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-pntB-ndh-3_S3_L001_R1_001 | 589,995 | 123,898,729 | 100.0% | 210.0 bases | 210 bases | 91.4% |
| errors | HRD-KHP-atpIC-pntB-ndh-3_S3_L001_R2_001 | 589,954 | 123,890,340 | 100.0% | 210.0 bases | 210 bases | 90.4% |
| total | 1,179,949 | 247,789,069 | 100.0% | 210.0 bases | 210 bases | 90.9% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_000913 | 4,641,652 | 48.6 | 1.4 | 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 | 3145 |
| 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 | 136 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.013 |
| reference sequence | pr(no read start) |
|---|---|
| NC_000913 | 0.90053 |
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 | 18:53:12 11 Nov 2015 | 18:53:33 11 Nov 2015 | 21 seconds |
| Read alignment to reference genome | 18:53:33 11 Nov 2015 | 18:54:45 11 Nov 2015 | 1 minute 12 seconds |
| Preprocessing alignments for candidate junction identification | 18:54:45 11 Nov 2015 | 18:55:12 11 Nov 2015 | 27 seconds |
| Preliminary analysis of coverage distribution | 18:55:12 11 Nov 2015 | 18:56:16 11 Nov 2015 | 1 minute 4 seconds |
| Identifying junction candidates | 18:56:16 11 Nov 2015 | 18:56:17 11 Nov 2015 | 1 second |
| Re-alignment to junction candidates | 18:56:17 11 Nov 2015 | 18:56:29 11 Nov 2015 | 12 seconds |
| Resolving alignments with junction candidates | 18:56:29 11 Nov 2015 | 18:57:16 11 Nov 2015 | 47 seconds |
| Creating BAM files | 18:57:16 11 Nov 2015 | 18:57:52 11 Nov 2015 | 36 seconds |
| Tabulating error counts | 18:57:52 11 Nov 2015 | 18:59:04 11 Nov 2015 | 1 minute 12 seconds |
| Re-calibrating base error rates | 18:59:04 11 Nov 2015 | 18:59:05 11 Nov 2015 | 1 second |
| Examining read alignment evidence | 18:59:05 11 Nov 2015 | 19:08:05 11 Nov 2015 | 9 minutes 0 seconds |
| Polymorphism statistics | 19:08:05 11 Nov 2015 | 19:08:05 11 Nov 2015 | 0 seconds |
| Output | 19:08:05 11 Nov 2015 | 19:08:33 11 Nov 2015 | 28 seconds |
| Total | 15 minutes 21 seconds | ||
