mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.35.4
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| read file | reads | bases | passed filters | average | longest | mapped | |
|---|---|---|---|---|---|---|---|
| errors | ATCC_S10_L001_R1_001 | 902,159 | 194,754,060 | 99.9% | 215.9 bases | 251 bases | 93.8% |
| total | 902,159 | 194,754,060 | 99.9% | 215.9 bases | 251 bases | 93.8% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | 6 | 31,282 | 120.8 | 3.8 | 2.0% | Aggregatibacter actinomycetemcomitans |
| coverage | distribution | 11 | 1,225 | NA | NA | 0.1% | Aggregatibacter actinomycetemcomitans |
| coverage | distribution | 3 | 104,543 | 103.4 | 4.4 | 5.6% | Aggregatibacter actinomycetemcomitans |
| coverage | distribution | 7 | 2,132 | NA | NA | 0.1% | Aggregatibacter actinomycetemcomitans |
| coverage | distribution | 9 | 1,416 | 100.0 | 2.1 | 0.1% | Aggregatibacter actinomycetemcomitans |
| coverage | distribution | 2 | 176,511 | 114.7 | 5.1 | 9.9% | Aggregatibacter actinomycetemcomitans |
| coverage | distribution | 12 | 486 | 125.1 | 1.0 | 0.0% | Aggregatibacter actinomycetemcomitans |
| coverage | distribution | 15 | 136 | 82.4 | 1.0 | 0.0% | Aggregatibacter actinomycetemcomitans |
| coverage | distribution | 14 | 192 | NA | NA | 0.0% | Aggregatibacter actinomycetemcomitans |
| coverage | distribution | 8 | 1,637 | NA | NA | 0.1% | Aggregatibacter actinomycetemcomitans |
| coverage | distribution | 4 | 47,299 | 104.1 | 3.1 | 2.6% | Aggregatibacter actinomycetemcomitans |
| coverage | distribution | 1 | 1,696,285 | 87.0 | 5.1 | 77.3% | Aggregatibacter actinomycetemcomitans |
| coverage | distribution | 10 | 1,369 | NA | NA | 0.1% | Aggregatibacter actinomycetemcomitans |
| coverage | distribution | 13 | 414 | NA | NA | 0.0% | Aggregatibacter actinomycetemcomitans |
| coverage | distribution | 16 | 105 | NA | NA | 0.0% | Aggregatibacter actinomycetemcomitans |
| coverage | distribution | 5 | 38,025 | 113.1 | 3.4 | 2.1% | Aggregatibacter actinomycetemcomitans |
| total | 2,103,057 | 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.
Insufficient coverage Reference sequence counted as entirely deleted due to low coverage. Try either the -t,--targeted-sequencing or the -c,--contig-reference option if you want mutations called for these reference sequences.
| option | limit | actual |
|---|---|---|
| Number of alignment pairs examined for constructing junction candidates | ≤ 100000 | 16773 |
| 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 | 400 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.097 |
| reference sequence | pr(no read start) |
|---|---|
| 6 | 0.82563 |
| 11 | NA |
| 3 | 0.84757 |
| 7 | NA |
| 9 | 0.83529 |
| 2 | 0.84588 |
| 12 | 0.89095 |
| 15 | 0.98897 |
| 14 | NA |
| 8 | NA |
| 4 | 0.84778 |
| 1 | 0.86762 |
| 10 | NA |
| 13 | NA |
| 16 | NA |
| 5 | 0.84494 |
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 |
| Minimum probablilty assigned that no mapped read will start at a given position and strand for junction prediction | 0.1 |
| Junction allow suboptimal matches | FALSE |
| 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 | 0.8 |
| 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 | 2.4.1 |
| R | 4.0.0 |
| step | start | end | elapsed |
|---|---|---|---|
| Read and reference sequence file input | 10:19:21 07 Feb 2022 | 10:19:41 07 Feb 2022 | 20 seconds |
| Read alignment to reference genome | 10:19:41 07 Feb 2022 | 10:20:40 07 Feb 2022 | 59 seconds |
| Preprocessing alignments for candidate junction identification | 10:20:40 07 Feb 2022 | 10:20:58 07 Feb 2022 | 18 seconds |
| Preliminary analysis of coverage distribution | 10:20:58 07 Feb 2022 | 10:21:53 07 Feb 2022 | 55 seconds |
| Identifying junction candidates | 10:21:53 07 Feb 2022 | 10:22:43 07 Feb 2022 | 50 seconds |
| Re-alignment to junction candidates | 10:22:43 07 Feb 2022 | 10:23:09 07 Feb 2022 | 26 seconds |
| Resolving best read alignments | 10:23:09 07 Feb 2022 | 10:23:37 07 Feb 2022 | 28 seconds |
| Creating BAM files | 10:23:37 07 Feb 2022 | 10:24:18 07 Feb 2022 | 41 seconds |
| Tabulating error counts | 10:24:18 07 Feb 2022 | 10:24:37 07 Feb 2022 | 19 seconds |
| Re-calibrating base error rates | 10:24:37 07 Feb 2022 | 10:24:49 07 Feb 2022 | 12 seconds |
| Examining read alignment evidence | 10:24:49 07 Feb 2022 | 10:28:38 07 Feb 2022 | 3 minutes 49 seconds |
| Polymorphism statistics | 10:28:38 07 Feb 2022 | 10:28:40 07 Feb 2022 | 2 seconds |
| Output | 10:28:40 07 Feb 2022 | 10:31:11 07 Feb 2022 | 2 minutes 31 seconds |
| Total | 11 minutes 50 seconds | ||
