mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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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-1-BOP-1000-ACEF-END-1_S5_L001_R1_001.good.fq | 418,159 | 60,392,328 | 100.0% | 144.4 bases | 149 bases | 98.4% |
| errors | Plate-1-BOP-1000-ACEF-END-1_S5_L001_R2_001.good.fq | 418,159 | 60,300,932 | 100.0% | 144.2 bases | 149 bases | 97.8% |
| errors | Plate-1-BOP-1000-ACEF-END-1_S5_L002_R1_001.good.fq | 389,068 | 56,211,721 | 100.0% | 144.5 bases | 149 bases | 98.5% |
| errors | Plate-1-BOP-1000-ACEF-END-1_S5_L002_R2_001.good.fq | 389,068 | 56,139,485 | 100.0% | 144.3 bases | 149 bases | 97.3% |
| errors | Plate-1-BOP-1000-ACEF-END-1_S5_L003_R1_001.good.fq | 404,021 | 58,320,411 | 100.0% | 144.3 bases | 149 bases | 98.3% |
| errors | Plate-1-BOP-1000-ACEF-END-1_S5_L003_R2_001.good.fq | 404,021 | 58,235,915 | 100.0% | 144.1 bases | 149 bases | 97.6% |
| errors | Plate-1-BOP-1000-ACEF-END-1_S5_L004_R1_001.good.fq | 410,173 | 59,178,788 | 100.0% | 144.3 bases | 149 bases | 98.5% |
| errors | Plate-1-BOP-1000-ACEF-END-1_S5_L004_R2_001.good.fq | 410,173 | 59,103,225 | 100.0% | 144.1 bases | 149 bases | 97.5% |
| total | 3,242,842 | 467,882,805 | 100.0% | 144.3 bases | 149 bases | 98.0% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_000913 | 4,641,652 | 98.3 | 2.8 | 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 | 20453 |
| 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 | 56 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.004 |
| reference sequence | pr(no read start) |
|---|---|
| NC_000913 | 0.74404 |
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 | ≤ 3 |
| Number of bases that at least one read must overlap each uniquely aligned side of a predicted junction | ≥ 1 |
| option | value |
|---|---|
| Mode | Consensus/Mixed Base |
| 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 | 10 |
| Polymorphism frequency cutoff | 0.2 |
| Polymorphism minimum variant coverage each strand | OFF |
| 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 | OFF |
| Skip base substitutions when they create a homopolymer flanked on each side by | OFF |
| program | version |
|---|---|
| bowtie2 | 2.2.6 |
| R | 3.4.4 |
| step | start | end | elapsed |
|---|---|---|---|
| Read and reference sequence file input | 18:16:52 12 Sep 2020 | 18:17:42 12 Sep 2020 | 50 seconds |
| Read alignment to reference genome | 18:17:43 12 Sep 2020 | 18:24:05 12 Sep 2020 | 6 minutes 22 seconds |
| Preprocessing alignments for candidate junction identification | 18:24:05 12 Sep 2020 | 18:24:55 12 Sep 2020 | 50 seconds |
| Preliminary analysis of coverage distribution | 18:24:55 12 Sep 2020 | 18:26:52 12 Sep 2020 | 1 minute 57 seconds |
| Identifying junction candidates | 18:26:52 12 Sep 2020 | 18:27:10 12 Sep 2020 | 18 seconds |
| Re-alignment to junction candidates | 18:27:10 12 Sep 2020 | 18:29:03 12 Sep 2020 | 1 minute 53 seconds |
| Resolving best read alignments | 18:29:03 12 Sep 2020 | 18:30:22 12 Sep 2020 | 1 minute 19 seconds |
| Creating BAM files | 18:30:22 12 Sep 2020 | 18:32:10 12 Sep 2020 | 1 minute 48 seconds |
| Tabulating error counts | 18:32:10 12 Sep 2020 | 18:32:46 12 Sep 2020 | 36 seconds |
| Re-calibrating base error rates | 18:32:46 12 Sep 2020 | 18:32:49 12 Sep 2020 | 3 seconds |
| Examining read alignment evidence | 18:32:49 12 Sep 2020 | 18:40:16 12 Sep 2020 | 7 minutes 27 seconds |
| Polymorphism statistics | 18:40:16 12 Sep 2020 | 18:40:16 12 Sep 2020 | 0 seconds |
| Output | 18:40:16 12 Sep 2020 | 18:40:35 12 Sep 2020 | 19 seconds |
| Total | 23 minutes 42 seconds | ||
