mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.33.1 revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| read file | reads | bases | passed filters | average | longest | mapped | |
|---|---|---|---|---|---|---|---|
| errors | Pputida_HGL_28_S318_L002_R1_001.good.fq | 1,334,032 | 182,867,921 | 100.0% | 137.1 bases | 150 bases | 94.9% |
| errors | Pputida_HGL_28_S318_L002_R2_001.good.fq | 1,334,032 | 182,867,921 | 100.0% | 137.1 bases | 150 bases | 93.0% |
| total | 2,668,064 | 365,735,842 | 100.0% | 137.1 bases | 150 bases | 94.0% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_002947 | 6,181,929 | 55.4 | 2.9 | 100.0% | Pseudomonas putida KT2440 chromosome, complete genome. |
| total | 6,181,929 | 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 | 49461 |
| 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 | 534 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.027 |
| reference sequence | pr(no read start) |
|---|---|
| NC_002947 | 0.83011 |
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 | 2.3.4.1 |
| R | 3.4.4 |
| step | start | end | elapsed |
|---|---|---|---|
| Read and reference sequence file input | 00:19:34 21 Aug 2019 | 00:20:11 21 Aug 2019 | 37 seconds |
| Read alignment to reference genome | 00:20:12 21 Aug 2019 | 00:26:01 21 Aug 2019 | 5 minutes 49 seconds |
| Preprocessing alignments for candidate junction identification | 00:26:01 21 Aug 2019 | 00:26:47 21 Aug 2019 | 46 seconds |
| Preliminary analysis of coverage distribution | 00:26:47 21 Aug 2019 | 00:28:17 21 Aug 2019 | 1 minute 30 seconds |
| Identifying junction candidates | 00:28:17 21 Aug 2019 | 00:32:55 21 Aug 2019 | 4 minutes 38 seconds |
| Re-alignment to junction candidates | 00:32:55 21 Aug 2019 | 00:34:23 21 Aug 2019 | 1 minute 28 seconds |
| Resolving best read alignments | 00:34:23 21 Aug 2019 | 00:35:27 21 Aug 2019 | 1 minute 4 seconds |
| Creating BAM files | 00:35:27 21 Aug 2019 | 00:36:44 21 Aug 2019 | 1 minute 17 seconds |
| Tabulating error counts | 00:36:44 21 Aug 2019 | 00:37:10 21 Aug 2019 | 26 seconds |
| Re-calibrating base error rates | 00:37:10 21 Aug 2019 | 00:37:11 21 Aug 2019 | 1 second |
| Examining read alignment evidence | 00:37:11 21 Aug 2019 | 00:42:23 21 Aug 2019 | 5 minutes 12 seconds |
| Polymorphism statistics | 00:42:23 21 Aug 2019 | 00:42:24 21 Aug 2019 | 1 second |
| Output | 00:42:24 21 Aug 2019 | 00:42:42 21 Aug 2019 | 18 seconds |
| Total | 23 minutes 7 seconds | ||
