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_92_S269_L002_R1_001.good.fq | 936,428 | 127,052,464 | 100.0% | 135.7 bases | 150 bases | 94.2% |
| errors | Pputida_HGL_92_S269_L002_R2_001.good.fq | 936,428 | 127,052,464 | 100.0% | 135.7 bases | 150 bases | 91.9% |
| total | 1,872,856 | 254,104,928 | 100.0% | 135.7 bases | 150 bases | 93.1% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_002947 | 6,181,929 | 38.1 | 2.1 | 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 | 33224 |
| 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 | 471 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.024 |
| reference sequence | pr(no read start) |
|---|---|
| NC_002947 | 0.87696 |
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 | 02:44:39 22 Aug 2019 | 02:45:08 22 Aug 2019 | 29 seconds |
| Read alignment to reference genome | 02:45:08 22 Aug 2019 | 02:49:25 22 Aug 2019 | 4 minutes 17 seconds |
| Preprocessing alignments for candidate junction identification | 02:49:25 22 Aug 2019 | 02:49:47 22 Aug 2019 | 22 seconds |
| Preliminary analysis of coverage distribution | 02:49:47 22 Aug 2019 | 02:50:39 22 Aug 2019 | 52 seconds |
| Identifying junction candidates | 02:50:39 22 Aug 2019 | 02:53:46 22 Aug 2019 | 3 minutes 7 seconds |
| Re-alignment to junction candidates | 02:53:46 22 Aug 2019 | 02:54:42 22 Aug 2019 | 56 seconds |
| Resolving best read alignments | 02:54:42 22 Aug 2019 | 02:55:24 22 Aug 2019 | 42 seconds |
| Creating BAM files | 02:55:24 22 Aug 2019 | 02:56:18 22 Aug 2019 | 54 seconds |
| Tabulating error counts | 02:56:18 22 Aug 2019 | 02:56:35 22 Aug 2019 | 17 seconds |
| Re-calibrating base error rates | 02:56:35 22 Aug 2019 | 02:56:37 22 Aug 2019 | 2 seconds |
| Examining read alignment evidence | 02:56:37 22 Aug 2019 | 03:00:21 22 Aug 2019 | 3 minutes 44 seconds |
| Polymorphism statistics | 03:00:21 22 Aug 2019 | 03:00:22 22 Aug 2019 | 1 second |
| Output | 03:00:22 22 Aug 2019 | 03:00:37 22 Aug 2019 | 15 seconds |
| Total | 15 minutes 58 seconds | ||
