mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.32.0b
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| read file | reads | bases | passed filters | average | longest | mapped | |
|---|---|---|---|---|---|---|---|
| errors | A3_F026_R1_F21_I0_S2181_L001_R2_001.good.fq | 392,124 | 56,073,732 | 100.0% | 143.0 bases | 143 bases | 97.8% |
| errors | A3_F026_R1_F21_I0_S2181_L001_R1_001.good.fq | 435,973 | 64,959,977 | 100.0% | 149.0 bases | 149 bases | 98.8% |
| total | 828,097 | 121,033,709 | 100.0% | 146.2 bases | 149 bases | 98.3% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | CP009273 | 4,631,469 | 23.4 | 1.5 | 100.0% | Escherichia coli BW25113, complete genome. |
| total | 4,631,469 | 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 | 3705 |
| 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 | 65 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.004 |
| reference sequence | pr(no read start) |
|---|---|
| CP009273 | 0.92759 |
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 | OFF |
| Consensus minimum coverage each strand | OFF |
| Polymorphism E-value cutoff | 2 |
| Polymorphism frequency cutoff | 0.025 |
| Polymorphism minimum coverage each strand | 2 |
| 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 | 2.3.2 |
| R | 3.4.2 |
| step | start | end | elapsed |
|---|---|---|---|
| Read and reference sequence file input | 17:51:14 15 Jun 2018 | 17:51:26 15 Jun 2018 | 12 seconds |
| Read alignment to reference genome | 17:51:26 15 Jun 2018 | 17:52:20 15 Jun 2018 | 54 seconds |
| Preprocessing alignments for candidate junction identification | 17:52:20 15 Jun 2018 | 17:52:29 15 Jun 2018 | 9 seconds |
| Preliminary analysis of coverage distribution | 17:52:29 15 Jun 2018 | 17:52:54 15 Jun 2018 | 25 seconds |
| Identifying junction candidates | 17:52:54 15 Jun 2018 | 17:52:54 15 Jun 2018 | 0 seconds |
| Re-alignment to junction candidates | 17:52:54 15 Jun 2018 | 17:53:04 15 Jun 2018 | 10 seconds |
| Resolving alignments with junction candidates | 17:53:04 15 Jun 2018 | 17:53:19 15 Jun 2018 | 15 seconds |
| Creating BAM files | 17:53:19 15 Jun 2018 | 17:53:40 15 Jun 2018 | 21 seconds |
| Tabulating error counts | 17:53:40 15 Jun 2018 | 17:53:50 15 Jun 2018 | 10 seconds |
| Re-calibrating base error rates | 17:53:50 15 Jun 2018 | 17:53:51 15 Jun 2018 | 1 second |
| Examining read alignment evidence | 17:53:51 15 Jun 2018 | 18:01:27 15 Jun 2018 | 7 minutes 36 seconds |
| Polymorphism statistics | 18:01:27 15 Jun 2018 | 18:01:28 15 Jun 2018 | 1 second |
| Output | 18:01:28 15 Jun 2018 | 18:01:34 15 Jun 2018 | 6 seconds |
| Total | 10 minutes 20 seconds | ||
