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 | ALE-52_S52_L001_R1_001.good.fq | 330,388 | 47,002,471 | 100.0% | 142.3 bases | 148 bases | 96.9% |
| errors | ALE-52_S52_L001_R2_001.good.fq | 330,388 | 47,009,378 | 100.0% | 142.3 bases | 148 bases | 96.1% |
| errors | ALE-52_S52_L002_R1_001.good.fq | 320,528 | 45,541,836 | 100.0% | 142.1 bases | 148 bases | 98.3% |
| errors | ALE-52_S52_L002_R2_001.good.fq | 320,528 | 45,559,893 | 100.0% | 142.1 bases | 148 bases | 96.7% |
| errors | ALE-52_S52_L003_R1_001.good.fq | 334,409 | 47,478,274 | 100.0% | 142.0 bases | 147 bases | 96.5% |
| errors | ALE-52_S52_L003_R2_001.good.fq | 334,409 | 47,211,560 | 100.0% | 141.2 bases | 147 bases | 97.2% |
| errors | ALE-52_S52_L004_R1_001.good.fq | 306,987 | 43,582,847 | 100.0% | 142.0 bases | 148 bases | 98.2% |
| errors | ALE-52_S52_L004_R2_001.good.fq | 306,987 | 43,604,602 | 100.0% | 142.0 bases | 148 bases | 96.4% |
| total | 2,584,624 | 366,990,861 | 100.0% | 142.0 bases | 148 bases | 97.0% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_002947 | 6,181,873 | 61.6 | 5.0 | 100.0% | Pseudomonas putida KT2440 chromosome, complete genome. |
| total | 6,181,873 | 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 | 27181 |
| 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 | 47 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.002 |
| reference sequence | pr(no read start) |
|---|---|
| NC_002947 | 0.82912 |
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 | 01:47:44 18 Feb 2020 | 01:48:22 18 Feb 2020 | 38 seconds |
| Read alignment to reference genome | 01:48:23 18 Feb 2020 | 01:53:45 18 Feb 2020 | 5 minutes 22 seconds |
| Preprocessing alignments for candidate junction identification | 01:53:45 18 Feb 2020 | 01:54:20 18 Feb 2020 | 35 seconds |
| Preliminary analysis of coverage distribution | 01:54:20 18 Feb 2020 | 01:55:50 18 Feb 2020 | 1 minute 30 seconds |
| Identifying junction candidates | 01:55:50 18 Feb 2020 | 01:56:30 18 Feb 2020 | 40 seconds |
| Re-alignment to junction candidates | 01:56:30 18 Feb 2020 | 01:58:04 18 Feb 2020 | 1 minute 34 seconds |
| Resolving best read alignments | 01:58:04 18 Feb 2020 | 01:58:59 18 Feb 2020 | 55 seconds |
| Creating BAM files | 01:58:59 18 Feb 2020 | 02:00:22 18 Feb 2020 | 1 minute 23 seconds |
| Tabulating error counts | 02:00:22 18 Feb 2020 | 02:00:50 18 Feb 2020 | 28 seconds |
| Re-calibrating base error rates | 02:00:50 18 Feb 2020 | 02:00:53 18 Feb 2020 | 3 seconds |
| Examining read alignment evidence | 02:00:53 18 Feb 2020 | 02:06:16 18 Feb 2020 | 5 minutes 23 seconds |
| Polymorphism statistics | 02:06:16 18 Feb 2020 | 02:06:17 18 Feb 2020 | 1 second |
| Output | 02:06:17 18 Feb 2020 | 02:06:35 18 Feb 2020 | 18 seconds |
| Total | 18 minutes 50 seconds | ||
