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_TALE__HGL_Pputida_112_S100_L001_R1_001.good.fq | 7,302,772 | 1,086,340,992 | 100.0% | 148.8 bases | 150 bases | 95.6% |
| errors | Pputida_TALE__HGL_Pputida_112_S100_L001_R2_001.good.fq | 7,302,772 | 1,086,340,992 | 100.0% | 148.8 bases | 150 bases | 95.0% |
| total | 14,605,544 | 2,172,681,984 | 100.0% | 148.8 bases | 150 bases | 95.3% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_002947 | 6,181,929 | 334.4 | 5.6 | 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 | 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 | 947 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.048 |
| reference sequence | pr(no read start) |
|---|---|
| NC_002947 | 0.49889 |
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 | 15:50:54 06 Apr 2020 | 15:54:46 06 Apr 2020 | 3 minutes 52 seconds |
| Read alignment to reference genome | 15:54:46 06 Apr 2020 | 16:28:00 06 Apr 2020 | 33 minutes 14 seconds |
| Preprocessing alignments for candidate junction identification | 16:28:00 06 Apr 2020 | 16:31:32 06 Apr 2020 | 3 minutes 32 seconds |
| Preliminary analysis of coverage distribution | 16:31:32 06 Apr 2020 | 16:38:08 06 Apr 2020 | 6 minutes 36 seconds |
| Identifying junction candidates | 16:38:08 06 Apr 2020 | 16:43:59 06 Apr 2020 | 5 minutes 51 seconds |
| Re-alignment to junction candidates | 16:43:59 06 Apr 2020 | 16:52:48 06 Apr 2020 | 8 minutes 49 seconds |
| Resolving best read alignments | 16:52:48 06 Apr 2020 | 17:00:00 06 Apr 2020 | 7 minutes 12 seconds |
| Creating BAM files | 17:00:00 06 Apr 2020 | 17:06:28 06 Apr 2020 | 6 minutes 28 seconds |
| Tabulating error counts | 17:06:28 06 Apr 2020 | 17:09:55 06 Apr 2020 | 3 minutes 27 seconds |
| Re-calibrating base error rates | 17:09:55 06 Apr 2020 | 17:09:57 06 Apr 2020 | 2 seconds |
| Examining read alignment evidence | 17:09:57 06 Apr 2020 | 17:42:32 06 Apr 2020 | 32 minutes 35 seconds |
| Polymorphism statistics | 17:42:32 06 Apr 2020 | 17:42:47 06 Apr 2020 | 15 seconds |
| Output | 17:42:47 06 Apr 2020 | 17:43:58 06 Apr 2020 | 1 minute 11 seconds |
| Total | 1 hour 53 minutes 4 seconds | ||
