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 | 30-END_S11_L001_R1_001_150407.good.fq | 211,462 | 40,137,093 | 100.0% | 189.8 bases | 275 bases | 97.0% |
| errors | 30-END_S11_L001_R1_001_150520.good.fq | 753,083 | 153,739,643 | 100.0% | 204.1 bases | 275 bases | 98.7% |
| errors | 30-END_S11_L001_R2_001_150407.good.fq | 211,462 | 42,003,100 | 100.0% | 198.6 bases | 275 bases | 63.7% |
| errors | 30-END_S11_L001_R2_001_150520.good.fq | 753,083 | 154,865,105 | 100.0% | 205.6 bases | 275 bases | 89.8% |
| errors | GLY_30_033_S332_L001_R1_001.good.fq | 1,105,423 | 156,478,389 | 100.0% | 141.6 bases | 149 bases | 98.5% |
| errors | GLY_30_033_S332_L001_R2_001.good.fq | 1,105,423 | 156,478,389 | 100.0% | 141.6 bases | 149 bases | 97.7% |
| errors | GLY_30_033_S332_L002_R1_001.good.fq | 1,081,049 | 152,669,416 | 100.0% | 141.2 bases | 149 bases | 98.4% |
| errors | GLY_30_033_S332_L002_R2_001.good.fq | 1,081,049 | 152,669,416 | 100.0% | 141.2 bases | 149 bases | 97.7% |
| total | 6,302,034 | 1,009,040,551 | 100.0% | 160.1 bases | 275 bases | 96.0% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_000913 | 4,641,652 | 191.4 | 4.1 | 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 | 20260 |
| 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 | 120 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.014 |
| reference sequence | pr(no read start) |
|---|---|
| NC_000913 | 0.60280 |
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 | 18:15:53 02 Jan 2019 | 18:17:29 02 Jan 2019 | 1 minute 36 seconds |
| Read alignment to reference genome | 18:17:29 02 Jan 2019 | 18:34:32 02 Jan 2019 | 17 minutes 3 seconds |
| Preprocessing alignments for candidate junction identification | 18:34:32 02 Jan 2019 | 18:35:54 02 Jan 2019 | 1 minute 22 seconds |
| Preliminary analysis of coverage distribution | 18:35:54 02 Jan 2019 | 18:40:17 02 Jan 2019 | 4 minutes 23 seconds |
| Identifying junction candidates | 18:40:17 02 Jan 2019 | 18:42:11 02 Jan 2019 | 1 minute 54 seconds |
| Re-alignment to junction candidates | 18:42:11 02 Jan 2019 | 18:46:51 02 Jan 2019 | 4 minutes 40 seconds |
| Resolving best read alignments | 18:46:51 02 Jan 2019 | 18:49:13 02 Jan 2019 | 2 minutes 22 seconds |
| Creating BAM files | 18:49:13 02 Jan 2019 | 18:53:08 02 Jan 2019 | 3 minutes 55 seconds |
| Tabulating error counts | 18:53:08 02 Jan 2019 | 18:54:35 02 Jan 2019 | 1 minute 27 seconds |
| Re-calibrating base error rates | 18:54:35 02 Jan 2019 | 18:54:37 02 Jan 2019 | 2 seconds |
| Examining read alignment evidence | 18:54:37 02 Jan 2019 | 20:27:10 02 Jan 2019 | 1 hour 32 minutes 33 seconds |
| Polymorphism statistics | 20:27:10 02 Jan 2019 | 20:27:12 02 Jan 2019 | 2 seconds |
| Output | 20:27:12 02 Jan 2019 | 20:27:55 02 Jan 2019 | 43 seconds |
| Total | 2 hours 12 minutes 2 seconds | ||
