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 | J3-A2_S91_R1_001.good.fq | 3,360,226 | 216,995,027 | 100.0% | 64.6 bases | 71 bases | 90.5% |
| total | 3,360,226 | 216,995,027 | 100.0% | 64.6 bases | 71 bases | 90.5% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | W3110S.gb | 4,646,334 | 44.3 | 12.3 | 100.0% | Escherichia coli str. K-12 substr. W3110 DNA, complete genome. |
| total | 4,646,334 | 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 | 12495 |
| 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 | 72 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.002 |
| reference sequence | pr(no read start) |
|---|---|
| W3110S.gb | 0.93060 |
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 | 10:23:44 11 Dec 2019 | 10:24:18 11 Dec 2019 | 34 seconds |
| Read alignment to reference genome | 10:24:18 11 Dec 2019 | 10:29:25 11 Dec 2019 | 5 minutes 7 seconds |
| Preprocessing alignments for candidate junction identification | 10:29:25 11 Dec 2019 | 10:30:07 11 Dec 2019 | 42 seconds |
| Preliminary analysis of coverage distribution | 10:30:07 11 Dec 2019 | 10:31:06 11 Dec 2019 | 59 seconds |
| Identifying junction candidates | 10:31:06 11 Dec 2019 | 10:31:07 11 Dec 2019 | 1 second |
| Re-alignment to junction candidates | 10:31:07 11 Dec 2019 | 10:32:11 11 Dec 2019 | 1 minute 4 seconds |
| Resolving best read alignments | 10:32:11 11 Dec 2019 | 10:33:16 11 Dec 2019 | 1 minute 5 seconds |
| Creating BAM files | 10:33:16 11 Dec 2019 | 10:34:11 11 Dec 2019 | 55 seconds |
| Tabulating error counts | 10:34:11 11 Dec 2019 | 10:34:28 11 Dec 2019 | 17 seconds |
| Re-calibrating base error rates | 10:34:28 11 Dec 2019 | 10:34:29 11 Dec 2019 | 1 second |
| Examining read alignment evidence | 10:34:29 11 Dec 2019 | 10:39:19 11 Dec 2019 | 4 minutes 50 seconds |
| Polymorphism statistics | 10:39:19 11 Dec 2019 | 10:39:21 11 Dec 2019 | 2 seconds |
| Output | 10:39:21 11 Dec 2019 | 10:42:42 11 Dec 2019 | 3 minutes 21 seconds |
| Total | 18 minutes 58 seconds | ||
