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 | 29-31_S29_L001_R1_001_150209.good.fq | 999,399 | 256,477,071 | 100.0% | 256.6 bases | 275 bases | 98.8% |
| errors | 29-31_S29_L001_R1_001_150513.good.fq | 1,040,342 | 273,086,495 | 100.0% | 262.5 bases | 276 bases | 98.6% |
| errors | 29-31_S29_L001_R2_001_150209.good.fq | 999,397 | 256,836,392 | 100.0% | 257.0 bases | 275 bases | 88.9% |
| errors | 29-31_S29_L001_R2_001_150513.good.fq | 1,040,342 | 274,048,086 | 100.0% | 263.4 bases | 276 bases | 74.0% |
| total | 4,079,480 | 1,060,448,044 | 100.0% | 259.9 bases | 276 bases | 90.0% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_000913 | 4,641,652 | 193.0 | 5.2 | 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 | 3373 |
| 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 | 223 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.027 |
| reference sequence | pr(no read start) |
|---|---|
| NC_000913 | 0.79240 |
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 | 2.3.4.1 |
| R | 3.4.4 |
| step | start | end | elapsed |
|---|---|---|---|
| Read and reference sequence file input | 18:04:38 07 Jan 2019 | 18:05:58 07 Jan 2019 | 1 minute 20 seconds |
| Read alignment to reference genome | 18:05:58 07 Jan 2019 | 18:31:34 07 Jan 2019 | 25 minutes 36 seconds |
| Preprocessing alignments for candidate junction identification | 18:31:34 07 Jan 2019 | 18:32:40 07 Jan 2019 | 1 minute 6 seconds |
| Preliminary analysis of coverage distribution | 18:32:40 07 Jan 2019 | 18:36:29 07 Jan 2019 | 3 minutes 49 seconds |
| Identifying junction candidates | 18:36:29 07 Jan 2019 | 18:36:36 07 Jan 2019 | 7 seconds |
| Re-alignment to junction candidates | 18:36:36 07 Jan 2019 | 18:41:31 07 Jan 2019 | 4 minutes 55 seconds |
| Resolving best read alignments | 18:41:31 07 Jan 2019 | 18:43:26 07 Jan 2019 | 1 minute 55 seconds |
| Creating BAM files | 18:43:26 07 Jan 2019 | 18:46:41 07 Jan 2019 | 3 minutes 15 seconds |
| Tabulating error counts | 18:46:41 07 Jan 2019 | 18:48:12 07 Jan 2019 | 1 minute 31 seconds |
| Re-calibrating base error rates | 18:48:12 07 Jan 2019 | 18:48:14 07 Jan 2019 | 2 seconds |
| Examining read alignment evidence | 18:48:14 07 Jan 2019 | 19:04:18 07 Jan 2019 | 16 minutes 4 seconds |
| Polymorphism statistics | 19:04:18 07 Jan 2019 | 19:04:19 07 Jan 2019 | 1 second |
| Output | 19:04:19 07 Jan 2019 | 19:04:41 07 Jan 2019 | 22 seconds |
| Total | 1 hour 3 seconds | ||
