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 | PAL28_S28_L007_R1_001.good.fq | 5,657,745 | 514,607,319 | 100.0% | 91.0 bases | 91 bases | 98.4% |
| errors | PAL28_S28_L007_R2_001.good.fq | 5,657,745 | 514,607,319 | 100.0% | 91.0 bases | 91 bases | 97.4% |
| total | 11,315,490 | 1,029,214,638 | 100.0% | 91.0 bases | 91 bases | 97.9% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | USA300TCH1516_ALE | 2,872,915 | 326.9 | 4.1 | 93.9% | Staphylococcus species strain strain. |
| coverage | distribution | CP000731 | 27,041 | 1309.7 | 10.0 | 3.4% | Staphylococcus aureus subsp. aureus USA300_TCH1516 plasmid |
| coverage | distribution | NC_012417 | 3,125 | 10155.8 | 73.9 | 2.7% | Staphylococcus aureus subsp. aureus USA300_TCH1516 plasmid |
| total | 2,903,081 | 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 | 64473 |
| Coverage evenness (position-hash) score of junction candidates | ≥ 2 | ≥ 4 |
| Test this many junction candidates (n). May be smaller if not enough passed the coverage evenness threshold | 100 ≤ n ≤ 5000 | 598 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.039 |
| reference sequence | pr(no read start) |
|---|---|
| USA300TCH1516_ALE | 0.28092 |
| CP000731 | 0.04415 |
| NC_012417 | 0.03140 |
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 | 11:51:31 23 May 2019 | 11:53:41 23 May 2019 | 2 minutes 10 seconds |
| Read alignment to reference genome | 11:53:41 23 May 2019 | 12:08:23 23 May 2019 | 14 minutes 42 seconds |
| Preprocessing alignments for candidate junction identification | 12:08:23 23 May 2019 | 12:10:29 23 May 2019 | 2 minutes 6 seconds |
| Preliminary analysis of coverage distribution | 12:10:29 23 May 2019 | 12:14:11 23 May 2019 | 3 minutes 42 seconds |
| Identifying junction candidates | 12:14:11 23 May 2019 | 12:15:09 23 May 2019 | 58 seconds |
| Re-alignment to junction candidates | 12:15:09 23 May 2019 | 12:19:56 23 May 2019 | 4 minutes 47 seconds |
| Resolving best read alignments | 12:19:56 23 May 2019 | 12:23:40 23 May 2019 | 3 minutes 44 seconds |
| Creating BAM files | 12:23:40 23 May 2019 | 12:27:02 23 May 2019 | 3 minutes 22 seconds |
| Tabulating error counts | 12:27:02 23 May 2019 | 12:28:34 23 May 2019 | 1 minute 32 seconds |
| Re-calibrating base error rates | 12:28:34 23 May 2019 | 12:28:37 23 May 2019 | 3 seconds |
| Examining read alignment evidence | 12:28:37 23 May 2019 | 13:52:07 23 May 2019 | 1 hour 23 minutes 30 seconds |
| Polymorphism statistics | 13:52:07 23 May 2019 | 13:52:09 23 May 2019 | 2 seconds |
| Output | 13:52:09 23 May 2019 | 13:52:58 23 May 2019 | 49 seconds |
| Total | 2 hours 1 minute 27 seconds | ||
