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-11_S11_L001_R1_001.good.fq | 364,543 | 51,429,169 | 100.0% | 141.1 bases | 149 bases | 93.0% |
| errors | ALE-11_S11_L001_R2_001.good.fq | 364,543 | 51,192,902 | 100.0% | 140.4 bases | 149 bases | 93.7% |
| errors | ALE-11_S11_L002_R1_001.good.fq | 360,280 | 50,715,558 | 100.0% | 140.8 bases | 149 bases | 94.2% |
| errors | ALE-11_S11_L002_R2_001.good.fq | 360,280 | 50,537,010 | 100.0% | 140.3 bases | 149 bases | 94.2% |
| errors | ALE-11_S11_L003_R1_001.good.fq | 372,950 | 52,458,048 | 100.0% | 140.7 bases | 149 bases | 94.1% |
| errors | ALE-11_S11_L003_R2_001.good.fq | 372,950 | 52,247,607 | 100.0% | 140.1 bases | 149 bases | 94.7% |
| errors | ALE-11_S11_L004_R1_001.good.fq | 346,930 | 48,822,709 | 100.0% | 140.7 bases | 149 bases | 94.0% |
| errors | ALE-11_S11_L004_R2_001.good.fq | 346,930 | 48,648,296 | 100.0% | 140.2 bases | 149 bases | 93.8% |
| total | 2,889,406 | 406,051,299 | 100.0% | 140.5 bases | 149 bases | 94.0% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_002947 | 6,181,873 | 59.4 | 2.3 | 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 | 76965 |
| 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 | 702 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.035 |
| reference sequence | pr(no read start) |
|---|---|
| NC_002947 | 0.81932 |
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 | 01:50:53 19 Feb 2020 | 01:51:35 19 Feb 2020 | 42 seconds |
| Read alignment to reference genome | 01:51:36 19 Feb 2020 | 01:57:53 19 Feb 2020 | 6 minutes 17 seconds |
| Preprocessing alignments for candidate junction identification | 01:57:53 19 Feb 2020 | 01:58:34 19 Feb 2020 | 41 seconds |
| Preliminary analysis of coverage distribution | 01:58:34 19 Feb 2020 | 02:00:10 19 Feb 2020 | 1 minute 36 seconds |
| Identifying junction candidates | 02:00:10 19 Feb 2020 | 02:12:05 19 Feb 2020 | 11 minutes 55 seconds |
| Re-alignment to junction candidates | 02:12:05 19 Feb 2020 | 02:14:09 19 Feb 2020 | 2 minutes 4 seconds |
| Resolving best read alignments | 02:14:09 19 Feb 2020 | 02:15:11 19 Feb 2020 | 1 minute 2 seconds |
| Creating BAM files | 02:15:11 19 Feb 2020 | 02:16:40 19 Feb 2020 | 1 minute 29 seconds |
| Tabulating error counts | 02:16:40 19 Feb 2020 | 02:17:09 19 Feb 2020 | 29 seconds |
| Re-calibrating base error rates | 02:17:09 19 Feb 2020 | 02:17:12 19 Feb 2020 | 3 seconds |
| Examining read alignment evidence | 02:17:12 19 Feb 2020 | 02:32:37 19 Feb 2020 | 15 minutes 25 seconds |
| Polymorphism statistics | 02:32:37 19 Feb 2020 | 02:32:40 19 Feb 2020 | 3 seconds |
| Output | 02:32:40 19 Feb 2020 | 02:37:06 19 Feb 2020 | 4 minutes 26 seconds |
| Total | 46 minutes 12 seconds | ||
