mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.26.0
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| read file | reads | bases | passed filters | average | longest | mapped | |
|---|---|---|---|---|---|---|---|
| errors | 2Glu_S3_L001_R2_001 | 959,824 | 273,909,494 | 100.0% | 285.4 bases | 301 bases | 76.2% |
| errors | 2Glu_S3_L001_R1_001 | 959,856 | 271,112,784 | 100.0% | 282.5 bases | 301 bases | 95.6% |
| total | 1,919,680 | 545,022,278 | 100.0% | 283.9 bases | 301 bases | 85.9% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_000913 | 4,641,652 | 102.5 | 3.9 | 100.0% | Escherichia coli str. K-12 substr. MG1655, complete genome. |
| total | 4,641,652 | 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 | 1990 |
| 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 | 120 |
| Total length of all junction candidates (factor times the reference genome length) | ≥ 0.1 | 0.016 |
| reference sequence | pr(no read start) |
|---|---|
| NC_000913 | 0.89916 |
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 | 0.05 |
| 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 | 02:13:33 16 Apr 2015 | 02:14:17 16 Apr 2015 | 44 seconds |
| Read alignment to reference genome | 02:14:18 16 Apr 2015 | 02:19:46 16 Apr 2015 | 5 minutes 28 seconds |
| Preprocessing alignments for candidate junction identification | 02:19:46 16 Apr 2015 | 02:20:41 16 Apr 2015 | 55 seconds |
| Preliminary analysis of coverage distribution | 02:20:41 16 Apr 2015 | 02:23:25 16 Apr 2015 | 2 minutes 44 seconds |
| Identifying junction candidates | 02:23:25 16 Apr 2015 | 02:23:26 16 Apr 2015 | 1 second |
| Re-alignment to junction candidates | 02:23:26 16 Apr 2015 | 02:23:51 16 Apr 2015 | 25 seconds |
| Resolving alignments with junction candidates | 02:23:51 16 Apr 2015 | 02:25:15 16 Apr 2015 | 1 minute 24 seconds |
| Creating BAM files | 02:25:15 16 Apr 2015 | 02:26:56 16 Apr 2015 | 1 minute 41 seconds |
| Tabulating error counts | 02:26:56 16 Apr 2015 | 02:29:31 16 Apr 2015 | 2 minutes 35 seconds |
| Re-calibrating base error rates | 02:29:31 16 Apr 2015 | 02:29:32 16 Apr 2015 | 1 second |
| Examining read alignment evidence | 02:29:32 16 Apr 2015 | 04:33:31 16 Apr 2015 | 2 hours 3 minutes 59 seconds |
| Polymorphism statistics | 04:33:31 16 Apr 2015 | 04:33:32 16 Apr 2015 | 1 second |
| Output | 04:33:32 16 Apr 2015 | 04:34:15 16 Apr 2015 | 43 seconds |
| Total | 2 hours 20 minutes 41 seconds | ||
