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 | 66_S66_L001_R1_001.good.fq | 456,240 | 66,642,113 | 100.0% | 146.1 bases | 149 bases | 99.2% |
| errors | 66_S66_L001_R2_001.good.fq | 456,240 | 66,632,627 | 100.0% | 146.0 bases | 149 bases | 98.3% |
| errors | 66_S66_L002_R1_001.good.fq | 438,803 | 64,108,245 | 100.0% | 146.1 bases | 149 bases | 99.1% |
| errors | 66_S66_L002_R2_001.good.fq | 438,803 | 64,105,149 | 100.0% | 146.1 bases | 149 bases | 97.8% |
| errors | 66_S66_L003_R1_001.good.fq | 459,389 | 67,121,616 | 100.0% | 146.1 bases | 149 bases | 99.2% |
| errors | 66_S66_L003_R2_001.good.fq | 459,389 | 67,109,679 | 100.0% | 146.1 bases | 149 bases | 98.4% |
| errors | 66_S66_L004_R1_001.good.fq | 470,420 | 68,685,426 | 100.0% | 146.0 bases | 149 bases | 99.3% |
| errors | 66_S66_L004_R2_001.good.fq | 470,420 | 68,668,437 | 100.0% | 146.0 bases | 149 bases | 98.7% |
| total | 3,649,704 | 533,073,292 | 100.0% | 146.1 bases | 149 bases | 98.8% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_002947_CJ-RC | 6,184,688 | 85.6 | 2.1 | 100.0% | Pseudomonas putida KT2440 chromosome, complete genome. |
| total | 6,184,688 | 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 | 8834 |
| Coverage evenness (position-hash) score of junction candidates | ≥ 2 | ≥ 2 |
| Test this many junction candidates (n). May be smaller if not enough passed the coverage evenness threshold | 100 ≤ n ≤ 5000 | 550 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.027 |
| reference sequence | pr(no read start) |
|---|---|
| NC_002947_CJ-RC | 0.77465 |
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 | ≤ 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 | 2.2.6 |
| R | 3.4.4 |
| step | start | end | elapsed |
|---|---|---|---|
| Read and reference sequence file input | 14:44:53 25 Oct 2024 | 14:45:58 25 Oct 2024 | 1 minute 5 seconds |
| Read alignment to reference genome | 14:45:58 25 Oct 2024 | 14:53:25 25 Oct 2024 | 7 minutes 27 seconds |
| Preprocessing alignments for candidate junction identification | 14:53:25 25 Oct 2024 | 14:54:12 25 Oct 2024 | 47 seconds |
| Preliminary analysis of coverage distribution | 14:54:12 25 Oct 2024 | 14:56:13 25 Oct 2024 | 2 minutes 1 second |
| Identifying junction candidates | 14:56:13 25 Oct 2024 | 14:56:16 25 Oct 2024 | 3 seconds |
| Re-alignment to junction candidates | 14:56:16 25 Oct 2024 | 14:58:21 25 Oct 2024 | 2 minutes 5 seconds |
| Resolving best read alignments | 14:58:21 25 Oct 2024 | 14:59:29 25 Oct 2024 | 1 minute 8 seconds |
| Creating BAM files | 14:59:29 25 Oct 2024 | 15:01:27 25 Oct 2024 | 1 minute 58 seconds |
| Tabulating error counts | 15:01:27 25 Oct 2024 | 15:02:14 25 Oct 2024 | 47 seconds |
| Re-calibrating base error rates | 15:02:14 25 Oct 2024 | 15:02:17 25 Oct 2024 | 3 seconds |
| Examining read alignment evidence | 15:02:17 25 Oct 2024 | 15:27:33 25 Oct 2024 | 25 minutes 16 seconds |
| Polymorphism statistics | 15:27:33 25 Oct 2024 | 15:27:34 25 Oct 2024 | 1 second |
| Output | 15:27:34 25 Oct 2024 | 15:28:02 25 Oct 2024 | 28 seconds |
| Total | 43 minutes 9 seconds | ||
