mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.29.0 revision 8f9c342918e4
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| read file | reads | bases | passed filters | average | longest | mapped | |
|---|---|---|---|---|---|---|---|
| errors | qtrim-12PD5-1_S12_L001_R2_001 | 1,201,367 | 180,232,953 | 100.0% | 150.0 bases | 151 bases | 98.1% |
| errors | qtrim-12PD5-1_S12_L001_R1_001 | 1,201,398 | 180,333,804 | 100.0% | 150.1 bases | 151 bases | 98.7% |
| total | 2,402,765 | 360,566,757 | 100.0% | 150.1 bases | 151 bases | 98.4% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_000913 | 4,641,652 | 76.7 | 1.4 | 98.3% | 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 | 1858 |
| 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 | 16 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.001 |
| reference sequence | pr(no read start) |
|---|---|
| NC_000913 | 0.78519 |
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 |
| Consensus frequency cutoff | 0.8 |
| Consensus minimum coverage each strand | OFF |
| Polymorphism E-value cutoff | 10 |
| Polymorphism frequency cutoff | 0.2 |
| Polymorphism minimum coverage each strand | OFF |
| Polymorphism bias cutoff | OFF |
| 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 | 16:18:16 02 Jan 2017 | 16:19:00 02 Jan 2017 | 44 seconds |
| Read alignment to reference genome | 16:19:01 02 Jan 2017 | 16:25:51 02 Jan 2017 | 6 minutes 50 seconds |
| Preprocessing alignments for candidate junction identification | 16:25:51 02 Jan 2017 | 16:26:56 02 Jan 2017 | 1 minute 5 seconds |
| Preliminary analysis of coverage distribution | 16:26:56 02 Jan 2017 | 16:29:03 02 Jan 2017 | 2 minutes 7 seconds |
| Identifying junction candidates | 16:29:03 02 Jan 2017 | 16:29:03 02 Jan 2017 | 0 seconds |
| Re-alignment to junction candidates | 16:29:03 02 Jan 2017 | 16:30:11 02 Jan 2017 | 1 minute 8 seconds |
| Resolving alignments with junction candidates | 16:30:11 02 Jan 2017 | 16:32:01 02 Jan 2017 | 1 minute 50 seconds |
| Creating BAM files | 16:32:01 02 Jan 2017 | 16:33:28 02 Jan 2017 | 1 minute 27 seconds |
| Tabulating error counts | 16:33:28 02 Jan 2017 | 16:35:04 02 Jan 2017 | 1 minute 36 seconds |
| Re-calibrating base error rates | 16:35:04 02 Jan 2017 | 16:35:05 02 Jan 2017 | 1 second |
| Examining read alignment evidence | 16:35:05 02 Jan 2017 | 16:47:20 02 Jan 2017 | 12 minutes 15 seconds |
| Polymorphism statistics | 16:47:20 02 Jan 2017 | 16:47:21 02 Jan 2017 | 1 second |
| Output | 16:47:21 02 Jan 2017 | 16:48:01 02 Jan 2017 | 40 seconds |
| Total | 29 minutes 44 seconds | ||
