mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.31.0 revision 69e7c3c0fa11
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| read file | reads | bases | passed filters | average | longest | mapped | |
|---|---|---|---|---|---|---|---|
| errors | PAL037_S37_R2_001.good.fq | 1,984,227 | 250,437,349 | 100.0% | 126.2 bases | 128 bases | 98.0% |
| errors | PAL037_S37_R1_001.good.fq | 1,984,227 | 250,437,349 | 100.0% | 126.2 bases | 128 bases | 99.2% |
| total | 3,968,454 | 500,874,698 | 100.0% | 126.2 bases | 128 bases | 98.6% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | CP016816 | 543,379 | 918.2 | 8.6 | 100.0% | Synthetic bacterium JCVI-Syn3.0 strain 6d, complete genome. |
| total | 543,379 | 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 | 10230 |
| Coverage evenness (position-hash) score of junction candidates | ≥ 2 | ≥ 4 |
| 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 | 0.049 |
| reference sequence | pr(no read start) |
|---|---|
| CP016816 | 0.12220 |
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 | 16:17:33 14 Nov 2017 | 16:18:18 14 Nov 2017 | 45 seconds |
| Read alignment to reference genome | 16:18:18 14 Nov 2017 | 16:20:34 14 Nov 2017 | 2 minutes 16 seconds |
| Preprocessing alignments for candidate junction identification | 16:20:34 14 Nov 2017 | 16:22:00 14 Nov 2017 | 1 minute 26 seconds |
| Preliminary analysis of coverage distribution | 16:22:00 14 Nov 2017 | 16:24:08 14 Nov 2017 | 2 minutes 8 seconds |
| Identifying junction candidates | 16:24:08 14 Nov 2017 | 16:24:13 14 Nov 2017 | 5 seconds |
| Re-alignment to junction candidates | 16:24:13 14 Nov 2017 | 16:24:45 14 Nov 2017 | 32 seconds |
| Resolving alignments with junction candidates | 16:24:45 14 Nov 2017 | 16:27:25 14 Nov 2017 | 2 minutes 40 seconds |
| Creating BAM files | 16:27:25 14 Nov 2017 | 16:28:41 14 Nov 2017 | 1 minute 16 seconds |
| Tabulating error counts | 16:28:41 14 Nov 2017 | 16:30:54 14 Nov 2017 | 2 minutes 13 seconds |
| Re-calibrating base error rates | 16:30:54 14 Nov 2017 | 16:30:55 14 Nov 2017 | 1 second |
| Examining read alignment evidence | 16:30:55 14 Nov 2017 | 16:47:38 14 Nov 2017 | 16 minutes 43 seconds |
| Polymorphism statistics | 16:47:38 14 Nov 2017 | 16:47:39 14 Nov 2017 | 1 second |
| Output | 16:47:39 14 Nov 2017 | 16:48:02 14 Nov 2017 | 23 seconds |
| Total | 30 minutes 29 seconds | ||
