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-ACEF-END-4_S77_L001_R1_001.good.fq | 326,916 | 45,121,634 | 100.0% | 138.0 bases | 148 bases | 99.4% |
| errors | Plate-3-BOP-1000-ACEF-END-4_S77_L001_R2_001.good.fq | 326,916 | 45,147,535 | 100.0% | 138.1 bases | 148 bases | 98.5% |
| errors | Plate-3-BOP-1000-ACEF-END-4_S77_L002_R1_001.good.fq | 302,220 | 41,739,604 | 100.0% | 138.1 bases | 148 bases | 99.5% |
| errors | Plate-3-BOP-1000-ACEF-END-4_S77_L002_R2_001.good.fq | 302,220 | 41,764,499 | 100.0% | 138.2 bases | 148 bases | 98.3% |
| errors | Plate-3-BOP-1000-ACEF-END-4_S77_L003_R1_001.good.fq | 316,679 | 43,683,545 | 100.0% | 137.9 bases | 148 bases | 99.3% |
| errors | Plate-3-BOP-1000-ACEF-END-4_S77_L003_R2_001.good.fq | 316,679 | 43,712,514 | 100.0% | 138.0 bases | 148 bases | 98.3% |
| errors | Plate-3-BOP-1000-ACEF-END-4_S77_L004_R1_001.good.fq | 336,424 | 46,438,506 | 100.0% | 138.0 bases | 148 bases | 99.5% |
| errors | Plate-3-BOP-1000-ACEF-END-4_S77_L004_R2_001.good.fq | 336,424 | 46,475,983 | 100.0% | 138.1 bases | 148 bases | 98.4% |
| total | 2,564,478 | 354,083,820 | 100.0% | 138.1 bases | 148 bases | 98.9% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_000913 | 4,641,652 | 73.6 | 4.6 | 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 | 8196 |
| 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 | 1312 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.086 |
| reference sequence | pr(no read start) |
|---|---|
| NC_000913 | 0.78923 |
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 | 2.3.4.1 |
| R | 3.4.4 |
| step | start | end | elapsed |
|---|---|---|---|
| Read and reference sequence file input | 19:56:06 25 Feb 2020 | 19:56:44 25 Feb 2020 | 38 seconds |
| Read alignment to reference genome | 19:56:45 25 Feb 2020 | 20:01:58 25 Feb 2020 | 5 minutes 13 seconds |
| Preprocessing alignments for candidate junction identification | 20:01:58 25 Feb 2020 | 20:02:34 25 Feb 2020 | 36 seconds |
| Preliminary analysis of coverage distribution | 20:02:34 25 Feb 2020 | 20:04:05 25 Feb 2020 | 1 minute 31 seconds |
| Identifying junction candidates | 20:04:05 25 Feb 2020 | 20:04:23 25 Feb 2020 | 18 seconds |
| Re-alignment to junction candidates | 20:04:23 25 Feb 2020 | 20:06:32 25 Feb 2020 | 2 minutes 9 seconds |
| Resolving best read alignments | 20:06:32 25 Feb 2020 | 20:07:30 25 Feb 2020 | 58 seconds |
| Creating BAM files | 20:07:30 25 Feb 2020 | 20:08:53 25 Feb 2020 | 1 minute 23 seconds |
| Tabulating error counts | 20:08:53 25 Feb 2020 | 20:09:21 25 Feb 2020 | 28 seconds |
| Re-calibrating base error rates | 20:09:21 25 Feb 2020 | 20:09:24 25 Feb 2020 | 3 seconds |
| Examining read alignment evidence | 20:09:24 25 Feb 2020 | 20:27:12 25 Feb 2020 | 17 minutes 48 seconds |
| Polymorphism statistics | 20:27:12 25 Feb 2020 | 20:27:13 25 Feb 2020 | 1 second |
| Output | 20:27:13 25 Feb 2020 | 20:27:42 25 Feb 2020 | 29 seconds |
| Total | 31 minutes 35 seconds | ||
