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-3-BOP-1000-RPE-END-3_S67_L001_R1_001.good.fq | 399,433 | 57,400,475 | 100.0% | 143.7 bases | 149 bases | 98.0% |
| errors | Plate-3-BOP-1000-RPE-END-3_S67_L001_R2_001.good.fq | 399,433 | 57,245,590 | 100.0% | 143.3 bases | 149 bases | 97.9% |
| errors | Plate-3-BOP-1000-RPE-END-3_S67_L002_R1_001.good.fq | 371,216 | 53,358,552 | 100.0% | 143.7 bases | 149 bases | 98.1% |
| errors | Plate-3-BOP-1000-RPE-END-3_S67_L002_R2_001.good.fq | 371,216 | 53,231,185 | 100.0% | 143.4 bases | 149 bases | 97.5% |
| errors | Plate-3-BOP-1000-RPE-END-3_S67_L003_R1_001.good.fq | 387,673 | 55,688,109 | 100.0% | 143.6 bases | 149 bases | 97.9% |
| errors | Plate-3-BOP-1000-RPE-END-3_S67_L003_R2_001.good.fq | 387,673 | 55,547,287 | 100.0% | 143.3 bases | 149 bases | 97.7% |
| errors | Plate-3-BOP-1000-RPE-END-3_S67_L004_R1_001.good.fq | 397,158 | 57,013,695 | 100.0% | 143.6 bases | 149 bases | 98.1% |
| errors | Plate-3-BOP-1000-RPE-END-3_S67_L004_R2_001.good.fq | 397,158 | 56,878,563 | 100.0% | 143.2 bases | 149 bases | 97.7% |
| total | 3,110,960 | 446,363,456 | 100.0% | 143.5 bases | 149 bases | 97.8% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_000913 | 4,641,652 | 92.9 | 4.2 | 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 | 18734 |
| 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 | 28 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.002 |
| reference sequence | pr(no read start) |
|---|---|
| NC_000913 | 0.75224 |
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 | 03:14:46 13 Sep 2020 | 03:15:33 13 Sep 2020 | 47 seconds |
| Read alignment to reference genome | 03:15:34 13 Sep 2020 | 03:21:32 13 Sep 2020 | 5 minutes 58 seconds |
| Preprocessing alignments for candidate junction identification | 03:21:32 13 Sep 2020 | 03:22:19 13 Sep 2020 | 47 seconds |
| Preliminary analysis of coverage distribution | 03:22:19 13 Sep 2020 | 03:24:09 13 Sep 2020 | 1 minute 50 seconds |
| Identifying junction candidates | 03:24:09 13 Sep 2020 | 03:24:25 13 Sep 2020 | 16 seconds |
| Re-alignment to junction candidates | 03:24:25 13 Sep 2020 | 03:26:10 13 Sep 2020 | 1 minute 45 seconds |
| Resolving best read alignments | 03:26:10 13 Sep 2020 | 03:27:24 13 Sep 2020 | 1 minute 14 seconds |
| Creating BAM files | 03:27:24 13 Sep 2020 | 03:29:05 13 Sep 2020 | 1 minute 41 seconds |
| Tabulating error counts | 03:29:05 13 Sep 2020 | 03:29:39 13 Sep 2020 | 34 seconds |
| Re-calibrating base error rates | 03:29:39 13 Sep 2020 | 03:29:42 13 Sep 2020 | 3 seconds |
| Examining read alignment evidence | 03:29:42 13 Sep 2020 | 03:59:45 13 Sep 2020 | 30 minutes 3 seconds |
| Polymorphism statistics | 03:59:45 13 Sep 2020 | 03:59:46 13 Sep 2020 | 1 second |
| Output | 03:59:46 13 Sep 2020 | 04:00:07 13 Sep 2020 | 21 seconds |
| Total | 45 minutes 20 seconds | ||
