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_40_S350_L002_R1_001.good.fq | 2,338,852 | 314,889,475 | 100.0% | 134.6 bases | 150 bases | 95.7% |
| errors | Pputida_HGL_40_S350_L002_R2_001.good.fq | 2,338,852 | 314,889,475 | 100.0% | 134.6 bases | 150 bases | 93.6% |
| total | 4,677,704 | 629,778,950 | 100.0% | 134.6 bases | 150 bases | 94.6% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_002947 | 6,181,929 | 96.3 | 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 | 50793 |
| 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 | 886 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.044 |
| reference sequence | pr(no read start) |
|---|---|
| NC_002947 | 0.72730 |
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 | 18:25:25 26 Mar 2020 | 18:26:38 26 Mar 2020 | 1 minute 13 seconds |
| Read alignment to reference genome | 18:26:38 26 Mar 2020 | 18:37:37 26 Mar 2020 | 10 minutes 59 seconds |
| Preprocessing alignments for candidate junction identification | 18:37:37 26 Mar 2020 | 18:38:42 26 Mar 2020 | 1 minute 5 seconds |
| Preliminary analysis of coverage distribution | 18:38:42 26 Mar 2020 | 18:41:16 26 Mar 2020 | 2 minutes 34 seconds |
| Identifying junction candidates | 18:41:16 26 Mar 2020 | 18:55:09 26 Mar 2020 | 13 minutes 53 seconds |
| Re-alignment to junction candidates | 18:55:09 26 Mar 2020 | 18:58:01 26 Mar 2020 | 2 minutes 52 seconds |
| Resolving best read alignments | 18:58:01 26 Mar 2020 | 18:59:56 26 Mar 2020 | 1 minute 55 seconds |
| Creating BAM files | 18:59:56 26 Mar 2020 | 19:02:18 26 Mar 2020 | 2 minutes 22 seconds |
| Tabulating error counts | 19:02:18 26 Mar 2020 | 19:03:09 26 Mar 2020 | 51 seconds |
| Re-calibrating base error rates | 19:03:09 26 Mar 2020 | 19:03:11 26 Mar 2020 | 2 seconds |
| Examining read alignment evidence | 19:03:11 26 Mar 2020 | 19:43:10 26 Mar 2020 | 39 minutes 59 seconds |
| Polymorphism statistics | 19:43:10 26 Mar 2020 | 19:43:12 26 Mar 2020 | 2 seconds |
| Output | 19:43:12 26 Mar 2020 | 19:45:48 26 Mar 2020 | 2 minutes 36 seconds |
| Total | 1 hour 20 minutes 23 seconds | ||
