mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.35.4 revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| read file | reads | bases | passed filters | average | longest | mapped | |
|---|---|---|---|---|---|---|---|
| errors | Pputida_sub_A5_F21_I1_R1_001.good.fq | 5,221,552 | 771,636,753 | 100.0% | 147.8 bases | 150 bases | 96.2% |
| errors | Pputida_sub_A5_F21_I1_R2_001.good.fq | 5,221,552 | 771,636,753 | 100.0% | 147.8 bases | 150 bases | 95.6% |
| total | 10,443,104 | 1,543,273,506 | 100.0% | 147.8 bases | 150 bases | 95.9% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_002947 | 6,186,878 | 233.2 | 4.7 | 100.0% | Pseudomonas putida KT2440 chromosome, complete genome. |
| total | 6,186,878 | 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 | 100011 |
| 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 | 763 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.038 |
| reference sequence | pr(no read start) |
|---|---|
| NC_002947 | 0.57406 |
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 |
| Minimum probablilty assigned that no mapped read will start at a given position and strand for junction prediction | 0.1 |
| Junction allow suboptimal matches | FALSE |
| 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 | 2.2.6 |
| R | 3.4.4 |
| step | start | end | elapsed |
|---|---|---|---|
| Read and reference sequence file input | 05:20:20 03 Feb 2021 | 05:30:06 03 Feb 2021 | 9 minutes 46 seconds |
| Read alignment to reference genome | 05:30:07 03 Feb 2021 | 06:50:55 03 Feb 2021 | 1 hour 20 minutes 48 seconds |
| Preprocessing alignments for candidate junction identification | 06:50:55 03 Feb 2021 | 07:00:17 03 Feb 2021 | 9 minutes 22 seconds |
| Preliminary analysis of coverage distribution | 07:00:17 03 Feb 2021 | 07:16:58 03 Feb 2021 | 16 minutes 41 seconds |
| Identifying junction candidates | 07:16:58 03 Feb 2021 | 07:30:02 03 Feb 2021 | 13 minutes 4 seconds |
| Re-alignment to junction candidates | 07:30:02 03 Feb 2021 | 07:51:36 03 Feb 2021 | 21 minutes 34 seconds |
| Resolving best read alignments | 07:51:36 03 Feb 2021 | 08:04:08 03 Feb 2021 | 12 minutes 32 seconds |
| Creating BAM files | 08:04:08 03 Feb 2021 | 08:19:04 03 Feb 2021 | 14 minutes 56 seconds |
| Tabulating error counts | 08:19:04 03 Feb 2021 | 08:26:19 03 Feb 2021 | 7 minutes 15 seconds |
| Re-calibrating base error rates | 08:26:19 03 Feb 2021 | 08:26:22 03 Feb 2021 | 3 seconds |
| Examining read alignment evidence | 08:26:22 03 Feb 2021 | 09:50:55 03 Feb 2021 | 1 hour 24 minutes 33 seconds |
| Polymorphism statistics | 09:50:55 03 Feb 2021 | 09:51:13 03 Feb 2021 | 18 seconds |
| Output | 09:51:13 03 Feb 2021 | 09:53:09 03 Feb 2021 | 1 minute 56 seconds |
| Total | 4 hours 32 minutes 48 seconds | ||
