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-1-BOP-1000-RPE-END-1_S29_L001_R1_001.good.fq | 570,100 | 80,510,757 | 100.0% | 141.2 bases | 149 bases | 97.1% |
| errors | Plate-1-BOP-1000-RPE-END-1_S29_L001_R2_001.good.fq | 570,100 | 80,251,393 | 100.0% | 140.8 bases | 149 bases | 97.3% |
| errors | Plate-1-BOP-1000-RPE-END-1_S29_L002_R1_001.good.fq | 526,535 | 74,407,512 | 100.0% | 141.3 bases | 149 bases | 97.2% |
| errors | Plate-1-BOP-1000-RPE-END-1_S29_L002_R2_001.good.fq | 526,535 | 74,201,898 | 100.0% | 140.9 bases | 149 bases | 96.9% |
| errors | Plate-1-BOP-1000-RPE-END-1_S29_L003_R1_001.good.fq | 554,214 | 78,267,004 | 100.0% | 141.2 bases | 149 bases | 97.0% |
| errors | Plate-1-BOP-1000-RPE-END-1_S29_L003_R2_001.good.fq | 554,214 | 78,025,544 | 100.0% | 140.8 bases | 149 bases | 97.1% |
| errors | Plate-1-BOP-1000-RPE-END-1_S29_L004_R1_001.good.fq | 567,869 | 80,174,464 | 100.0% | 141.2 bases | 149 bases | 97.3% |
| errors | Plate-1-BOP-1000-RPE-END-1_S29_L004_R2_001.good.fq | 567,869 | 79,957,606 | 100.0% | 140.8 bases | 149 bases | 97.1% |
| total | 4,437,436 | 625,796,178 | 100.0% | 141.0 bases | 149 bases | 97.1% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_000913 | 4,641,652 | 121.7 | 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 | 58343 |
| 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 | 157 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.010 |
| reference sequence | pr(no read start) |
|---|---|
| NC_000913 | 0.68566 |
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 | 06:01:38 12 Sep 2020 | 06:02:45 12 Sep 2020 | 1 minute 7 seconds |
| Read alignment to reference genome | 06:02:45 12 Sep 2020 | 06:11:09 12 Sep 2020 | 8 minutes 24 seconds |
| Preprocessing alignments for candidate junction identification | 06:11:09 12 Sep 2020 | 06:12:17 12 Sep 2020 | 1 minute 8 seconds |
| Preliminary analysis of coverage distribution | 06:12:17 12 Sep 2020 | 06:14:47 12 Sep 2020 | 2 minutes 30 seconds |
| Identifying junction candidates | 06:14:47 12 Sep 2020 | 06:16:33 12 Sep 2020 | 1 minute 46 seconds |
| Re-alignment to junction candidates | 06:16:33 12 Sep 2020 | 06:19:08 12 Sep 2020 | 2 minutes 35 seconds |
| Resolving best read alignments | 06:19:08 12 Sep 2020 | 06:20:56 12 Sep 2020 | 1 minute 48 seconds |
| Creating BAM files | 06:20:56 12 Sep 2020 | 06:23:14 12 Sep 2020 | 2 minutes 18 seconds |
| Tabulating error counts | 06:23:14 12 Sep 2020 | 06:24:01 12 Sep 2020 | 47 seconds |
| Re-calibrating base error rates | 06:24:01 12 Sep 2020 | 06:24:04 12 Sep 2020 | 3 seconds |
| Examining read alignment evidence | 06:24:04 12 Sep 2020 | 06:33:56 12 Sep 2020 | 9 minutes 52 seconds |
| Polymorphism statistics | 06:33:56 12 Sep 2020 | 06:33:57 12 Sep 2020 | 1 second |
| Output | 06:33:57 12 Sep 2020 | 06:34:20 12 Sep 2020 | 23 seconds |
| Total | 32 minutes 42 seconds | ||
