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_F85_I1_R1_001.good.fq | 8,862,650 | 1,320,281,569 | 100.0% | 149.0 bases | 149 bases | 96.3% |
| errors | Pputida_sub_A5_F85_I1_R2_001.good.fq | 8,862,650 | 1,320,281,569 | 100.0% | 149.0 bases | 149 bases | 95.9% |
| total | 17,725,300 | 2,640,563,138 | 100.0% | 149.0 bases | 149 bases | 96.1% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_002947 | 6,186,878 | 413.5 | 7.5 | 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 | 100000 |
| Coverage evenness (position-hash) score of junction candidates | ≥ 2 | ≥ 4 |
| Test this many junction candidates (n). May be smaller if not enough passed the coverage evenness threshold | 100 ≤ n ≤ 5000 | 635 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.031 |
| reference sequence | pr(no read start) |
|---|---|
| NC_002947 | 0.38651 |
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 | 08:33:42 05 Mar 2021 | 08:38:51 05 Mar 2021 | 5 minutes 9 seconds |
| Read alignment to reference genome | 08:38:52 05 Mar 2021 | 09:22:33 05 Mar 2021 | 43 minutes 41 seconds |
| Preprocessing alignments for candidate junction identification | 09:22:33 05 Mar 2021 | 09:26:51 05 Mar 2021 | 4 minutes 18 seconds |
| Preliminary analysis of coverage distribution | 09:26:51 05 Mar 2021 | 09:35:31 05 Mar 2021 | 8 minutes 40 seconds |
| Identifying junction candidates | 09:35:31 05 Mar 2021 | 09:37:01 05 Mar 2021 | 1 minute 30 seconds |
| Re-alignment to junction candidates | 09:37:01 05 Mar 2021 | 09:48:53 05 Mar 2021 | 11 minutes 52 seconds |
| Resolving best read alignments | 09:48:53 05 Mar 2021 | 09:54:43 05 Mar 2021 | 5 minutes 50 seconds |
| Creating BAM files | 09:54:43 05 Mar 2021 | 10:02:41 05 Mar 2021 | 7 minutes 58 seconds |
| Tabulating error counts | 10:02:41 05 Mar 2021 | 10:06:26 05 Mar 2021 | 3 minutes 45 seconds |
| Re-calibrating base error rates | 10:06:26 05 Mar 2021 | 10:06:28 05 Mar 2021 | 2 seconds |
| Examining read alignment evidence | 10:06:28 05 Mar 2021 | 10:51:55 05 Mar 2021 | 45 minutes 27 seconds |
| Polymorphism statistics | 10:51:55 05 Mar 2021 | 10:52:14 05 Mar 2021 | 19 seconds |
| Output | 10:52:14 05 Mar 2021 | 10:53:12 05 Mar 2021 | 58 seconds |
| Total | 2 hours 19 minutes 29 seconds | ||
