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 | R2_Lane4_BC05_R1.good.fq | 1,847,947 | 140,346,285 | 100.0% | 75.9 bases | 76 bases | 97.9% |
| errors | R2_Lane4_BC05_R2.good.fq | 1,847,947 | 140,346,285 | 100.0% | 75.9 bases | 76 bases | 96.3% |
| total | 3,695,894 | 280,692,570 | 100.0% | 75.9 bases | 76 bases | 97.1% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | REL606 | 4,629,812 | 59.3 | 2.5 | 100.0% | Escherichia coli strain REL606. |
| total | 4,629,812 | 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 | 3880 |
| 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 | 52 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.002 |
| reference sequence | pr(no read start) |
|---|---|
| REL606 | 0.71287 |
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 | 06:25:33 02 Feb 2019 | 06:26:11 02 Feb 2019 | 38 seconds |
| Read alignment to reference genome | 06:26:11 02 Feb 2019 | 06:31:13 02 Feb 2019 | 5 minutes 2 seconds |
| Preprocessing alignments for candidate junction identification | 06:31:13 02 Feb 2019 | 06:31:54 02 Feb 2019 | 41 seconds |
| Preliminary analysis of coverage distribution | 06:31:54 02 Feb 2019 | 06:33:26 02 Feb 2019 | 1 minute 32 seconds |
| Identifying junction candidates | 06:33:26 02 Feb 2019 | 06:33:27 02 Feb 2019 | 1 second |
| Re-alignment to junction candidates | 06:33:27 02 Feb 2019 | 06:34:46 02 Feb 2019 | 1 minute 19 seconds |
| Resolving best read alignments | 06:34:46 02 Feb 2019 | 06:35:51 02 Feb 2019 | 1 minute 5 seconds |
| Creating BAM files | 06:35:51 02 Feb 2019 | 06:37:15 02 Feb 2019 | 1 minute 24 seconds |
| Tabulating error counts | 06:37:15 02 Feb 2019 | 06:37:38 02 Feb 2019 | 23 seconds |
| Re-calibrating base error rates | 06:37:38 02 Feb 2019 | 06:37:39 02 Feb 2019 | 1 second |
| Examining read alignment evidence | 06:37:39 02 Feb 2019 | 06:41:37 02 Feb 2019 | 3 minutes 58 seconds |
| Polymorphism statistics | 06:41:37 02 Feb 2019 | 06:41:37 02 Feb 2019 | 0 seconds |
| Output | 06:41:37 02 Feb 2019 | 06:41:47 02 Feb 2019 | 10 seconds |
| Total | 16 minutes 14 seconds | ||
