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-3-BOP27-ACNB-END-2_S53_L001_R1_001.good.fq | 249,449 | 35,447,453 | 100.0% | 142.1 bases | 149 bases | 98.3% |
| errors | Plate-3-BOP27-ACNB-END-2_S53_L001_R2_001.good.fq | 249,449 | 35,373,601 | 100.0% | 141.8 bases | 149 bases | 98.0% |
| errors | Plate-3-BOP27-ACNB-END-2_S53_L002_R1_001.good.fq | 234,518 | 33,346,293 | 100.0% | 142.2 bases | 149 bases | 98.4% |
| errors | Plate-3-BOP27-ACNB-END-2_S53_L002_R2_001.good.fq | 234,518 | 33,286,315 | 100.0% | 141.9 bases | 149 bases | 97.7% |
| errors | Plate-3-BOP27-ACNB-END-2_S53_L003_R1_001.good.fq | 242,863 | 34,494,467 | 100.0% | 142.0 bases | 149 bases | 98.3% |
| errors | Plate-3-BOP27-ACNB-END-2_S53_L003_R2_001.good.fq | 242,863 | 34,422,195 | 100.0% | 141.7 bases | 149 bases | 97.9% |
| errors | Plate-3-BOP27-ACNB-END-2_S53_L004_R1_001.good.fq | 252,584 | 35,874,414 | 100.0% | 142.0 bases | 149 bases | 98.4% |
| errors | Plate-3-BOP27-ACNB-END-2_S53_L004_R2_001.good.fq | 252,584 | 35,810,183 | 100.0% | 141.8 bases | 149 bases | 97.7% |
| total | 1,958,828 | 278,054,921 | 100.0% | 141.9 bases | 149 bases | 98.1% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_000913 | 4,641,652 | 58.3 | 2.9 | 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 | 9897 |
| 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 | 947 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.062 |
| reference sequence | pr(no read start) |
|---|---|
| NC_000913 | 0.82930 |
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 | ≤ 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 | 17:43:21 12 Sep 2020 | 17:43:52 12 Sep 2020 | 31 seconds |
| Read alignment to reference genome | 17:43:52 12 Sep 2020 | 17:47:40 12 Sep 2020 | 3 minutes 48 seconds |
| Preprocessing alignments for candidate junction identification | 17:47:40 12 Sep 2020 | 17:48:10 12 Sep 2020 | 30 seconds |
| Preliminary analysis of coverage distribution | 17:48:10 12 Sep 2020 | 17:49:13 12 Sep 2020 | 1 minute 3 seconds |
| Identifying junction candidates | 17:49:13 12 Sep 2020 | 17:49:18 12 Sep 2020 | 5 seconds |
| Re-alignment to junction candidates | 17:49:18 12 Sep 2020 | 17:50:42 12 Sep 2020 | 1 minute 24 seconds |
| Resolving best read alignments | 17:50:42 12 Sep 2020 | 17:51:28 12 Sep 2020 | 46 seconds |
| Creating BAM files | 17:51:28 12 Sep 2020 | 17:52:33 12 Sep 2020 | 1 minute 5 seconds |
| Tabulating error counts | 17:52:33 12 Sep 2020 | 17:52:54 12 Sep 2020 | 21 seconds |
| Re-calibrating base error rates | 17:52:54 12 Sep 2020 | 17:52:57 12 Sep 2020 | 3 seconds |
| Examining read alignment evidence | 17:52:57 12 Sep 2020 | 18:06:42 12 Sep 2020 | 13 minutes 45 seconds |
| Polymorphism statistics | 18:06:42 12 Sep 2020 | 18:06:43 12 Sep 2020 | 1 second |
| Output | 18:06:43 12 Sep 2020 | 18:07:23 12 Sep 2020 | 40 seconds |
| Total | 24 minutes 2 seconds | ||
