mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.30.1 revision 4379201f728c
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| read file | reads | bases | passed filters | average | longest | mapped | |
|---|---|---|---|---|---|---|---|
| errors | DH1_S9_L001_R2_001 | 2,665,703 | 392,482,013 | 100.0% | 147.2 bases | 151 bases | 97.0% |
| errors | DH1_S9_L001_R1_001 | 2,665,722 | 392,509,856 | 100.0% | 147.2 bases | 151 bases | 97.7% |
| total | 5,331,425 | 784,991,869 | 100.0% | 147.2 bases | 151 bases | 97.3% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | DH1 | 4,630,707 | 164.8 | 2.5 | 100.0% | Escherichia coli DH1, complete genome. |
| total | 4,630,707 | 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 | 1404 |
| 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 | 124 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.008 |
| reference sequence | pr(no read start) |
|---|---|
| DH1 | 0.59432 |
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 |
| program | version |
|---|---|
| bowtie2 | 2.2.8 |
| R | 3.3.1 |
| step | start | end | elapsed |
|---|---|---|---|
| Read and reference sequence file input | 15:55:49 30 Jun 2017 | 15:57:07 30 Jun 2017 | 1 minute 18 seconds |
| Read alignment to reference genome | 15:57:08 30 Jun 2017 | 16:00:48 30 Jun 2017 | 3 minutes 40 seconds |
| Preprocessing alignments for candidate junction identification | 16:00:48 30 Jun 2017 | 16:03:07 30 Jun 2017 | 2 minutes 19 seconds |
| Preliminary analysis of coverage distribution | 16:03:07 30 Jun 2017 | 16:06:29 30 Jun 2017 | 3 minutes 22 seconds |
| Identifying junction candidates | 16:06:29 30 Jun 2017 | 16:06:31 30 Jun 2017 | 2 seconds |
| Re-alignment to junction candidates | 16:06:31 30 Jun 2017 | 16:07:18 30 Jun 2017 | 47 seconds |
| Resolving alignments with junction candidates | 16:07:18 30 Jun 2017 | 16:11:20 30 Jun 2017 | 4 minutes 2 seconds |
| Creating BAM files | 16:11:20 30 Jun 2017 | 16:13:22 30 Jun 2017 | 2 minutes 2 seconds |
| Tabulating error counts | 16:13:22 30 Jun 2017 | 16:16:44 30 Jun 2017 | 3 minutes 22 seconds |
| Re-calibrating base error rates | 16:16:44 30 Jun 2017 | 16:16:45 30 Jun 2017 | 1 second |
| Examining read alignment evidence | 16:16:45 30 Jun 2017 | 16:40:49 30 Jun 2017 | 24 minutes 4 seconds |
| Polymorphism statistics | 16:40:49 30 Jun 2017 | 16:40:51 30 Jun 2017 | 2 seconds |
| Output | 16:40:51 30 Jun 2017 | 16:41:17 30 Jun 2017 | 26 seconds |
| Total | 45 minutes 27 seconds | ||
