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 | 1Xyl_S2_L001_R2_001 | 1,583,932 | 446,191,413 | 100.0% | 281.7 bases | 301 bases | 76.6% |
| errors | 1Xyl_S2_L001_R1_001 | 1,583,993 | 441,719,997 | 100.0% | 278.9 bases | 301 bases | 93.0% |
| total | 3,167,925 | 887,911,410 | 100.0% | 280.3 bases | 301 bases | 84.8% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_000913 | 4,641,652 | 158.7 | 4.4 | 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 | 2686 |
| 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 | 219 |
| Total length of all junction candidates (factor times the reference genome length) | ≥ 0.1 | 0.029 |
| reference sequence | pr(no read start) |
|---|---|
| NC_000913 | 0.85551 |
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 | 05:36:23 16 Apr 2015 | 05:37:35 16 Apr 2015 | 1 minute 12 seconds |
| Read alignment to reference genome | 05:37:35 16 Apr 2015 | 05:46:58 16 Apr 2015 | 9 minutes 23 seconds |
| Preprocessing alignments for candidate junction identification | 05:46:58 16 Apr 2015 | 05:48:30 16 Apr 2015 | 1 minute 32 seconds |
| Preliminary analysis of coverage distribution | 05:48:30 16 Apr 2015 | 05:52:57 16 Apr 2015 | 4 minutes 27 seconds |
| Identifying junction candidates | 05:52:57 16 Apr 2015 | 05:52:59 16 Apr 2015 | 2 seconds |
| Re-alignment to junction candidates | 05:52:59 16 Apr 2015 | 05:53:46 16 Apr 2015 | 47 seconds |
| Resolving alignments with junction candidates | 05:53:46 16 Apr 2015 | 05:56:07 16 Apr 2015 | 2 minutes 21 seconds |
| Creating BAM files | 05:56:07 16 Apr 2015 | 05:58:50 16 Apr 2015 | 2 minutes 43 seconds |
| Tabulating error counts | 05:58:50 16 Apr 2015 | 06:02:56 16 Apr 2015 | 4 minutes 6 seconds |
| Re-calibrating base error rates | 06:02:56 16 Apr 2015 | 06:02:57 16 Apr 2015 | 1 second |
| Examining read alignment evidence | 06:02:57 16 Apr 2015 | 09:32:03 16 Apr 2015 | 3 hours 29 minutes 6 seconds |
| Polymorphism statistics | 09:32:03 16 Apr 2015 | 09:32:06 16 Apr 2015 | 3 seconds |
| Output | 09:32:06 16 Apr 2015 | 09:33:12 16 Apr 2015 | 1 minute 6 seconds |
| Total | 3 hours 56 minutes 49 seconds | ||
