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-3_S7_L001_R1_001.good.fq | 450,606 | 64,932,376 | 100.0% | 144.1 bases | 149 bases | 98.8% |
| errors | Plate-1-BOP-1000-ACEF-END-3_S7_L001_R2_001.good.fq | 450,606 | 64,832,446 | 100.0% | 143.9 bases | 149 bases | 98.3% |
| errors | Plate-1-BOP-1000-ACEF-END-3_S7_L002_R1_001.good.fq | 419,652 | 60,498,548 | 100.0% | 144.2 bases | 149 bases | 98.8% |
| errors | Plate-1-BOP-1000-ACEF-END-3_S7_L002_R2_001.good.fq | 419,652 | 60,419,744 | 100.0% | 144.0 bases | 149 bases | 97.9% |
| errors | Plate-1-BOP-1000-ACEF-END-3_S7_L003_R1_001.good.fq | 438,427 | 63,167,066 | 100.0% | 144.1 bases | 149 bases | 98.7% |
| errors | Plate-1-BOP-1000-ACEF-END-3_S7_L003_R2_001.good.fq | 438,427 | 63,078,117 | 100.0% | 143.9 bases | 149 bases | 98.2% |
| errors | Plate-1-BOP-1000-ACEF-END-3_S7_L004_R1_001.good.fq | 448,664 | 64,617,948 | 100.0% | 144.0 bases | 149 bases | 98.9% |
| errors | Plate-1-BOP-1000-ACEF-END-3_S7_L004_R2_001.good.fq | 448,664 | 64,539,679 | 100.0% | 143.8 bases | 149 bases | 98.1% |
| total | 3,514,698 | 506,085,924 | 100.0% | 144.0 bases | 149 bases | 98.5% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_000913 | 4,641,652 | 106.3 | 3.0 | 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 | 16370 |
| 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 | 1121 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.073 |
| reference sequence | pr(no read start) |
|---|---|
| NC_000913 | 0.72594 |
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 | 00:57:46 26 Feb 2020 | 00:58:38 26 Feb 2020 | 52 seconds |
| Read alignment to reference genome | 00:58:38 26 Feb 2020 | 01:05:38 26 Feb 2020 | 7 minutes 0 seconds |
| Preprocessing alignments for candidate junction identification | 01:05:38 26 Feb 2020 | 01:06:27 26 Feb 2020 | 49 seconds |
| Preliminary analysis of coverage distribution | 01:06:27 26 Feb 2020 | 01:08:34 26 Feb 2020 | 2 minutes 7 seconds |
| Identifying junction candidates | 01:08:34 26 Feb 2020 | 01:08:51 26 Feb 2020 | 17 seconds |
| Re-alignment to junction candidates | 01:08:51 26 Feb 2020 | 01:11:35 26 Feb 2020 | 2 minutes 44 seconds |
| Resolving best read alignments | 01:11:35 26 Feb 2020 | 01:12:52 26 Feb 2020 | 1 minute 17 seconds |
| Creating BAM files | 01:12:52 26 Feb 2020 | 01:14:50 26 Feb 2020 | 1 minute 58 seconds |
| Tabulating error counts | 01:14:50 26 Feb 2020 | 01:15:29 26 Feb 2020 | 39 seconds |
| Re-calibrating base error rates | 01:15:29 26 Feb 2020 | 01:15:32 26 Feb 2020 | 3 seconds |
| Examining read alignment evidence | 01:15:32 26 Feb 2020 | 01:22:58 26 Feb 2020 | 7 minutes 26 seconds |
| Polymorphism statistics | 01:22:58 26 Feb 2020 | 01:22:58 26 Feb 2020 | 0 seconds |
| Output | 01:22:58 26 Feb 2020 | 01:23:22 26 Feb 2020 | 24 seconds |
| Total | 25 minutes 36 seconds | ||
