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 | Coumaric-4_S20_L001_R1_001.good.fq | 183,721 | 26,934,194 | 100.0% | 146.6 bases | 149 bases | 93.8% |
| errors | Coumaric-4_S20_L001_R2_001.good.fq | 183,721 | 26,911,066 | 100.0% | 146.5 bases | 149 bases | 93.2% |
| errors | Coumaric-4_S20_L002_R1_001.good.fq | 164,749 | 24,149,606 | 100.0% | 146.6 bases | 149 bases | 93.8% |
| errors | Coumaric-4_S20_L002_R2_001.good.fq | 164,749 | 24,131,564 | 100.0% | 146.5 bases | 149 bases | 92.8% |
| errors | Coumaric-4_S20_L003_R1_001.good.fq | 170,561 | 25,005,777 | 100.0% | 146.6 bases | 149 bases | 93.9% |
| errors | Coumaric-4_S20_L003_R2_001.good.fq | 170,561 | 24,986,008 | 100.0% | 146.5 bases | 149 bases | 93.1% |
| errors | Coumaric-4_S20_L004_R1_001.good.fq | 158,646 | 23,248,666 | 100.0% | 146.5 bases | 149 bases | 93.8% |
| errors | Coumaric-4_S20_L004_R2_001.good.fq | 158,646 | 23,230,031 | 100.0% | 146.4 bases | 149 bases | 92.6% |
| total | 1,355,354 | 198,596,912 | 100.0% | 146.5 bases | 149 bases | 93.4% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_002947 | 6,181,873 | 30.3 | 2.0 | 100.0% | Pseudomonas putida KT2440 chromosome, complete genome. |
| total | 6,181,873 | 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 | 13868 |
| 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 | 824 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.041 |
| reference sequence | pr(no read start) |
|---|---|
| NC_002947 | 0.91039 |
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 | 21:15:47 17 Feb 2020 | 21:16:08 17 Feb 2020 | 21 seconds |
| Read alignment to reference genome | 21:16:09 17 Feb 2020 | 21:19:04 17 Feb 2020 | 2 minutes 55 seconds |
| Preprocessing alignments for candidate junction identification | 21:19:04 17 Feb 2020 | 21:19:23 17 Feb 2020 | 19 seconds |
| Preliminary analysis of coverage distribution | 21:19:23 17 Feb 2020 | 21:20:06 17 Feb 2020 | 43 seconds |
| Identifying junction candidates | 21:20:06 17 Feb 2020 | 21:20:14 17 Feb 2020 | 8 seconds |
| Re-alignment to junction candidates | 21:20:14 17 Feb 2020 | 21:21:15 17 Feb 2020 | 1 minute 1 second |
| Resolving best read alignments | 21:21:15 17 Feb 2020 | 21:21:44 17 Feb 2020 | 29 seconds |
| Creating BAM files | 21:21:44 17 Feb 2020 | 21:22:25 17 Feb 2020 | 41 seconds |
| Tabulating error counts | 21:22:25 17 Feb 2020 | 21:22:39 17 Feb 2020 | 14 seconds |
| Re-calibrating base error rates | 21:22:39 17 Feb 2020 | 21:22:42 17 Feb 2020 | 3 seconds |
| Examining read alignment evidence | 21:22:42 17 Feb 2020 | 21:25:43 17 Feb 2020 | 3 minutes 1 second |
| Polymorphism statistics | 21:25:43 17 Feb 2020 | 21:25:44 17 Feb 2020 | 1 second |
| Output | 21:25:44 17 Feb 2020 | 21:26:05 17 Feb 2020 | 21 seconds |
| Total | 10 minutes 17 seconds | ||
