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 | Plate-1-BOP-1000-ACEF-END-4_S8_L001_R1_001.good.fq | 392,231 | 56,255,787 | 100.0% | 143.4 bases | 149 bases | 98.1% |
| errors | Plate-1-BOP-1000-ACEF-END-4_S8_L001_R2_001.good.fq | 392,231 | 56,084,128 | 100.0% | 143.0 bases | 149 bases | 98.0% |
| errors | Plate-1-BOP-1000-ACEF-END-4_S8_L002_R1_001.good.fq | 363,986 | 52,240,691 | 100.0% | 143.5 bases | 149 bases | 98.2% |
| errors | Plate-1-BOP-1000-ACEF-END-4_S8_L002_R2_001.good.fq | 363,986 | 52,097,322 | 100.0% | 143.1 bases | 149 bases | 97.6% |
| errors | Plate-1-BOP-1000-ACEF-END-4_S8_L003_R1_001.good.fq | 380,461 | 54,561,108 | 100.0% | 143.4 bases | 149 bases | 98.0% |
| errors | Plate-1-BOP-1000-ACEF-END-4_S8_L003_R2_001.good.fq | 380,461 | 54,390,034 | 100.0% | 143.0 bases | 149 bases | 97.8% |
| errors | Plate-1-BOP-1000-ACEF-END-4_S8_L004_R1_001.good.fq | 388,301 | 55,653,554 | 100.0% | 143.3 bases | 149 bases | 98.2% |
| errors | Plate-1-BOP-1000-ACEF-END-4_S8_L004_R2_001.good.fq | 388,301 | 55,501,351 | 100.0% | 142.9 bases | 149 bases | 97.9% |
| total | 3,049,958 | 436,783,975 | 100.0% | 143.2 bases | 149 bases | 98.0% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_000913 | 4,641,652 | 91.0 | 2.9 | 100.0% | Escherichia coli str. K-12 substr. MG1655, complete genome. |
| total | 4,641,652 | 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 | 15458 |
| 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 | 1497 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.098 |
| reference sequence | pr(no read start) |
|---|---|
| NC_000913 | 0.75529 |
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 | 03:27:34 27 Feb 2020 | 03:28:19 27 Feb 2020 | 45 seconds |
| Read alignment to reference genome | 03:28:20 27 Feb 2020 | 03:34:28 27 Feb 2020 | 6 minutes 8 seconds |
| Preprocessing alignments for candidate junction identification | 03:34:28 27 Feb 2020 | 03:35:11 27 Feb 2020 | 43 seconds |
| Preliminary analysis of coverage distribution | 03:35:11 27 Feb 2020 | 03:37:01 27 Feb 2020 | 1 minute 50 seconds |
| Identifying junction candidates | 03:37:01 27 Feb 2020 | 03:37:13 27 Feb 2020 | 12 seconds |
| Re-alignment to junction candidates | 03:37:13 27 Feb 2020 | 03:39:43 27 Feb 2020 | 2 minutes 30 seconds |
| Resolving best read alignments | 03:39:43 27 Feb 2020 | 03:40:50 27 Feb 2020 | 1 minute 7 seconds |
| Creating BAM files | 03:40:50 27 Feb 2020 | 03:42:32 27 Feb 2020 | 1 minute 42 seconds |
| Tabulating error counts | 03:42:32 27 Feb 2020 | 03:43:05 27 Feb 2020 | 33 seconds |
| Re-calibrating base error rates | 03:43:05 27 Feb 2020 | 03:43:08 27 Feb 2020 | 3 seconds |
| Examining read alignment evidence | 03:43:08 27 Feb 2020 | 03:49:32 27 Feb 2020 | 6 minutes 24 seconds |
| Polymorphism statistics | 03:49:32 27 Feb 2020 | 03:49:32 27 Feb 2020 | 0 seconds |
| Output | 03:49:32 27 Feb 2020 | 03:49:52 27 Feb 2020 | 20 seconds |
| Total | 22 minutes 17 seconds | ||
