mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.32.1 revision aa8f2595a244
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| read file | reads | bases | passed filters | average | longest | mapped | |
|---|---|---|---|---|---|---|---|
| errors | T1000_847_TGTTAACT-AGCCAACT.R2.good.fq | 1,616,083 | 168,933,082 | 100.0% | 104.5 bases | 139 bases | 90.9% |
| errors | T1000_847_TGTTAACT-AGCCAACT.R1.good.fq | 1,616,083 | 168,933,082 | 100.0% | 104.5 bases | 139 bases | 90.9% |
| total | 3,232,166 | 337,866,164 | 100.0% | 104.5 bases | 139 bases | 90.9% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_000913 | 4,641,652 | 64.2 | 4.1 | 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 | 4725 |
| 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 | 855 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.052 |
| reference sequence | pr(no read start) |
|---|---|
| NC_000913 | 0.78735 |
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 | 0.75 |
| Consensus minimum variant coverage each strand | OFF |
| Consensus minimum total coverage each strand | OFF |
| Consensus minimum variant coverage | OFF |
| Consensus minimum total coverage | OFF |
| Polymorphism E-value cutoff | 10 |
| Polymorphism frequency cutoff | 0.2 |
| Polymorphism minimum variant coverage each strand | OFF |
| Polymorphism minimum total coverage each strand | OFF |
| Polymorphism minimum variant coverage | OFF |
| Polymorphism minimum total coverage | 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 | 02:27:08 20 Jul 2018 | 02:27:42 20 Jul 2018 | 34 seconds |
| Read alignment to reference genome | 02:27:42 20 Jul 2018 | 02:29:26 20 Jul 2018 | 1 minute 44 seconds |
| Preprocessing alignments for candidate junction identification | 02:29:26 20 Jul 2018 | 02:30:07 20 Jul 2018 | 41 seconds |
| Preliminary analysis of coverage distribution | 02:30:07 20 Jul 2018 | 02:31:11 20 Jul 2018 | 1 minute 4 seconds |
| Identifying junction candidates | 02:31:11 20 Jul 2018 | 02:31:20 20 Jul 2018 | 9 seconds |
| Re-alignment to junction candidates | 02:31:20 20 Jul 2018 | 02:31:46 20 Jul 2018 | 26 seconds |
| Resolving best read alignments | 02:31:46 20 Jul 2018 | 02:32:53 20 Jul 2018 | 1 minute 7 seconds |
| Creating BAM files | 02:32:53 20 Jul 2018 | 02:33:50 20 Jul 2018 | 57 seconds |
| Tabulating error counts | 02:33:50 20 Jul 2018 | 02:34:15 20 Jul 2018 | 25 seconds |
| Re-calibrating base error rates | 02:34:15 20 Jul 2018 | 02:34:16 20 Jul 2018 | 1 second |
| Examining read alignment evidence | 02:34:16 20 Jul 2018 | 02:39:03 20 Jul 2018 | 4 minutes 47 seconds |
| Polymorphism statistics | 02:39:03 20 Jul 2018 | 02:39:03 20 Jul 2018 | 0 seconds |
| Output | 02:39:03 20 Jul 2018 | 02:40:04 20 Jul 2018 | 1 minute 1 second |
| Total | 12 minutes 56 seconds | ||
