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 | glucose-1_S35_L001_R1_001.good.fq | 189,109 | 27,690,913 | 100.0% | 146.4 bases | 148 bases | 97.6% |
| errors | glucose-1_S35_L001_R2_001.good.fq | 189,109 | 27,675,181 | 100.0% | 146.3 bases | 148 bases | 96.8% |
| errors | glucose-1_S35_L002_R1_001.good.fq | 174,807 | 25,596,639 | 100.0% | 146.4 bases | 148 bases | 97.5% |
| errors | glucose-1_S35_L002_R2_001.good.fq | 174,807 | 25,581,869 | 100.0% | 146.3 bases | 148 bases | 96.4% |
| errors | glucose-1_S35_L003_R1_001.good.fq | 176,551 | 25,851,116 | 100.0% | 146.4 bases | 148 bases | 97.5% |
| errors | glucose-1_S35_L003_R2_001.good.fq | 176,551 | 25,835,428 | 100.0% | 146.3 bases | 148 bases | 96.7% |
| errors | glucose-1_S35_L004_R1_001.good.fq | 164,313 | 24,055,590 | 100.0% | 146.4 bases | 148 bases | 97.5% |
| errors | glucose-1_S35_L004_R2_001.good.fq | 164,313 | 24,041,101 | 100.0% | 146.3 bases | 148 bases | 96.2% |
| total | 1,409,560 | 206,327,837 | 100.0% | 146.4 bases | 148 bases | 97.0% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_002947 | 6,181,873 | 32.4 | 1.7 | 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 | 17735 |
| 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 | 843 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.041 |
| reference sequence | pr(no read start) |
|---|---|
| NC_002947 | 0.90385 |
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 | 11:47:55 18 Feb 2020 | 11:48:17 18 Feb 2020 | 22 seconds |
| Read alignment to reference genome | 11:48:18 18 Feb 2020 | 11:51:23 18 Feb 2020 | 3 minutes 5 seconds |
| Preprocessing alignments for candidate junction identification | 11:51:23 18 Feb 2020 | 11:51:43 18 Feb 2020 | 20 seconds |
| Preliminary analysis of coverage distribution | 11:51:43 18 Feb 2020 | 11:52:31 18 Feb 2020 | 48 seconds |
| Identifying junction candidates | 11:52:31 18 Feb 2020 | 11:52:36 18 Feb 2020 | 5 seconds |
| Re-alignment to junction candidates | 11:52:36 18 Feb 2020 | 11:53:40 18 Feb 2020 | 1 minute 4 seconds |
| Resolving best read alignments | 11:53:40 18 Feb 2020 | 11:54:11 18 Feb 2020 | 31 seconds |
| Creating BAM files | 11:54:11 18 Feb 2020 | 11:54:55 18 Feb 2020 | 44 seconds |
| Tabulating error counts | 11:54:55 18 Feb 2020 | 11:55:10 18 Feb 2020 | 15 seconds |
| Re-calibrating base error rates | 11:55:10 18 Feb 2020 | 11:55:12 18 Feb 2020 | 2 seconds |
| Examining read alignment evidence | 11:55:12 18 Feb 2020 | 11:58:28 18 Feb 2020 | 3 minutes 16 seconds |
| Polymorphism statistics | 11:58:28 18 Feb 2020 | 11:58:29 18 Feb 2020 | 1 second |
| Output | 11:58:29 18 Feb 2020 | 11:58:49 18 Feb 2020 | 20 seconds |
| Total | 10 minutes 53 seconds | ||
