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 | 6_D16_AGTCAA_L001_R1_001 | 17,868,162 | 1,804,684,362 | 100.0% | 101.0 bases | 101 bases | 99.6% |
| total | 17,868,162 | 1,804,684,362 | 100.0% | 101.0 bases | 101 bases | 99.6% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_007779 | 4,646,332 | 399.7 | 2.1 | 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 | 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 | 108 |
| Total length of all junction candidates (factor times the reference genome length) | ≥ 0.1 | 0.005 |
| reference sequence | pr(no read start) |
|---|---|
| NC_007779 | 0.19151 |
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 | 20:57:00 04 Mar 2015 | 20:59:22 04 Mar 2015 | 2 minutes 22 seconds |
| Read alignment to reference genome | 20:59:23 04 Mar 2015 | 21:08:10 04 Mar 2015 | 8 minutes 47 seconds |
| Preprocessing alignments for candidate junction identification | 21:08:10 04 Mar 2015 | 21:13:32 04 Mar 2015 | 5 minutes 22 seconds |
| Preliminary analysis of coverage distribution | 21:13:32 04 Mar 2015 | 21:25:45 04 Mar 2015 | 12 minutes 13 seconds |
| Identifying junction candidates | 21:25:45 04 Mar 2015 | 21:25:50 04 Mar 2015 | 5 seconds |
| Re-alignment to junction candidates | 21:25:50 04 Mar 2015 | 21:27:44 04 Mar 2015 | 1 minute 54 seconds |
| Resolving alignments with junction candidates | 21:27:44 04 Mar 2015 | 21:35:02 04 Mar 2015 | 7 minutes 18 seconds |
| Creating BAM files | 21:35:02 04 Mar 2015 | 21:46:01 04 Mar 2015 | 10 minutes 59 seconds |
| Tabulating error counts | 21:46:01 04 Mar 2015 | 21:49:34 04 Mar 2015 | 3 minutes 33 seconds |
| Re-calibrating base error rates | 21:49:34 04 Mar 2015 | 21:49:36 04 Mar 2015 | 2 seconds |
| Examining read alignment evidence | 21:49:36 04 Mar 2015 | 23:41:40 04 Mar 2015 | 1 hour 52 minutes 4 seconds |
| Polymorphism statistics | 23:41:40 04 Mar 2015 | 23:41:42 04 Mar 2015 | 2 seconds |
| Output | 23:41:42 04 Mar 2015 | 23:43:28 04 Mar 2015 | 1 minute 46 seconds |
| Total | 2 hours 46 minutes 27 seconds | ||
