mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.26.1
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| read file | reads | bases | passed filters | average | longest | mapped | |
|---|---|---|---|---|---|---|---|
| errors | HRD-KHP-atpIC-ndh-3_S6_L001_R2_001 | 551,245 | 115,760,933 | 100.0% | 210.0 bases | 210 bases | 92.4% |
| errors | HRD-KHP-atpIC-ndh-3_S6_L001_R1_001 | 551,279 | 115,767,664 | 100.0% | 210.0 bases | 210 bases | 93.7% |
| total | 1,102,524 | 231,528,597 | 100.0% | 210.0 bases | 210 bases | 93.0% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_000913 | 4,641,652 | 46.4 | 1.3 | 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 | 3468 |
| 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 | 99 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.009 |
| reference sequence | pr(no read start) |
|---|---|
| NC_000913 | 0.90457 |
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 | ≤ 3 |
| Number of bases that at least one read must overlap each uniquely aligned side of a predicted junction | ≥ 1 |
| option | value |
|---|---|
| Mode | Consensus/Mixed Base |
| Ploidy | 1 (haploid) |
| Consensus mutation E-value cutoff | 10 |
| Polymorphism E-value cutoff | 10 |
| Polymorphism frequency cutoff | 0.1 |
| Polymorphism minimum coverage each strand | 2 |
| Polymorphism bias cutoff | 0.05 |
| Predict indel polymorphisms | YES |
| Skip indel polymorphisms in homopolymers runs of | OFF |
| Skip base substitutions when they create a homopolymer flanked on each side by | OFF |
| step | start | end | elapsed |
|---|---|---|---|
| Read and reference sequence file input | 18:24:51 11 Nov 2015 | 18:25:11 11 Nov 2015 | 20 seconds |
| Read alignment to reference genome | 18:25:11 11 Nov 2015 | 18:26:16 11 Nov 2015 | 1 minute 5 seconds |
| Preprocessing alignments for candidate junction identification | 18:26:16 11 Nov 2015 | 18:26:41 11 Nov 2015 | 25 seconds |
| Preliminary analysis of coverage distribution | 18:26:41 11 Nov 2015 | 18:27:43 11 Nov 2015 | 1 minute 2 seconds |
| Identifying junction candidates | 18:27:43 11 Nov 2015 | 18:27:43 11 Nov 2015 | 0 seconds |
| Re-alignment to junction candidates | 18:27:43 11 Nov 2015 | 18:27:55 11 Nov 2015 | 12 seconds |
| Resolving alignments with junction candidates | 18:27:55 11 Nov 2015 | 18:28:39 11 Nov 2015 | 44 seconds |
| Creating BAM files | 18:28:39 11 Nov 2015 | 18:29:13 11 Nov 2015 | 34 seconds |
| Tabulating error counts | 18:29:13 11 Nov 2015 | 18:30:22 11 Nov 2015 | 1 minute 9 seconds |
| Re-calibrating base error rates | 18:30:22 11 Nov 2015 | 18:30:23 11 Nov 2015 | 1 second |
| Examining read alignment evidence | 18:30:23 11 Nov 2015 | 18:39:02 11 Nov 2015 | 8 minutes 39 seconds |
| Polymorphism statistics | 18:39:02 11 Nov 2015 | 18:39:02 11 Nov 2015 | 0 seconds |
| Output | 18:39:02 11 Nov 2015 | 18:39:32 11 Nov 2015 | 30 seconds |
| Total | 14 minutes 41 seconds | ||
