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-27-PFKA-END-2_S62_L001_R1_001.good.fq | 341,429 | 49,167,735 | 100.0% | 144.0 bases | 149 bases | 97.1% |
| errors | Plate-3-BOP-27-PFKA-END-2_S62_L001_R2_001.good.fq | 341,429 | 48,900,986 | 100.0% | 143.2 bases | 149 bases | 97.6% |
| errors | Plate-3-BOP-27-PFKA-END-2_S62_L002_R1_001.good.fq | 312,772 | 45,070,486 | 100.0% | 144.1 bases | 149 bases | 97.3% |
| errors | Plate-3-BOP-27-PFKA-END-2_S62_L002_R2_001.good.fq | 312,772 | 44,836,679 | 100.0% | 143.4 bases | 149 bases | 97.6% |
| errors | Plate-3-BOP-27-PFKA-END-2_S62_L003_R1_001.good.fq | 331,726 | 47,733,963 | 100.0% | 143.9 bases | 149 bases | 97.1% |
| errors | Plate-3-BOP-27-PFKA-END-2_S62_L003_R2_001.good.fq | 331,726 | 47,476,826 | 100.0% | 143.1 bases | 149 bases | 97.5% |
| errors | Plate-3-BOP-27-PFKA-END-2_S62_L004_R1_001.good.fq | 331,106 | 47,656,721 | 100.0% | 143.9 bases | 149 bases | 97.3% |
| errors | Plate-3-BOP-27-PFKA-END-2_S62_L004_R2_001.good.fq | 331,106 | 47,408,941 | 100.0% | 143.2 bases | 149 bases | 97.7% |
| total | 2,634,066 | 378,252,337 | 100.0% | 143.6 bases | 149 bases | 97.4% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_000913 | 4,641,652 | 75.9 | 7.0 | 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 | 16289 |
| 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 | 1501 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.097 |
| reference sequence | pr(no read start) |
|---|---|
| NC_000913 | 0.78517 |
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 | 23:43:48 12 Sep 2020 | 23:44:29 12 Sep 2020 | 41 seconds |
| Read alignment to reference genome | 23:44:29 12 Sep 2020 | 23:49:39 12 Sep 2020 | 5 minutes 10 seconds |
| Preprocessing alignments for candidate junction identification | 23:49:39 12 Sep 2020 | 23:50:19 12 Sep 2020 | 40 seconds |
| Preliminary analysis of coverage distribution | 23:50:19 12 Sep 2020 | 23:51:52 12 Sep 2020 | 1 minute 33 seconds |
| Identifying junction candidates | 23:51:52 12 Sep 2020 | 23:52:06 12 Sep 2020 | 14 seconds |
| Re-alignment to junction candidates | 23:52:06 12 Sep 2020 | 23:54:10 12 Sep 2020 | 2 minutes 4 seconds |
| Resolving best read alignments | 23:54:10 12 Sep 2020 | 23:55:15 12 Sep 2020 | 1 minute 5 seconds |
| Creating BAM files | 23:55:15 12 Sep 2020 | 23:56:42 12 Sep 2020 | 1 minute 27 seconds |
| Tabulating error counts | 23:56:42 12 Sep 2020 | 23:57:11 12 Sep 2020 | 29 seconds |
| Re-calibrating base error rates | 23:57:11 12 Sep 2020 | 23:57:14 12 Sep 2020 | 3 seconds |
| Examining read alignment evidence | 23:57:14 12 Sep 2020 | 00:19:59 13 Sep 2020 | 22 minutes 45 seconds |
| Polymorphism statistics | 00:19:59 13 Sep 2020 | 00:20:00 13 Sep 2020 | 1 second |
| Output | 00:20:00 13 Sep 2020 | 00:20:32 13 Sep 2020 | 32 seconds |
| Total | 36 minutes 44 seconds | ||
