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 | Plate-1-BOP-1000-RPE-END-2_S30_L001_R1_001.good.fq | 628,860 | 82,378,390 | 100.0% | 131.0 bases | 149 bases | 96.2% |
| errors | Plate-1-BOP-1000-RPE-END-2_S30_L001_R2_001.good.fq | 628,860 | 81,737,917 | 100.0% | 130.0 bases | 149 bases | 97.8% |
| errors | Plate-1-BOP-1000-RPE-END-2_S30_L002_R1_001.good.fq | 574,792 | 75,320,658 | 100.0% | 131.0 bases | 149 bases | 96.3% |
| errors | Plate-1-BOP-1000-RPE-END-2_S30_L002_R2_001.good.fq | 574,792 | 74,781,050 | 100.0% | 130.1 bases | 149 bases | 97.6% |
| errors | Plate-1-BOP-1000-RPE-END-2_S30_L003_R1_001.good.fq | 616,069 | 80,663,943 | 100.0% | 130.9 bases | 149 bases | 96.0% |
| errors | Plate-1-BOP-1000-RPE-END-2_S30_L003_R2_001.good.fq | 616,069 | 80,063,343 | 100.0% | 130.0 bases | 149 bases | 97.5% |
| errors | Plate-1-BOP-1000-RPE-END-2_S30_L004_R1_001.good.fq | 630,655 | 82,587,705 | 100.0% | 131.0 bases | 149 bases | 96.4% |
| errors | Plate-1-BOP-1000-RPE-END-2_S30_L004_R2_001.good.fq | 630,655 | 82,019,660 | 100.0% | 130.1 bases | 149 bases | 97.6% |
| total | 4,900,752 | 639,552,666 | 100.0% | 130.5 bases | 149 bases | 96.9% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_000913 | 4,641,652 | 123.9 | 4.1 | 100.0% | Escherichia coli str. K-12 substr. MG1655, complete genome. |
| total | 4,641,652 | 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 | 55753 |
| 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 | 259 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.017 |
| reference sequence | pr(no read start) |
|---|---|
| NC_000913 | 0.65300 |
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 | 13:38:50 28 Feb 2020 | 13:39:59 28 Feb 2020 | 1 minute 9 seconds |
| Read alignment to reference genome | 13:40:00 28 Feb 2020 | 13:49:05 28 Feb 2020 | 9 minutes 5 seconds |
| Preprocessing alignments for candidate junction identification | 13:49:05 28 Feb 2020 | 13:50:12 28 Feb 2020 | 1 minute 7 seconds |
| Preliminary analysis of coverage distribution | 13:50:12 28 Feb 2020 | 13:52:45 28 Feb 2020 | 2 minutes 33 seconds |
| Identifying junction candidates | 13:52:45 28 Feb 2020 | 13:55:43 28 Feb 2020 | 2 minutes 58 seconds |
| Re-alignment to junction candidates | 13:55:43 28 Feb 2020 | 13:58:47 28 Feb 2020 | 3 minutes 4 seconds |
| Resolving best read alignments | 13:58:47 28 Feb 2020 | 14:00:29 28 Feb 2020 | 1 minute 42 seconds |
| Creating BAM files | 14:00:29 28 Feb 2020 | 14:02:50 28 Feb 2020 | 2 minutes 21 seconds |
| Tabulating error counts | 14:02:50 28 Feb 2020 | 14:03:39 28 Feb 2020 | 49 seconds |
| Re-calibrating base error rates | 14:03:39 28 Feb 2020 | 14:03:42 28 Feb 2020 | 3 seconds |
| Examining read alignment evidence | 14:03:42 28 Feb 2020 | 14:12:36 28 Feb 2020 | 8 minutes 54 seconds |
| Polymorphism statistics | 14:12:36 28 Feb 2020 | 14:12:37 28 Feb 2020 | 1 second |
| Output | 14:12:37 28 Feb 2020 | 14:13:04 28 Feb 2020 | 27 seconds |
| Total | 34 minutes 13 seconds | ||
