mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.35.4 revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| read file | reads | bases | passed filters | average | longest | mapped | |
|---|---|---|---|---|---|---|---|
| errors | X_end_X_A5_F53_I1_S128_L004_R1_001.good.fq | 3,837,144 | 373,186,916 | 100.0% | 97.3 bases | 101 bases | 98.1% |
| errors | X_end_X_A5_F53_I1_S128_L004_R2_001.good.fq | 3,837,144 | 373,186,916 | 100.0% | 97.3 bases | 101 bases | 97.7% |
| total | 7,674,288 | 746,373,832 | 100.0% | 97.3 bases | 101 bases | 97.9% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | JE3692-4 | 6,192,177 | 119.7 | 3.0 | 100.0% | Pseudomonas putida KT2440 complete genome. |
| total | 6,192,177 | 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 | 100001 |
| 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 | 434 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.014 |
| reference sequence | pr(no read start) |
|---|---|
| JE3692-4 | 0.60140 |
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 |
| Minimum probablilty assigned that no mapped read will start at a given position and strand for junction prediction | 0.1 |
| Junction allow suboptimal matches | FALSE |
| 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 | 2.2.6 |
| R | 3.4.4 |
| step | start | end | elapsed |
|---|---|---|---|
| Read and reference sequence file input | 20:17:52 01 Feb 2024 | 20:20:21 01 Feb 2024 | 2 minutes 29 seconds |
| Read alignment to reference genome | 20:20:21 01 Feb 2024 | 20:32:10 01 Feb 2024 | 11 minutes 49 seconds |
| Preprocessing alignments for candidate junction identification | 20:32:10 01 Feb 2024 | 20:33:37 01 Feb 2024 | 1 minute 27 seconds |
| Preliminary analysis of coverage distribution | 20:33:37 01 Feb 2024 | 20:35:50 01 Feb 2024 | 2 minutes 13 seconds |
| Identifying junction candidates | 20:35:50 01 Feb 2024 | 20:39:28 01 Feb 2024 | 3 minutes 38 seconds |
| Re-alignment to junction candidates | 20:39:28 01 Feb 2024 | 20:42:38 01 Feb 2024 | 3 minutes 10 seconds |
| Resolving best read alignments | 20:42:38 01 Feb 2024 | 20:44:44 01 Feb 2024 | 2 minutes 6 seconds |
| Creating BAM files | 20:44:44 01 Feb 2024 | 20:46:41 01 Feb 2024 | 1 minute 57 seconds |
| Tabulating error counts | 20:46:41 01 Feb 2024 | 20:47:52 01 Feb 2024 | 1 minute 11 seconds |
| Re-calibrating base error rates | 20:47:52 01 Feb 2024 | 20:47:53 01 Feb 2024 | 1 second |
| Examining read alignment evidence | 20:47:53 01 Feb 2024 | 21:00:54 01 Feb 2024 | 13 minutes 1 second |
| Polymorphism statistics | 21:00:54 01 Feb 2024 | 21:00:55 01 Feb 2024 | 1 second |
| Output | 21:00:55 01 Feb 2024 | 21:01:14 01 Feb 2024 | 19 seconds |
| Total | 43 minutes 22 seconds | ||
