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_PALE__HGL_Pputida_152_S140_L001_R1_001.good.fq | 8,820,600 | 1,313,741,367 | 100.0% | 148.9 bases | 150 bases | 96.0% |
| errors | Pputida_PALE__HGL_Pputida_152_S140_L001_R2_001.good.fq | 8,820,600 | 1,313,741,367 | 100.0% | 148.9 bases | 150 bases | 95.4% |
| total | 17,641,200 | 2,627,482,734 | 100.0% | 148.9 bases | 150 bases | 95.7% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_002947 | 6,186,878 | 367.9 | 4.9 | 100.0% | Pseudomonas putida KT2440 chromosome, complete genome. |
| total | 6,186,878 | 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 | 876 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.044 |
| reference sequence | pr(no read start) |
|---|---|
| NC_002947 | 0.44198 |
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 | ≤ 0 |
| Number of bases that at least one read must overlap each uniquely aligned side of a predicted junction | ≥ 6 |
| option | value |
|---|---|
| Mode | Full Polymorphism |
| 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 | 2 |
| Polymorphism frequency cutoff | 0.05 |
| Polymorphism minimum variant coverage each strand | 2 |
| 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 | ≥3 bases |
| Skip base substitutions when they create a homopolymer flanked on each side by | ≥5 bases |
| program | version |
|---|---|
| bowtie2 | 2.3.4.1 |
| R | 3.4.4 |
| step | start | end | elapsed |
|---|---|---|---|
| Read and reference sequence file input | 08:28:41 02 Apr 2020 | 08:33:12 02 Apr 2020 | 4 minutes 31 seconds |
| Read alignment to reference genome | 08:33:12 02 Apr 2020 | 09:10:42 02 Apr 2020 | 37 minutes 30 seconds |
| Preprocessing alignments for candidate junction identification | 09:10:42 02 Apr 2020 | 09:14:53 02 Apr 2020 | 4 minutes 11 seconds |
| Preliminary analysis of coverage distribution | 09:14:53 02 Apr 2020 | 09:22:35 02 Apr 2020 | 7 minutes 42 seconds |
| Identifying junction candidates | 09:22:35 02 Apr 2020 | 09:28:45 02 Apr 2020 | 6 minutes 10 seconds |
| Re-alignment to junction candidates | 09:28:45 02 Apr 2020 | 09:38:35 02 Apr 2020 | 9 minutes 50 seconds |
| Resolving best read alignments | 09:38:35 02 Apr 2020 | 09:46:49 02 Apr 2020 | 8 minutes 14 seconds |
| Creating BAM files | 09:46:49 02 Apr 2020 | 09:53:30 02 Apr 2020 | 6 minutes 41 seconds |
| Tabulating error counts | 09:53:30 02 Apr 2020 | 09:57:50 02 Apr 2020 | 4 minutes 20 seconds |
| Re-calibrating base error rates | 09:57:50 02 Apr 2020 | 09:57:51 02 Apr 2020 | 1 second |
| Examining read alignment evidence | 09:57:51 02 Apr 2020 | 12:44:28 02 Apr 2020 | 2 hours 46 minutes 37 seconds |
| Polymorphism statistics | 12:44:28 02 Apr 2020 | 12:45:03 02 Apr 2020 | 35 seconds |
| Output | 12:45:03 02 Apr 2020 | 12:50:40 02 Apr 2020 | 5 minutes 37 seconds |
| Total | 4 hours 21 minutes 59 seconds | ||
