13:53:53 05 Mar 2015 | 2 seconds |
| Examining read alignment evidence | 13:53:53 05 Mar 2015 | 15:34:03 05 Mar 2015 | 1 hour 40 minutes 10 seconds |
| Polymorphism statistics | 15:34:03 05 Mar 2015 | 15:34:05 05 Mar 2015 | 2 seconds |
| Output | 15:34:05 05 Mar 2015 | 15:35:52 05 Mar 2015 | 1 minute 47 seconds |
| Total | 2 hours 24 minutes 49 seconds | ||
