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 | PAL040_S40_R1_001.good.fq | 4,039,123 | 510,706,529 | 100.0% | 126.4 bases | 128 bases | 99.5% |
| errors | PAL040_S40_R2_001.good.fq | 4,039,123 | 510,706,529 | 100.0% | 126.4 bases | 128 bases | 98.6% |
| total | 8,078,246 | 1,021,413,058 | 100.0% | 126.4 bases | 128 bases | 99.0% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | CP016816 | 543,379 | 1877.2 | 29.9 | 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 | 12733 |
| 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 | 153 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.075 |
| reference sequence | pr(no read start) |
|---|---|
| CP016816 | 0.04050 |
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 | 20:02:24 14 Nov 2017 | 20:04:03 14 Nov 2017 | 1 minute 39 seconds |
| Read alignment to reference genome | 20:04:03 14 Nov 2017 | 20:08:40 14 Nov 2017 | 4 minutes 37 seconds |
| Preprocessing alignments for candidate junction identification | 20:08:40 14 Nov 2017 | 20:11:34 14 Nov 2017 | 2 minutes 54 seconds |
| Preliminary analysis of coverage distribution | 20:11:34 14 Nov 2017 | 20:16:03 14 Nov 2017 | 4 minutes 29 seconds |
| Identifying junction candidates | 20:16:03 14 Nov 2017 | 20:16:12 14 Nov 2017 | 9 seconds |
| Re-alignment to junction candidates | 20:16:12 14 Nov 2017 | 20:17:27 14 Nov 2017 | 1 minute 15 seconds |
| Resolving alignments with junction candidates | 20:17:27 14 Nov 2017 | 20:22:51 14 Nov 2017 | 5 minutes 24 seconds |
| Creating BAM files | 20:22:51 14 Nov 2017 | 20:25:27 14 Nov 2017 | 2 minutes 36 seconds |
| Tabulating error counts | 20:25:27 14 Nov 2017 | 20:29:58 14 Nov 2017 | 4 minutes 31 seconds |
| Re-calibrating base error rates | 20:29:58 14 Nov 2017 | 20:30:00 14 Nov 2017 | 2 seconds |
| Examining read alignment evidence | 20:30:00 14 Nov 2017 | 21:03:02 14 Nov 2017 | 33 minutes 2 seconds |
| Polymorphism statistics | 21:03:02 14 Nov 2017 | 21:03:06 14 Nov 2017 | 4 seconds |
| Output | 21:03:06 14 Nov 2017 | 21:04:02 14 Nov 2017 | 56 seconds |
| Total | 1 hour 1 minute 38 seconds | ||
