mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.35.4 revision f352f80f4bc9
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-PFKA-END-3_S42_L001_R1_001.good.fq | 415,411 | 58,244,315 | 100.0% | 140.2 bases | 149 bases | 97.0% |
| errors | Plate-3-BOP-1000-PFKA-END-3_S42_L001_R2_001.good.fq | 415,411 | 57,941,457 | 100.0% | 139.5 bases | 149 bases | 97.7% |
| errors | Plate-3-BOP-1000-PFKA-END-3_S42_L002_R1_001.good.fq | 382,956 | 53,730,735 | 100.0% | 140.3 bases | 149 bases | 97.0% |
| errors | Plate-3-BOP-1000-PFKA-END-3_S42_L002_R2_001.good.fq | 382,956 | 53,478,069 | 100.0% | 139.6 bases | 149 bases | 97.3% |
| errors | Plate-3-BOP-1000-PFKA-END-3_S42_L003_R1_001.good.fq | 401,258 | 56,204,024 | 100.0% | 140.1 bases | 149 bases | 96.8% |
| errors | Plate-3-BOP-1000-PFKA-END-3_S42_L003_R2_001.good.fq | 401,258 | 55,903,997 | 100.0% | 139.3 bases | 149 bases | 97.5% |
| errors | Plate-3-BOP-1000-PFKA-END-3_S42_L004_R1_001.good.fq | 415,946 | 58,271,420 | 100.0% | 140.1 bases | 149 bases | 97.1% |
| errors | Plate-3-BOP-1000-PFKA-END-3_S42_L004_R2_001.good.fq | 415,946 | 57,997,054 | 100.0% | 139.4 bases | 149 bases | 97.4% |
| total | 3,231,142 | 451,771,071 | 100.0% | 139.8 bases | 149 bases | 97.2% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_000913 | 4,641,652 | 93.1 | 3.9 | 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 | 20311 |
| 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 | 55 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.004 |
| reference sequence | pr(no read start) |
|---|---|
| NC_000913 | 0.74224 |
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 |
| Minimum probablilty assigned that no mapped read will start at a given position and strand for junction prediction | 0.1 |
| Junction allow suboptimal matches | FALSE |
| 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 | 10:35:03 06 Apr 2022 | 10:36:01 06 Apr 2022 | 58 seconds |
| Read alignment to reference genome | 10:36:01 06 Apr 2022 | 10:42:27 06 Apr 2022 | 6 minutes 26 seconds |
| Preprocessing alignments for candidate junction identification | 10:42:27 06 Apr 2022 | 10:43:07 06 Apr 2022 | 40 seconds |
| Preliminary analysis of coverage distribution | 10:43:07 06 Apr 2022 | 10:45:02 06 Apr 2022 | 1 minute 55 seconds |
| Identifying junction candidates | 10:45:02 06 Apr 2022 | 10:45:13 06 Apr 2022 | 11 seconds |
| Re-alignment to junction candidates | 10:45:13 06 Apr 2022 | 10:46:43 06 Apr 2022 | 1 minute 30 seconds |
| Resolving best read alignments | 10:46:43 06 Apr 2022 | 10:47:41 06 Apr 2022 | 58 seconds |
| Creating BAM files | 10:47:41 06 Apr 2022 | 10:49:23 06 Apr 2022 | 1 minute 42 seconds |
| Tabulating error counts | 10:49:23 06 Apr 2022 | 10:50:05 06 Apr 2022 | 42 seconds |
| Re-calibrating base error rates | 10:50:05 06 Apr 2022 | 10:50:08 06 Apr 2022 | 3 seconds |
| Examining read alignment evidence | 10:50:08 06 Apr 2022 | 11:21:54 06 Apr 2022 | 31 minutes 46 seconds |
| Polymorphism statistics | 11:21:54 06 Apr 2022 | 11:21:55 06 Apr 2022 | 1 second |
| Output | 11:21:55 06 Apr 2022 | 11:22:14 06 Apr 2022 | 19 seconds |
| Total | 47 minutes 11 seconds | ||
