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-53_S53_L001_R1_001.good.fq | 375,976 | 52,983,070 | 100.0% | 140.9 bases | 149 bases | 93.4% |
| errors | ALE-53_S53_L001_R2_001.good.fq | 375,976 | 52,789,229 | 100.0% | 140.4 bases | 149 bases | 93.8% |
| errors | ALE-53_S53_L002_R1_001.good.fq | 370,983 | 52,176,305 | 100.0% | 140.6 bases | 149 bases | 94.8% |
| errors | ALE-53_S53_L002_R2_001.good.fq | 370,983 | 52,043,927 | 100.0% | 140.3 bases | 149 bases | 94.3% |
| errors | ALE-53_S53_L003_R1_001.good.fq | 384,094 | 53,974,393 | 100.0% | 140.5 bases | 149 bases | 94.7% |
| errors | ALE-53_S53_L003_R2_001.good.fq | 384,094 | 53,793,512 | 100.0% | 140.1 bases | 149 bases | 95.0% |
| errors | ALE-53_S53_L004_R1_001.good.fq | 355,676 | 50,001,284 | 100.0% | 140.6 bases | 149 bases | 94.6% |
| errors | ALE-53_S53_L004_R2_001.good.fq | 355,676 | 49,873,247 | 100.0% | 140.2 bases | 149 bases | 94.0% |
| total | 2,973,458 | 417,634,967 | 100.0% | 140.5 bases | 149 bases | 94.3% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_002947 | 6,181,873 | 63.9 | 2.2 | 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 | 71840 |
| 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 | 756 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.038 |
| reference sequence | pr(no read start) |
|---|---|
| NC_002947 | 0.81337 |
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 | 14:16:33 18 Feb 2020 | 14:17:17 18 Feb 2020 | 44 seconds |
| Read alignment to reference genome | 14:17:17 18 Feb 2020 | 14:23:53 18 Feb 2020 | 6 minutes 36 seconds |
| Preprocessing alignments for candidate junction identification | 14:23:53 18 Feb 2020 | 14:24:35 18 Feb 2020 | 42 seconds |
| Preliminary analysis of coverage distribution | 14:24:35 18 Feb 2020 | 14:26:16 18 Feb 2020 | 1 minute 41 seconds |
| Identifying junction candidates | 14:26:16 18 Feb 2020 | 14:39:02 18 Feb 2020 | 12 minutes 46 seconds |
| Re-alignment to junction candidates | 14:39:02 18 Feb 2020 | 14:41:12 18 Feb 2020 | 2 minutes 10 seconds |
| Resolving best read alignments | 14:41:12 18 Feb 2020 | 14:42:17 18 Feb 2020 | 1 minute 5 seconds |
| Creating BAM files | 14:42:17 18 Feb 2020 | 14:43:50 18 Feb 2020 | 1 minute 33 seconds |
| Tabulating error counts | 14:43:50 18 Feb 2020 | 14:44:20 18 Feb 2020 | 30 seconds |
| Re-calibrating base error rates | 14:44:20 18 Feb 2020 | 14:44:23 18 Feb 2020 | 3 seconds |
| Examining read alignment evidence | 14:44:23 18 Feb 2020 | 14:50:17 18 Feb 2020 | 5 minutes 54 seconds |
| Polymorphism statistics | 14:50:17 18 Feb 2020 | 14:50:18 18 Feb 2020 | 1 second |
| Output | 14:50:18 18 Feb 2020 | 14:51:11 18 Feb 2020 | 53 seconds |
| Total | 34 minutes 38 seconds | ||
