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-1000-RPE-END-1_S65_L001_R1_001.good.fq | 414,637 | 59,743,173 | 100.0% | 144.1 bases | 149 bases | 98.8% |
| errors | Plate-3-BOP-1000-RPE-END-1_S65_L001_R2_001.good.fq | 414,637 | 59,646,839 | 100.0% | 143.9 bases | 149 bases | 98.3% |
| errors | Plate-3-BOP-1000-RPE-END-1_S65_L002_R1_001.good.fq | 385,443 | 55,562,126 | 100.0% | 144.2 bases | 149 bases | 98.8% |
| errors | Plate-3-BOP-1000-RPE-END-1_S65_L002_R2_001.good.fq | 385,443 | 55,481,469 | 100.0% | 143.9 bases | 149 bases | 98.0% |
| errors | Plate-3-BOP-1000-RPE-END-1_S65_L003_R1_001.good.fq | 401,378 | 57,829,042 | 100.0% | 144.1 bases | 149 bases | 98.7% |
| errors | Plate-3-BOP-1000-RPE-END-1_S65_L003_R2_001.good.fq | 401,378 | 57,736,262 | 100.0% | 143.8 bases | 149 bases | 98.1% |
| errors | Plate-3-BOP-1000-RPE-END-1_S65_L004_R1_001.good.fq | 410,185 | 59,066,843 | 100.0% | 144.0 bases | 149 bases | 98.8% |
| errors | Plate-3-BOP-1000-RPE-END-1_S65_L004_R2_001.good.fq | 410,185 | 58,986,250 | 100.0% | 143.8 bases | 149 bases | 98.1% |
| total | 3,223,286 | 464,052,004 | 100.0% | 144.0 bases | 149 bases | 98.4% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_000913 | 4,641,652 | 91.9 | 3.0 | 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 | 15876 |
| 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 | 1265 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.082 |
| reference sequence | pr(no read start) |
|---|---|
| NC_000913 | 0.74767 |
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 | 04:16:25 11 Sep 2020 | 04:17:14 11 Sep 2020 | 49 seconds |
| Read alignment to reference genome | 04:17:14 11 Sep 2020 | 04:23:23 11 Sep 2020 | 6 minutes 9 seconds |
| Preprocessing alignments for candidate junction identification | 04:23:23 11 Sep 2020 | 04:24:12 11 Sep 2020 | 49 seconds |
| Preliminary analysis of coverage distribution | 04:24:12 11 Sep 2020 | 04:26:06 11 Sep 2020 | 1 minute 54 seconds |
| Identifying junction candidates | 04:26:06 11 Sep 2020 | 04:26:25 11 Sep 2020 | 19 seconds |
| Re-alignment to junction candidates | 04:26:25 11 Sep 2020 | 04:28:52 11 Sep 2020 | 2 minutes 27 seconds |
| Resolving best read alignments | 04:28:52 11 Sep 2020 | 04:30:12 11 Sep 2020 | 1 minute 20 seconds |
| Creating BAM files | 04:30:12 11 Sep 2020 | 04:31:57 11 Sep 2020 | 1 minute 45 seconds |
| Tabulating error counts | 04:31:57 11 Sep 2020 | 04:32:32 11 Sep 2020 | 35 seconds |
| Re-calibrating base error rates | 04:32:32 11 Sep 2020 | 04:32:35 11 Sep 2020 | 3 seconds |
| Examining read alignment evidence | 04:32:35 11 Sep 2020 | 05:04:16 11 Sep 2020 | 31 minutes 41 seconds |
| Polymorphism statistics | 05:04:16 11 Sep 2020 | 05:04:16 11 Sep 2020 | 0 seconds |
| Output | 05:04:16 11 Sep 2020 | 05:04:41 11 Sep 2020 | 25 seconds |
| Total | 48 minutes 16 seconds | ||
