mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.35.4 revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| read file | reads | bases | passed filters | average | longest | mapped | |
|---|---|---|---|---|---|---|---|
| errors | PAL25_S25_L007_R1_001_val_1.good.fq | 5,266,303 | 523,921,557 | 100.0% | 99.5 bases | 100 bases | 96.6% |
| errors | PAL25_S25_L007_R2_001_val_2.good.fq | 5,252,503 | 518,558,760 | 100.0% | 98.7 bases | 100 bases | 96.3% |
| total | 10,518,806 | 1,042,480,317 | 100.0% | 99.1 bases | 100 bases | 96.4% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_000913_3_pae_pgi | 4,640,912 | 216.9 | 3.2 | 100.0% | Escherichia coli str. K-12 substr. MG1655, P. aerophilum pgi gene, complete genome. |
| total | 4,640,912 | 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 | 100000 |
| Coverage evenness (position-hash) score of junction candidates | ≥ 2 | ≥ 3 |
| Test this many junction candidates (n). May be smaller if not enough passed the coverage evenness threshold | 100 ≤ n ≤ 5000 | 2033 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.091 |
| reference sequence | pr(no read start) |
|---|---|
| NC_000913_3_pae_pgi | 0.46942 |
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 |
| Minimum probablilty assigned that no mapped read will start at a given position and strand for junction prediction | 0.1 |
| Junction allow suboptimal matches | FALSE |
| 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 | 2.2.6 |
| R | 3.4.4 |
| step | start | end | elapsed |
|---|---|---|---|
| Read and reference sequence file input | 18:17:48 19 Dec 2020 | 18:26:11 19 Dec 2020 | 8 minutes 23 seconds |
| Read alignment to reference genome | 18:26:12 19 Dec 2020 | 19:29:47 19 Dec 2020 | 1 hour 3 minutes 35 seconds |
| Preprocessing alignments for candidate junction identification | 19:29:47 19 Dec 2020 | 19:38:02 19 Dec 2020 | 8 minutes 15 seconds |
| Preliminary analysis of coverage distribution | 19:38:02 19 Dec 2020 | 19:52:47 19 Dec 2020 | 14 minutes 45 seconds |
| Identifying junction candidates | 19:52:47 19 Dec 2020 | 20:25:58 19 Dec 2020 | 33 minutes 11 seconds |
| Re-alignment to junction candidates | 20:25:58 19 Dec 2020 | 20:47:00 19 Dec 2020 | 21 minutes 2 seconds |
| Resolving best read alignments | 20:47:00 19 Dec 2020 | 20:56:49 19 Dec 2020 | 9 minutes 49 seconds |
| Creating BAM files | 20:56:49 19 Dec 2020 | 21:10:02 19 Dec 2020 | 13 minutes 13 seconds |
| Tabulating error counts | 21:10:02 19 Dec 2020 | 21:14:54 19 Dec 2020 | 4 minutes 52 seconds |
| Re-calibrating base error rates | 21:14:54 19 Dec 2020 | 21:14:57 19 Dec 2020 | 3 seconds |
| Examining read alignment evidence | 21:14:57 19 Dec 2020 | 22:13:17 19 Dec 2020 | 58 minutes 20 seconds |
| Polymorphism statistics | 22:13:17 19 Dec 2020 | 22:13:28 19 Dec 2020 | 11 seconds |
| Output | 22:13:28 19 Dec 2020 | 22:16:31 19 Dec 2020 | 3 minutes 3 seconds |
| Total | 3 hours 58 minutes 42 seconds | ||
