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 | 3_S3_L001_R1_001.good.fq | 420,103 | 61,498,833 | 100.0% | 146.4 bases | 149 bases | 99.0% |
| errors | 3_S3_L001_R2_001.good.fq | 420,103 | 61,490,604 | 100.0% | 146.4 bases | 149 bases | 98.1% |
| errors | 3_S3_L002_R1_001.good.fq | 412,794 | 60,417,149 | 100.0% | 146.4 bases | 149 bases | 99.0% |
| errors | 3_S3_L002_R2_001.good.fq | 412,794 | 60,411,574 | 100.0% | 146.3 bases | 149 bases | 97.6% |
| errors | 3_S3_L003_R1_001.good.fq | 423,868 | 62,036,889 | 100.0% | 146.4 bases | 149 bases | 99.1% |
| errors | 3_S3_L003_R2_001.good.fq | 423,868 | 62,025,539 | 100.0% | 146.3 bases | 149 bases | 98.3% |
| errors | 3_S3_L004_R1_001.good.fq | 438,802 | 64,186,930 | 100.0% | 146.3 bases | 149 bases | 99.2% |
| errors | 3_S3_L004_R2_001.good.fq | 438,802 | 64,172,412 | 100.0% | 146.2 bases | 149 bases | 98.5% |
| total | 3,391,134 | 496,239,930 | 100.0% | 146.3 bases | 149 bases | 98.6% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_002947_CJ-RC | 6,184,688 | 79.3 | 2.7 | 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 | 11822 |
| 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 | 612 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.030 |
| reference sequence | pr(no read start) |
|---|---|
| NC_002947_CJ-RC | 0.79033 |
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 | 12:34:39 26 Oct 2024 | 12:35:38 26 Oct 2024 | 59 seconds |
| Read alignment to reference genome | 12:35:39 26 Oct 2024 | 12:42:47 26 Oct 2024 | 7 minutes 8 seconds |
| Preprocessing alignments for candidate junction identification | 12:42:47 26 Oct 2024 | 12:43:32 26 Oct 2024 | 45 seconds |
| Preliminary analysis of coverage distribution | 12:43:32 26 Oct 2024 | 12:45:25 26 Oct 2024 | 1 minute 53 seconds |
| Identifying junction candidates | 12:45:25 26 Oct 2024 | 12:45:27 26 Oct 2024 | 2 seconds |
| Re-alignment to junction candidates | 12:45:27 26 Oct 2024 | 12:47:28 26 Oct 2024 | 2 minutes 1 second |
| Resolving best read alignments | 12:47:28 26 Oct 2024 | 12:48:30 26 Oct 2024 | 1 minute 2 seconds |
| Creating BAM files | 12:48:30 26 Oct 2024 | 12:50:21 26 Oct 2024 | 1 minute 51 seconds |
| Tabulating error counts | 12:50:21 26 Oct 2024 | 12:51:04 26 Oct 2024 | 43 seconds |
| Re-calibrating base error rates | 12:51:04 26 Oct 2024 | 12:51:07 26 Oct 2024 | 3 seconds |
| Examining read alignment evidence | 12:51:07 26 Oct 2024 | 13:00:14 26 Oct 2024 | 9 minutes 7 seconds |
| Polymorphism statistics | 13:00:14 26 Oct 2024 | 13:00:14 26 Oct 2024 | 0 seconds |
| Output | 13:00:14 26 Oct 2024 | 13:00:29 26 Oct 2024 | 15 seconds |
| Total | 25 minutes 49 seconds | ||
