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 | SNFM_15_40_1_S213_S1991_L006_R1_001.good.fq | 1,387,416 | 187,138,928 | 100.0% | 134.9 bases | 141 bases | 90.3% |
| errors | SNFM_15_40_1_S213_S1991_L006_R2_001.good.fq | 1,387,416 | 187,138,928 | 100.0% | 134.9 bases | 141 bases | 89.0% |
| errors | SNFM_15_40_1_S213_S1991_L008_R1_001.good.fq | 601,153 | 80,752,576 | 100.0% | 134.3 bases | 141 bases | 90.1% |
| errors | SNFM_15_40_1_S213_S1991_L008_R2_001.good.fq | 601,153 | 80,752,576 | 100.0% | 134.3 bases | 141 bases | 87.8% |
| total | 3,977,138 | 535,783,008 | 100.0% | 134.7 bases | 141 bases | 89.4% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | USA300TCH1516_ALE | 2,872,915 | 154.7 | 2.7 | 93.7% | Staphylococcus species strain strain. |
| coverage | distribution | CP000731 | 27,041 | 486.5 | 6.6 | 2.7% | Staphylococcus aureus subsp. aureus USA300_TCH1516 plasmid |
| coverage | distribution | NC_012417 | 3,125 | 5660.4 | 21.5 | 3.6% | 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 | 100000 |
| 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 | 253 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.025 |
| reference sequence | pr(no read start) |
|---|---|
| USA300TCH1516_ALE | 0.61844 |
| CP000731 | 0.29843 |
| NC_012417 | 0.03111 |
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 | 22:57:06 23 May 2019 | 22:58:00 23 May 2019 | 54 seconds |
| Read alignment to reference genome | 22:58:00 23 May 2019 | 23:07:37 23 May 2019 | 9 minutes 37 seconds |
| Preprocessing alignments for candidate junction identification | 23:07:37 23 May 2019 | 23:08:35 23 May 2019 | 58 seconds |
| Preliminary analysis of coverage distribution | 23:08:35 23 May 2019 | 23:10:21 23 May 2019 | 1 minute 46 seconds |
| Identifying junction candidates | 23:10:21 23 May 2019 | 23:11:46 23 May 2019 | 1 minute 25 seconds |
| Re-alignment to junction candidates | 23:11:46 23 May 2019 | 23:14:36 23 May 2019 | 2 minutes 50 seconds |
| Resolving best read alignments | 23:14:36 23 May 2019 | 23:16:08 23 May 2019 | 1 minute 32 seconds |
| Creating BAM files | 23:16:08 23 May 2019 | 23:17:39 23 May 2019 | 1 minute 31 seconds |
| Tabulating error counts | 23:17:39 23 May 2019 | 23:18:20 23 May 2019 | 41 seconds |
| Re-calibrating base error rates | 23:18:20 23 May 2019 | 23:18:22 23 May 2019 | 2 seconds |
| Examining read alignment evidence | 23:18:22 23 May 2019 | 23:25:54 23 May 2019 | 7 minutes 32 seconds |
| Polymorphism statistics | 23:25:54 23 May 2019 | 23:25:57 23 May 2019 | 3 seconds |
| Output | 23:25:57 23 May 2019 | 23:26:16 23 May 2019 | 19 seconds |
| Total | 29 minutes 10 seconds | ||
