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 | Coumaric-2_S18_L001_R1_001.good.fq | 214,265 | 31,135,283 | 100.0% | 145.3 bases | 148 bases | 97.3% |
| errors | Coumaric-2_S18_L001_R2_001.good.fq | 214,265 | 31,100,393 | 100.0% | 145.1 bases | 148 bases | 96.7% |
| errors | Coumaric-2_S18_L002_R1_001.good.fq | 196,444 | 28,538,196 | 100.0% | 145.3 bases | 148 bases | 97.3% |
| errors | Coumaric-2_S18_L002_R2_001.good.fq | 196,444 | 28,508,944 | 100.0% | 145.1 bases | 148 bases | 96.7% |
| errors | Coumaric-2_S18_L003_R1_001.good.fq | 203,065 | 29,514,827 | 100.0% | 145.3 bases | 148 bases | 97.3% |
| errors | Coumaric-2_S18_L003_R2_001.good.fq | 203,065 | 29,485,721 | 100.0% | 145.2 bases | 148 bases | 96.8% |
| errors | Coumaric-2_S18_L004_R1_001.good.fq | 189,124 | 27,477,501 | 100.0% | 145.3 bases | 148 bases | 97.3% |
| errors | Coumaric-2_S18_L004_R2_001.good.fq | 189,124 | 27,448,530 | 100.0% | 145.1 bases | 148 bases | 96.5% |
| total | 1,605,796 | 233,209,395 | 100.0% | 145.2 bases | 148 bases | 97.0% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_002947 | 6,181,873 | 36.5 | 1.9 | 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 | 16608 |
| Coverage evenness (position-hash) score of junction candidates | ≥ 2 | ≥ 2 |
| Test this many junction candidates (n). May be smaller if not enough passed the coverage evenness threshold | 100 ≤ n ≤ 5000 | 1247 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.061 |
| reference sequence | pr(no read start) |
|---|---|
| NC_002947 | 0.89116 |
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 | 06:49:33 18 Feb 2020 | 06:49:58 18 Feb 2020 | 25 seconds |
| Read alignment to reference genome | 06:49:59 18 Feb 2020 | 06:53:24 18 Feb 2020 | 3 minutes 25 seconds |
| Preprocessing alignments for candidate junction identification | 06:53:24 18 Feb 2020 | 06:53:47 18 Feb 2020 | 23 seconds |
| Preliminary analysis of coverage distribution | 06:53:47 18 Feb 2020 | 06:54:40 18 Feb 2020 | 53 seconds |
| Identifying junction candidates | 06:54:40 18 Feb 2020 | 06:55:03 18 Feb 2020 | 23 seconds |
| Re-alignment to junction candidates | 06:55:03 18 Feb 2020 | 06:56:21 18 Feb 2020 | 1 minute 18 seconds |
| Resolving best read alignments | 06:56:21 18 Feb 2020 | 06:56:57 18 Feb 2020 | 36 seconds |
| Creating BAM files | 06:56:57 18 Feb 2020 | 06:57:45 18 Feb 2020 | 48 seconds |
| Tabulating error counts | 06:57:45 18 Feb 2020 | 06:58:02 18 Feb 2020 | 17 seconds |
| Re-calibrating base error rates | 06:58:02 18 Feb 2020 | 06:58:04 18 Feb 2020 | 2 seconds |
| Examining read alignment evidence | 06:58:04 18 Feb 2020 | 07:01:40 18 Feb 2020 | 3 minutes 36 seconds |
| Polymorphism statistics | 07:01:40 18 Feb 2020 | 07:01:41 18 Feb 2020 | 1 second |
| Output | 07:01:41 18 Feb 2020 | 07:02:08 18 Feb 2020 | 27 seconds |
| Total | 12 minutes 34 seconds | ||
