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_3_121_1_S172_S2002_L006_R1_001.good.fq | 1,047,182 | 146,394,178 | 100.0% | 139.8 bases | 141 bases | 97.1% |
| errors | SNFR_3_121_1_S172_S2002_L006_R2_001.good.fq | 1,047,182 | 146,394,178 | 100.0% | 139.8 bases | 141 bases | 95.6% |
| errors | SNFR_3_121_1_S172_S2002_L008_R1_001.good.fq | 452,036 | 63,134,714 | 100.0% | 139.7 bases | 141 bases | 97.1% |
| errors | SNFR_3_121_1_S172_S2002_L008_R2_001.good.fq | 452,036 | 63,134,714 | 100.0% | 139.7 bases | 141 bases | 94.1% |
| total | 2,998,436 | 419,057,784 | 100.0% | 139.8 bases | 141 bases | 96.1% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | USA300TCH1516_ALE | 2,872,915 | 130.3 | 2.8 | 93.2% | Staphylococcus species strain strain. |
| coverage | distribution | CP000731 | 27,041 | 502.2 | 5.5 | 3.4% | Staphylococcus aureus subsp. aureus USA300_TCH1516 plasmid |
| coverage | distribution | NC_012417 | 3,125 | 4547.4 | 19.0 | 3.4% | 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 | 60636 |
| 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 | 299 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.030 |
| reference sequence | pr(no read start) |
|---|---|
| USA300TCH1516_ALE | 0.67389 |
| CP000731 | 0.30245 |
| NC_012417 | 0.04366 |
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 | 12:35:25 25 May 2019 | 12:36:05 25 May 2019 | 40 seconds |
| Read alignment to reference genome | 12:36:06 25 May 2019 | 12:43:00 25 May 2019 | 6 minutes 54 seconds |
| Preprocessing alignments for candidate junction identification | 12:43:00 25 May 2019 | 12:43:41 25 May 2019 | 41 seconds |
| Preliminary analysis of coverage distribution | 12:43:41 25 May 2019 | 12:45:07 25 May 2019 | 1 minute 26 seconds |
| Identifying junction candidates | 12:45:07 25 May 2019 | 12:46:14 25 May 2019 | 1 minute 7 seconds |
| Re-alignment to junction candidates | 12:46:14 25 May 2019 | 12:48:25 25 May 2019 | 2 minutes 11 seconds |
| Resolving best read alignments | 12:48:25 25 May 2019 | 12:49:31 25 May 2019 | 1 minute 6 seconds |
| Creating BAM files | 12:49:31 25 May 2019 | 12:50:47 25 May 2019 | 1 minute 16 seconds |
| Tabulating error counts | 12:50:47 25 May 2019 | 12:51:20 25 May 2019 | 33 seconds |
| Re-calibrating base error rates | 12:51:20 25 May 2019 | 12:51:22 25 May 2019 | 2 seconds |
| Examining read alignment evidence | 12:51:22 25 May 2019 | 12:57:36 25 May 2019 | 6 minutes 14 seconds |
| Polymorphism statistics | 12:57:36 25 May 2019 | 12:57:36 25 May 2019 | 0 seconds |
| Output | 12:57:36 25 May 2019 | 12:57:51 25 May 2019 | 15 seconds |
| Total | 22 minutes 25 seconds | ||
