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-BOP27-ACNB-END-1_S16_L001_R1_001.good.fq | 349,512 | 50,361,199 | 100.0% | 144.1 bases | 149 bases | 97.6% |
| errors | Plate-1-BOP27-ACNB-END-1_S16_L001_R2_001.good.fq | 349,512 | 50,094,370 | 100.0% | 143.3 bases | 149 bases | 97.9% |
| errors | Plate-1-BOP27-ACNB-END-1_S16_L002_R1_001.good.fq | 324,405 | 46,752,388 | 100.0% | 144.1 bases | 149 bases | 97.8% |
| errors | Plate-1-BOP27-ACNB-END-1_S16_L002_R2_001.good.fq | 324,405 | 46,526,957 | 100.0% | 143.4 bases | 149 bases | 97.8% |
| errors | Plate-1-BOP27-ACNB-END-1_S16_L003_R1_001.good.fq | 340,788 | 49,076,069 | 100.0% | 144.0 bases | 149 bases | 97.5% |
| errors | Plate-1-BOP27-ACNB-END-1_S16_L003_R2_001.good.fq | 340,788 | 48,815,439 | 100.0% | 143.2 bases | 149 bases | 97.8% |
| errors | Plate-1-BOP27-ACNB-END-1_S16_L004_R1_001.good.fq | 340,417 | 49,008,881 | 100.0% | 144.0 bases | 149 bases | 97.7% |
| errors | Plate-1-BOP27-ACNB-END-1_S16_L004_R2_001.good.fq | 340,417 | 48,764,280 | 100.0% | 143.2 bases | 149 bases | 97.9% |
| total | 2,710,244 | 389,399,583 | 100.0% | 143.7 bases | 149 bases | 97.8% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_000913 | 4,641,652 | 83.2 | 6.6 | 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 | 6978 |
| 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 | 695 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.046 |
| reference sequence | pr(no read start) |
|---|---|
| NC_000913 | 0.78105 |
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 | 00:48:36 13 Sep 2020 | 00:49:18 13 Sep 2020 | 42 seconds |
| Read alignment to reference genome | 00:49:18 13 Sep 2020 | 00:54:33 13 Sep 2020 | 5 minutes 15 seconds |
| Preprocessing alignments for candidate junction identification | 00:54:33 13 Sep 2020 | 00:55:15 13 Sep 2020 | 42 seconds |
| Preliminary analysis of coverage distribution | 00:55:15 13 Sep 2020 | 00:56:52 13 Sep 2020 | 1 minute 37 seconds |
| Identifying junction candidates | 00:56:52 13 Sep 2020 | 00:56:58 13 Sep 2020 | 6 seconds |
| Re-alignment to junction candidates | 00:56:58 13 Sep 2020 | 00:58:50 13 Sep 2020 | 1 minute 52 seconds |
| Resolving best read alignments | 00:58:50 13 Sep 2020 | 00:59:58 13 Sep 2020 | 1 minute 8 seconds |
| Creating BAM files | 00:59:58 13 Sep 2020 | 01:01:28 13 Sep 2020 | 1 minute 30 seconds |
| Tabulating error counts | 01:01:28 13 Sep 2020 | 01:01:57 13 Sep 2020 | 29 seconds |
| Re-calibrating base error rates | 01:01:57 13 Sep 2020 | 01:02:00 13 Sep 2020 | 3 seconds |
| Examining read alignment evidence | 01:02:00 13 Sep 2020 | 01:08:04 13 Sep 2020 | 6 minutes 4 seconds |
| Polymorphism statistics | 01:08:04 13 Sep 2020 | 01:08:04 13 Sep 2020 | 0 seconds |
| Output | 01:08:04 13 Sep 2020 | 01:08:16 13 Sep 2020 | 12 seconds |
| Total | 19 minutes 40 seconds | ||
