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-RPE-END-1_S44_L001_R1_001.good.fq | 404,801 | 57,742,934 | 100.0% | 142.6 bases | 149 bases | 98.0% |
| errors | Plate-3-BOP-27-RPE-END-1_S44_L001_R2_001.good.fq | 404,801 | 57,560,878 | 100.0% | 142.2 bases | 149 bases | 97.8% |
| errors | Plate-3-BOP-27-RPE-END-1_S44_L002_R1_001.good.fq | 380,304 | 54,282,980 | 100.0% | 142.7 bases | 149 bases | 98.1% |
| errors | Plate-3-BOP-27-RPE-END-1_S44_L002_R2_001.good.fq | 380,304 | 54,129,521 | 100.0% | 142.3 bases | 149 bases | 97.4% |
| errors | Plate-3-BOP-27-RPE-END-1_S44_L003_R1_001.good.fq | 389,645 | 55,527,308 | 100.0% | 142.5 bases | 149 bases | 97.9% |
| errors | Plate-3-BOP-27-RPE-END-1_S44_L003_R2_001.good.fq | 389,645 | 55,350,000 | 100.0% | 142.1 bases | 149 bases | 97.6% |
| errors | Plate-3-BOP-27-RPE-END-1_S44_L004_R1_001.good.fq | 408,516 | 58,206,181 | 100.0% | 142.5 bases | 149 bases | 98.1% |
| errors | Plate-3-BOP-27-RPE-END-1_S44_L004_R2_001.good.fq | 408,516 | 58,041,352 | 100.0% | 142.1 bases | 149 bases | 97.6% |
| total | 3,166,532 | 450,841,154 | 100.0% | 142.4 bases | 149 bases | 97.8% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_000913 | 4,641,652 | 88.6 | 8.8 | 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 | 15797 |
| 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 | 1441 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.093 |
| reference sequence | pr(no read start) |
|---|---|
| NC_000913 | 0.75160 |
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 | 14:40:18 11 Sep 2020 | 14:41:06 11 Sep 2020 | 48 seconds |
| Read alignment to reference genome | 14:41:06 11 Sep 2020 | 14:47:14 11 Sep 2020 | 6 minutes 8 seconds |
| Preprocessing alignments for candidate junction identification | 14:47:14 11 Sep 2020 | 14:48:03 11 Sep 2020 | 49 seconds |
| Preliminary analysis of coverage distribution | 14:48:03 11 Sep 2020 | 14:49:57 11 Sep 2020 | 1 minute 54 seconds |
| Identifying junction candidates | 14:49:57 11 Sep 2020 | 14:50:15 11 Sep 2020 | 18 seconds |
| Re-alignment to junction candidates | 14:50:15 11 Sep 2020 | 14:52:40 11 Sep 2020 | 2 minutes 25 seconds |
| Resolving best read alignments | 14:52:40 11 Sep 2020 | 14:53:58 11 Sep 2020 | 1 minute 18 seconds |
| Creating BAM files | 14:53:58 11 Sep 2020 | 14:55:43 11 Sep 2020 | 1 minute 45 seconds |
| Tabulating error counts | 14:55:43 11 Sep 2020 | 14:56:17 11 Sep 2020 | 34 seconds |
| Re-calibrating base error rates | 14:56:17 11 Sep 2020 | 14:56:20 11 Sep 2020 | 3 seconds |
| Examining read alignment evidence | 14:56:20 11 Sep 2020 | 15:29:04 11 Sep 2020 | 32 minutes 44 seconds |
| Polymorphism statistics | 15:29:04 11 Sep 2020 | 15:29:05 11 Sep 2020 | 1 second |
| Output | 15:29:05 11 Sep 2020 | 15:29:33 11 Sep 2020 | 28 seconds |
| Total | 49 minutes 15 seconds | ||
