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 | ALE-2_S2_L001_R1_001.good.fq | 318,341 | 44,519,839 | 100.0% | 139.8 bases | 149 bases | 94.1% |
| errors | ALE-2_S2_L001_R2_001.good.fq | 318,341 | 44,348,856 | 100.0% | 139.3 bases | 149 bases | 94.6% |
| errors | ALE-2_S2_L002_R1_001.good.fq | 311,132 | 43,418,809 | 100.0% | 139.6 bases | 149 bases | 95.2% |
| errors | ALE-2_S2_L002_R2_001.good.fq | 311,132 | 43,292,756 | 100.0% | 139.1 bases | 149 bases | 95.1% |
| errors | ALE-2_S2_L003_R1_001.good.fq | 327,427 | 45,666,754 | 100.0% | 139.5 bases | 149 bases | 95.2% |
| errors | ALE-2_S2_L003_R2_001.good.fq | 327,427 | 45,505,159 | 100.0% | 139.0 bases | 149 bases | 95.7% |
| errors | ALE-2_S2_L004_R1_001.good.fq | 300,277 | 41,879,010 | 100.0% | 139.5 bases | 149 bases | 95.1% |
| errors | ALE-2_S2_L004_R2_001.good.fq | 300,277 | 41,764,118 | 100.0% | 139.1 bases | 149 bases | 94.8% |
| total | 2,514,354 | 350,395,301 | 100.0% | 139.4 bases | 149 bases | 95.0% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_002947 | 6,181,873 | 53.9 | 2.6 | 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 | 51689 |
| 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 | 536 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.027 |
| reference sequence | pr(no read start) |
|---|---|
| NC_002947 | 0.83782 |
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 | 17:11:35 18 Feb 2020 | 17:12:12 18 Feb 2020 | 37 seconds |
| Read alignment to reference genome | 17:12:13 18 Feb 2020 | 17:17:41 18 Feb 2020 | 5 minutes 28 seconds |
| Preprocessing alignments for candidate junction identification | 17:17:41 18 Feb 2020 | 17:18:16 18 Feb 2020 | 35 seconds |
| Preliminary analysis of coverage distribution | 17:18:16 18 Feb 2020 | 17:19:40 18 Feb 2020 | 1 minute 24 seconds |
| Identifying junction candidates | 17:19:40 18 Feb 2020 | 17:23:29 18 Feb 2020 | 3 minutes 49 seconds |
| Re-alignment to junction candidates | 17:23:29 18 Feb 2020 | 17:25:16 18 Feb 2020 | 1 minute 47 seconds |
| Resolving best read alignments | 17:25:16 18 Feb 2020 | 17:26:10 18 Feb 2020 | 54 seconds |
| Creating BAM files | 17:26:10 18 Feb 2020 | 17:27:28 18 Feb 2020 | 1 minute 18 seconds |
| Tabulating error counts | 17:27:28 18 Feb 2020 | 17:27:54 18 Feb 2020 | 26 seconds |
| Re-calibrating base error rates | 17:27:54 18 Feb 2020 | 17:27:57 18 Feb 2020 | 3 seconds |
| Examining read alignment evidence | 17:27:57 18 Feb 2020 | 17:40:20 18 Feb 2020 | 12 minutes 23 seconds |
| Polymorphism statistics | 17:40:20 18 Feb 2020 | 17:40:22 18 Feb 2020 | 2 seconds |
| Output | 17:40:22 18 Feb 2020 | 17:44:22 18 Feb 2020 | 4 minutes 0 seconds |
| Total | 32 minutes 46 seconds | ||
