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 | SNFR_15_116_0_S2363_L001_R1_001.good.fq | 281,112 | 39,607,740 | 100.0% | 140.9 bases | 141 bases | 98.8% |
| errors | SNFR_15_116_0_S2363_L001_R2_001.good.fq | 281,112 | 39,607,740 | 100.0% | 140.9 bases | 141 bases | 91.5% |
| total | 562,224 | 79,215,480 | 100.0% | 140.9 bases | 141 bases | 95.1% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | USA300TCH1516_ALE | 2,872,915 | 26.1 | 1.6 | 100.0% | Staphylococcus species strain strain. |
| coverage | distribution | CP000731 | 27,041 | NA | NA | 0.0% | Staphylococcus aureus subsp. aureus USA300_TCH1516 plasmid |
| coverage | distribution | NC_012417 | 3,125 | NA | NA | 0.0% | 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.
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 | 1064 |
| 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 | 18 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.002 |
| reference sequence | pr(no read start) |
|---|---|
| USA300TCH1516_ALE | 0.92129 |
| CP000731 | NA |
| NC_012417 | NA |
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 | 18:12:44 25 May 2019 | 18:12:53 25 May 2019 | 9 seconds |
| Read alignment to reference genome | 18:12:53 25 May 2019 | 18:14:18 25 May 2019 | 1 minute 25 seconds |
| Preprocessing alignments for candidate junction identification | 18:14:18 25 May 2019 | 18:14:25 25 May 2019 | 7 seconds |
| Preliminary analysis of coverage distribution | 18:14:25 25 May 2019 | 18:14:43 25 May 2019 | 18 seconds |
| Identifying junction candidates | 18:14:43 25 May 2019 | 18:14:43 25 May 2019 | 0 seconds |
| Re-alignment to junction candidates | 18:14:43 25 May 2019 | 18:15:00 25 May 2019 | 17 seconds |
| Resolving best read alignments | 18:15:00 25 May 2019 | 18:15:10 25 May 2019 | 10 seconds |
| Creating BAM files | 18:15:10 25 May 2019 | 18:15:26 25 May 2019 | 16 seconds |
| Tabulating error counts | 18:15:26 25 May 2019 | 18:15:32 25 May 2019 | 6 seconds |
| Re-calibrating base error rates | 18:15:32 25 May 2019 | 18:15:33 25 May 2019 | 1 second |
| Examining read alignment evidence | 18:15:33 25 May 2019 | 18:19:40 25 May 2019 | 4 minutes 7 seconds |
| Polymorphism statistics | 18:19:40 25 May 2019 | 18:19:41 25 May 2019 | 1 second |
| Output | 18:19:41 25 May 2019 | 18:19:44 25 May 2019 | 3 seconds |
| Total | 7 minutes 0 seconds | ||
