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 | KT2440_Van_A2_F110_I1_R1_S45_L001_R1_001.good.fq | 339,079 | 43,102,258 | 100.0% | 127.1 bases | 135 bases | 94.2% |
| errors | KT2440_Van_A2_F110_I1_R1_S45_L001_R2_001.good.fq | 339,079 | 43,102,424 | 100.0% | 127.1 bases | 135 bases | 91.2% |
| errors | KT2440_Van_A2_F110_I1_R1_S45_L002_R1_001.good.fq | 331,210 | 42,149,544 | 100.0% | 127.3 bases | 135 bases | 95.5% |
| errors | KT2440_Van_A2_F110_I1_R1_S45_L002_R2_001.good.fq | 331,210 | 42,148,579 | 100.0% | 127.3 bases | 135 bases | 93.6% |
| errors | KT2440_Van_A2_F110_I1_R1_S45_L003_R1_001.good.fq | 337,990 | 43,067,462 | 100.0% | 127.4 bases | 135 bases | 94.1% |
| errors | KT2440_Van_A2_F110_I1_R1_S45_L003_R2_001.good.fq | 337,990 | 43,066,195 | 100.0% | 127.4 bases | 135 bases | 92.1% |
| errors | KT2440_Van_A2_F110_I1_R1_S45_L004_R1_001.good.fq | 337,807 | 42,906,926 | 100.0% | 127.0 bases | 135 bases | 95.6% |
| errors | KT2440_Van_A2_F110_I1_R1_S45_L004_R2_001.good.fq | 337,807 | 42,906,478 | 100.0% | 127.0 bases | 135 bases | 93.9% |
| total | 2,692,172 | 342,449,866 | 100.0% | 127.2 bases | 135 bases | 93.8% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | KT2440 | 6,185,276 | 50.0 | 3.3 | 100.0% | tig00000001|arrow. |
| total | 6,185,276 | 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 | 1850 |
| 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 | 87 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.004 |
| reference sequence | pr(no read start) |
|---|---|
| KT2440 | 0.86838 |
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 | ≤ 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 | 22:01:14 01 May 2023 | 22:01:59 01 May 2023 | 45 seconds |
| Read alignment to reference genome | 22:02:00 01 May 2023 | 22:08:01 01 May 2023 | 6 minutes 1 second |
| Preprocessing alignments for candidate junction identification | 22:08:01 01 May 2023 | 22:08:35 01 May 2023 | 34 seconds |
| Preliminary analysis of coverage distribution | 22:08:35 01 May 2023 | 22:10:09 01 May 2023 | 1 minute 34 seconds |
| Identifying junction candidates | 22:10:09 01 May 2023 | 22:10:10 01 May 2023 | 1 second |
| Re-alignment to junction candidates | 22:10:10 01 May 2023 | 22:11:30 01 May 2023 | 1 minute 20 seconds |
| Resolving best read alignments | 22:11:30 01 May 2023 | 22:12:16 01 May 2023 | 46 seconds |
| Creating BAM files | 22:12:16 01 May 2023 | 22:13:42 01 May 2023 | 1 minute 26 seconds |
| Tabulating error counts | 22:13:42 01 May 2023 | 22:14:10 01 May 2023 | 28 seconds |
| Re-calibrating base error rates | 22:14:10 01 May 2023 | 22:14:13 01 May 2023 | 3 seconds |
| Examining read alignment evidence | 22:14:13 01 May 2023 | 22:20:32 01 May 2023 | 6 minutes 19 seconds |
| Polymorphism statistics | 22:20:32 01 May 2023 | 22:20:33 01 May 2023 | 1 second |
| Output | 22:20:33 01 May 2023 | 22:20:59 01 May 2023 | 26 seconds |
| Total | 19 minutes 44 seconds | ||
