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 | Glu_KHP_A8_F380_I3_R1_S32_L008_R1_001.good.fq | 3,967,315 | 392,764,185 | 100.0% | 99.0 bases | 99 bases | 93.5% |
| errors | Glu_KHP_A8_F380_I3_R1_S32_L008_R2_001.good.fq | 3,850,383 | 381,187,917 | 100.0% | 99.0 bases | 99 bases | 88.5% |
| total | 7,817,698 | 773,952,102 | 100.0% | 99.0 bases | 99 bases | 91.1% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_000913 | 4,641,652 | 150.7 | 2.0 | 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 | 100027 |
| 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 | 1789 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.079 |
| reference sequence | pr(no read start) |
|---|---|
| NC_000913 | 0.54408 |
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 | 08:55:11 23 May 2019 | 08:56:33 23 May 2019 | 1 minute 22 seconds |
| Read alignment to reference genome | 08:56:33 23 May 2019 | 09:10:58 23 May 2019 | 14 minutes 25 seconds |
| Preprocessing alignments for candidate junction identification | 09:10:58 23 May 2019 | 09:12:34 23 May 2019 | 1 minute 36 seconds |
| Preliminary analysis of coverage distribution | 09:12:34 23 May 2019 | 09:15:38 23 May 2019 | 3 minutes 4 seconds |
| Identifying junction candidates | 09:15:38 23 May 2019 | 09:27:55 23 May 2019 | 12 minutes 17 seconds |
| Re-alignment to junction candidates | 09:27:55 23 May 2019 | 09:32:47 23 May 2019 | 4 minutes 52 seconds |
| Resolving best read alignments | 09:32:47 23 May 2019 | 09:35:14 23 May 2019 | 2 minutes 27 seconds |
| Creating BAM files | 09:35:14 23 May 2019 | 09:38:01 23 May 2019 | 2 minutes 47 seconds |
| Tabulating error counts | 09:38:01 23 May 2019 | 09:39:03 23 May 2019 | 1 minute 2 seconds |
| Re-calibrating base error rates | 09:39:03 23 May 2019 | 09:39:04 23 May 2019 | 1 second |
| Examining read alignment evidence | 09:39:04 23 May 2019 | 09:49:53 23 May 2019 | 10 minutes 49 seconds |
| Polymorphism statistics | 09:49:53 23 May 2019 | 09:49:56 23 May 2019 | 3 seconds |
| Output | 09:49:56 23 May 2019 | 09:51:12 23 May 2019 | 1 minute 16 seconds |
| Total | 56 minutes 1 second | ||
