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-76_S76_L001_R1_001.good.fq | 318,359 | 45,771,029 | 100.0% | 143.8 bases | 149 bases | 91.6% |
| errors | ALE-76_S76_L001_R2_001.good.fq | 318,359 | 45,495,632 | 100.0% | 142.9 bases | 149 bases | 92.9% |
| errors | ALE-76_S76_L002_R1_001.good.fq | 305,644 | 43,876,720 | 100.0% | 143.6 bases | 149 bases | 93.3% |
| errors | ALE-76_S76_L002_R2_001.good.fq | 305,644 | 43,641,762 | 100.0% | 142.8 bases | 149 bases | 93.7% |
| errors | ALE-76_S76_L003_R1_001.good.fq | 324,360 | 46,546,685 | 100.0% | 143.5 bases | 149 bases | 93.1% |
| errors | ALE-76_S76_L003_R2_001.good.fq | 324,360 | 46,282,816 | 100.0% | 142.7 bases | 149 bases | 94.1% |
| errors | ALE-76_S76_L004_R1_001.good.fq | 292,862 | 42,008,085 | 100.0% | 143.4 bases | 149 bases | 93.2% |
| errors | ALE-76_S76_L004_R2_001.good.fq | 292,862 | 41,782,586 | 100.0% | 142.7 bases | 149 bases | 93.3% |
| total | 2,482,450 | 355,405,315 | 100.0% | 143.2 bases | 149 bases | 93.2% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_002947 | 6,181,873 | 53.8 | 2.1 | 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 | 62042 |
| 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 | 532 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.026 |
| reference sequence | pr(no read start) |
|---|---|
| NC_002947 | 0.84368 |
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 | 05:35:03 19 Feb 2020 | 05:35:40 19 Feb 2020 | 37 seconds |
| Read alignment to reference genome | 05:35:41 19 Feb 2020 | 05:41:11 19 Feb 2020 | 5 minutes 30 seconds |
| Preprocessing alignments for candidate junction identification | 05:41:11 19 Feb 2020 | 05:41:45 19 Feb 2020 | 34 seconds |
| Preliminary analysis of coverage distribution | 05:41:45 19 Feb 2020 | 05:43:09 19 Feb 2020 | 1 minute 24 seconds |
| Identifying junction candidates | 05:43:09 19 Feb 2020 | 05:51:07 19 Feb 2020 | 7 minutes 58 seconds |
| Re-alignment to junction candidates | 05:51:07 19 Feb 2020 | 05:52:49 19 Feb 2020 | 1 minute 42 seconds |
| Resolving best read alignments | 05:52:49 19 Feb 2020 | 05:53:43 19 Feb 2020 | 54 seconds |
| Creating BAM files | 05:53:43 19 Feb 2020 | 05:55:00 19 Feb 2020 | 1 minute 17 seconds |
| Tabulating error counts | 05:55:00 19 Feb 2020 | 05:55:25 19 Feb 2020 | 25 seconds |
| Re-calibrating base error rates | 05:55:25 19 Feb 2020 | 05:55:28 19 Feb 2020 | 3 seconds |
| Examining read alignment evidence | 05:55:28 19 Feb 2020 | 06:00:29 19 Feb 2020 | 5 minutes 1 second |
| Polymorphism statistics | 06:00:29 19 Feb 2020 | 06:00:30 19 Feb 2020 | 1 second |
| Output | 06:00:30 19 Feb 2020 | 06:01:04 19 Feb 2020 | 34 seconds |
| Total | 26 minutes 0 seconds | ||
