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-BOP-1000-ACNB-END-1_S50_L001_R1_001.good.fq | 376,096 | 53,384,568 | 100.0% | 141.9 bases | 149 bases | 96.3% |
| errors | Plate-3-BOP-1000-ACNB-END-1_S50_L001_R2_001.good.fq | 376,096 | 52,971,375 | 100.0% | 140.8 bases | 149 bases | 97.5% |
| errors | Plate-3-BOP-1000-ACNB-END-1_S50_L002_R1_001.good.fq | 344,424 | 48,895,433 | 100.0% | 142.0 bases | 149 bases | 96.5% |
| errors | Plate-3-BOP-1000-ACNB-END-1_S50_L002_R2_001.good.fq | 344,424 | 48,554,791 | 100.0% | 141.0 bases | 149 bases | 97.3% |
| errors | Plate-3-BOP-1000-ACNB-END-1_S50_L003_R1_001.good.fq | 365,418 | 51,829,710 | 100.0% | 141.8 bases | 149 bases | 96.2% |
| errors | Plate-3-BOP-1000-ACNB-END-1_S50_L003_R2_001.good.fq | 365,418 | 51,439,969 | 100.0% | 140.8 bases | 149 bases | 97.3% |
| errors | Plate-3-BOP-1000-ACNB-END-1_S50_L004_R1_001.good.fq | 369,439 | 52,402,470 | 100.0% | 141.8 bases | 149 bases | 96.4% |
| errors | Plate-3-BOP-1000-ACNB-END-1_S50_L004_R2_001.good.fq | 369,439 | 52,007,538 | 100.0% | 140.8 bases | 149 bases | 97.5% |
| total | 2,910,754 | 411,485,854 | 100.0% | 141.4 bases | 149 bases | 96.9% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_000913 | 4,641,652 | 84.3 | 3.9 | 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 | 22442 |
| 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 | 0.003 |
| reference sequence | pr(no read start) |
|---|---|
| NC_000913 | 0.76778 |
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 | 2.3.4.1 |
| R | 3.4.4 |
| step | start | end | elapsed |
|---|---|---|---|
| Read and reference sequence file input | 10:23:25 25 Feb 2020 | 10:24:08 25 Feb 2020 | 43 seconds |
| Read alignment to reference genome | 10:24:09 25 Feb 2020 | 10:30:21 25 Feb 2020 | 6 minutes 12 seconds |
| Preprocessing alignments for candidate junction identification | 10:30:21 25 Feb 2020 | 10:31:03 25 Feb 2020 | 42 seconds |
| Preliminary analysis of coverage distribution | 10:31:03 25 Feb 2020 | 10:32:47 25 Feb 2020 | 1 minute 44 seconds |
| Identifying junction candidates | 10:32:47 25 Feb 2020 | 10:33:15 25 Feb 2020 | 28 seconds |
| Re-alignment to junction candidates | 10:33:15 25 Feb 2020 | 10:35:06 25 Feb 2020 | 1 minute 51 seconds |
| Resolving best read alignments | 10:35:06 25 Feb 2020 | 10:36:09 25 Feb 2020 | 1 minute 3 seconds |
| Creating BAM files | 10:36:09 25 Feb 2020 | 10:37:44 25 Feb 2020 | 1 minute 35 seconds |
| Tabulating error counts | 10:37:44 25 Feb 2020 | 10:38:16 25 Feb 2020 | 32 seconds |
| Re-calibrating base error rates | 10:38:16 25 Feb 2020 | 10:38:19 25 Feb 2020 | 3 seconds |
| Examining read alignment evidence | 10:38:19 25 Feb 2020 | 11:00:24 25 Feb 2020 | 22 minutes 5 seconds |
| Polymorphism statistics | 11:00:24 25 Feb 2020 | 11:00:25 25 Feb 2020 | 1 second |
| Output | 11:00:25 25 Feb 2020 | 11:00:51 25 Feb 2020 | 26 seconds |
| Total | 37 minutes 25 seconds | ||
