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 | TF_KALE_argR_A6_F60_I3_R1_S41_L001_R1_001.good.fq | 249,232 | 32,144,090 | 100.0% | 129.0 bases | 137 bases | 97.7% |
| errors | TF_KALE_argR_A6_F60_I3_R1_S41_L001_R2_001.good.fq | 249,232 | 32,145,711 | 100.0% | 129.0 bases | 137 bases | 95.8% |
| errors | TF_KALE_argR_A6_F60_I3_R1_S41_L002_R1_001.good.fq | 248,323 | 32,043,903 | 100.0% | 129.0 bases | 137 bases | 98.4% |
| errors | TF_KALE_argR_A6_F60_I3_R1_S41_L002_R2_001.good.fq | 248,323 | 32,045,390 | 100.0% | 129.0 bases | 137 bases | 97.1% |
| errors | TF_KALE_argR_A6_F60_I3_R1_S41_L003_R1_001.good.fq | 248,089 | 31,983,932 | 100.0% | 128.9 bases | 137 bases | 98.4% |
| errors | TF_KALE_argR_A6_F60_I3_R1_S41_L003_R2_001.good.fq | 248,089 | 31,984,765 | 100.0% | 128.9 bases | 137 bases | 97.3% |
| errors | TF_KALE_argR_A6_F60_I3_R1_S41_L004_R1_001.good.fq | 254,187 | 32,719,807 | 100.0% | 128.7 bases | 137 bases | 98.7% |
| errors | TF_KALE_argR_A6_F60_I3_R1_S41_L004_R2_001.good.fq | 254,187 | 32,721,632 | 100.0% | 128.7 bases | 137 bases | 97.9% |
| total | 1,999,662 | 257,789,230 | 100.0% | 128.9 bases | 137 bases | 97.6% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_000913 | 4,641,652 | 52.9 | 3.3 | 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 | 1246 |
| 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 | 98 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.006 |
| reference sequence | pr(no read start) |
|---|---|
| NC_000913 | 0.86699 |
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 | 21:17:49 22 Apr 2021 | 21:18:23 22 Apr 2021 | 34 seconds |
| Read alignment to reference genome | 21:18:23 22 Apr 2021 | 21:22:28 22 Apr 2021 | 4 minutes 5 seconds |
| Preprocessing alignments for candidate junction identification | 21:22:28 22 Apr 2021 | 21:22:51 22 Apr 2021 | 23 seconds |
| Preliminary analysis of coverage distribution | 21:22:51 22 Apr 2021 | 21:23:59 22 Apr 2021 | 1 minute 8 seconds |
| Identifying junction candidates | 21:23:59 22 Apr 2021 | 21:23:59 22 Apr 2021 | 0 seconds |
| Re-alignment to junction candidates | 21:23:59 22 Apr 2021 | 21:24:58 22 Apr 2021 | 59 seconds |
| Resolving best read alignments | 21:24:58 22 Apr 2021 | 21:25:31 22 Apr 2021 | 33 seconds |
| Creating BAM files | 21:25:31 22 Apr 2021 | 21:26:35 22 Apr 2021 | 1 minute 4 seconds |
| Tabulating error counts | 21:26:35 22 Apr 2021 | 21:26:58 22 Apr 2021 | 23 seconds |
| Re-calibrating base error rates | 21:26:58 22 Apr 2021 | 21:27:01 22 Apr 2021 | 3 seconds |
| Examining read alignment evidence | 21:27:01 22 Apr 2021 | 21:31:49 22 Apr 2021 | 4 minutes 48 seconds |
| Polymorphism statistics | 21:31:49 22 Apr 2021 | 21:31:50 22 Apr 2021 | 1 second |
| Output | 21:31:50 22 Apr 2021 | 21:31:57 22 Apr 2021 | 7 seconds |
| Total | 14 minutes 8 seconds | ||
