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 | C13-Redo-Population-6-23_S15_L001_R1_001.good.fq | 1,371,085 | 347,897,161 | 100.0% | 253.7 bases | 281 bases | 98.6% |
| errors | C13-Redo-Population-6-23_S15_L001_R2_001.good.fq | 1,371,085 | 349,664,454 | 100.0% | 255.0 bases | 281 bases | 90.3% |
| total | 2,742,170 | 697,561,615 | 100.0% | 254.4 bases | 281 bases | 94.4% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_000913 | 4,641,652 | 136.8 | 10.4 | 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 | 3433 |
| 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 | 396 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.048 |
| reference sequence | pr(no read start) |
|---|---|
| NC_000913 | 0.83156 |
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 | 07:50:13 16 May 2019 | 07:50:56 16 May 2019 | 43 seconds |
| Read alignment to reference genome | 07:50:56 16 May 2019 | 08:05:58 16 May 2019 | 15 minutes 2 seconds |
| Preprocessing alignments for candidate junction identification | 08:05:58 16 May 2019 | 08:06:42 16 May 2019 | 44 seconds |
| Preliminary analysis of coverage distribution | 08:06:42 16 May 2019 | 08:09:24 16 May 2019 | 2 minutes 42 seconds |
| Identifying junction candidates | 08:09:24 16 May 2019 | 08:09:27 16 May 2019 | 3 seconds |
| Re-alignment to junction candidates | 08:09:27 16 May 2019 | 08:13:07 16 May 2019 | 3 minutes 40 seconds |
| Resolving best read alignments | 08:13:07 16 May 2019 | 08:14:27 16 May 2019 | 1 minute 20 seconds |
| Creating BAM files | 08:14:27 16 May 2019 | 08:16:50 16 May 2019 | 2 minutes 23 seconds |
| Tabulating error counts | 08:16:50 16 May 2019 | 08:17:52 16 May 2019 | 1 minute 2 seconds |
| Re-calibrating base error rates | 08:17:52 16 May 2019 | 08:17:53 16 May 2019 | 1 second |
| Examining read alignment evidence | 08:17:53 16 May 2019 | 09:36:13 16 May 2019 | 1 hour 18 minutes 20 seconds |
| Polymorphism statistics | 09:36:13 16 May 2019 | 09:36:14 16 May 2019 | 1 second |
| Output | 09:36:14 16 May 2019 | 09:36:30 16 May 2019 | 16 seconds |
| Total | 1 hour 46 minutes 17 seconds | ||
