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-2-BOP-27-ACNB-ALE-1-flask-16_S26_L001_R1_001.good.fq | 178,681 | 22,232,276 | 100.0% | 124.4 bases | 149 bases | 94.6% |
| errors | Plate-2-BOP-27-ACNB-ALE-1-flask-16_S26_L001_R2_001.good.fq | 178,681 | 21,946,569 | 100.0% | 122.8 bases | 149 bases | 97.5% |
| errors | Plate-2-BOP-27-ACNB-ALE-1-flask-16_S26_L002_R1_001.good.fq | 141,163 | 17,473,640 | 100.0% | 123.8 bases | 149 bases | 94.3% |
| errors | Plate-2-BOP-27-ACNB-ALE-1-flask-16_S26_L002_R2_001.good.fq | 141,163 | 17,245,349 | 100.0% | 122.2 bases | 149 bases | 97.0% |
| errors | Plate-2-BOP-27-ACNB-ALE-1-flask-16_S26_L003_R1_001.good.fq | 162,463 | 20,159,347 | 100.0% | 124.1 bases | 149 bases | 94.4% |
| errors | Plate-2-BOP-27-ACNB-ALE-1-flask-16_S26_L003_R2_001.good.fq | 162,463 | 19,882,899 | 100.0% | 122.4 bases | 149 bases | 97.5% |
| errors | Plate-2-BOP-27-ACNB-ALE-1-flask-16_S26_L004_R1_001.good.fq | 140,007 | 17,301,548 | 100.0% | 123.6 bases | 149 bases | 94.2% |
| errors | Plate-2-BOP-27-ACNB-ALE-1-flask-16_S26_L004_R2_001.good.fq | 140,007 | 17,068,743 | 100.0% | 121.9 bases | 149 bases | 97.0% |
| total | 1,244,628 | 153,310,371 | 100.0% | 123.2 bases | 149 bases | 95.8% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_000913 | 4,641,652 | 31.6 | 2.4 | 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 | 18427 |
| 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 | 99 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.006 |
| reference sequence | pr(no read start) |
|---|---|
| NC_000913 | 0.88523 |
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 | 07:37:42 27 Feb 2020 | 07:38:00 27 Feb 2020 | 18 seconds |
| Read alignment to reference genome | 07:38:01 27 Feb 2020 | 07:40:18 27 Feb 2020 | 2 minutes 17 seconds |
| Preprocessing alignments for candidate junction identification | 07:40:18 27 Feb 2020 | 07:40:34 27 Feb 2020 | 16 seconds |
| Preliminary analysis of coverage distribution | 07:40:34 27 Feb 2020 | 07:41:07 27 Feb 2020 | 33 seconds |
| Identifying junction candidates | 07:41:07 27 Feb 2020 | 07:41:36 27 Feb 2020 | 29 seconds |
| Re-alignment to junction candidates | 07:41:36 27 Feb 2020 | 07:42:19 27 Feb 2020 | 43 seconds |
| Resolving best read alignments | 07:42:19 27 Feb 2020 | 07:42:45 27 Feb 2020 | 26 seconds |
| Creating BAM files | 07:42:45 27 Feb 2020 | 07:43:14 27 Feb 2020 | 29 seconds |
| Tabulating error counts | 07:43:14 27 Feb 2020 | 07:43:25 27 Feb 2020 | 11 seconds |
| Re-calibrating base error rates | 07:43:25 27 Feb 2020 | 07:43:28 27 Feb 2020 | 3 seconds |
| Examining read alignment evidence | 07:43:28 27 Feb 2020 | 07:45:46 27 Feb 2020 | 2 minutes 18 seconds |
| Polymorphism statistics | 07:45:46 27 Feb 2020 | 07:45:47 27 Feb 2020 | 1 second |
| Output | 07:45:47 27 Feb 2020 | 07:45:59 27 Feb 2020 | 12 seconds |
| Total | 8 minutes 16 seconds | ||
