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 | 4_D16_CTTGTA_L003_R1_001 | 15,484,463 | 1,563,930,763 | 100.0% | 101.0 bases | 101 bases | 98.4% |
| total | 15,484,463 | 1,563,930,763 | 100.0% | 101.0 bases | 101 bases | 98.4% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_007779 | 4,646,332 | 341.6 | 2.3 | 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 | 126 |
| Total length of all junction candidates (factor times the reference genome length) | ≥ 0.1 | 0.006 |
| reference sequence | pr(no read start) |
|---|---|
| NC_007779 | 0.23728 |
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 | 04:44:03 04 Mar 2015 | 04:46:12 04 Mar 2015 | 2 minutes 9 seconds |
| Read alignment to reference genome | 04:46:13 04 Mar 2015 | 04:53:36 04 Mar 2015 | 7 minutes 23 seconds |
| Preprocessing alignments for candidate junction identification | 04:53:36 04 Mar 2015 | 04:58:09 04 Mar 2015 | 4 minutes 33 seconds |
| Preliminary analysis of coverage distribution | 04:58:09 04 Mar 2015 | 05:08:28 04 Mar 2015 | 10 minutes 19 seconds |
| Identifying junction candidates | 05:08:28 04 Mar 2015 | 05:08:34 04 Mar 2015 | 6 seconds |
| Re-alignment to junction candidates | 05:08:34 04 Mar 2015 | 05:10:12 04 Mar 2015 | 1 minute 38 seconds |
| Resolving alignments with junction candidates | 05:10:12 04 Mar 2015 | 05:16:55 04 Mar 2015 | 6 minutes 43 seconds |
| Creating BAM files | 05:16:55 04 Mar 2015 | 05:26:11 04 Mar 2015 | 9 minutes 16 seconds |
| Tabulating error counts | 05:26:11 04 Mar 2015 | 05:29:13 04 Mar 2015 | 3 minutes 2 seconds |
| Re-calibrating base error rates | 05:29:13 04 Mar 2015 | 05:29:15 04 Mar 2015 | 2 seconds |
| Examining read alignment evidence | 05:29:15 04 Mar 2015 | 07:27:45 04 Mar 2015 | 1 hour 58 minutes 30 seconds |
| Polymorphism statistics | 07:27:45 04 Mar 2015 | 07:27:47 04 Mar 2015 | 2 seconds |
| Output | 07:27:47 04 Mar 2015 | 07:29:27 04 Mar 2015 | 1 minute 40 seconds |
| Total | 2 hours 45 minutes 23 seconds | ||
