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-2-BOP-27-SUCB-ALE-4-flask-8_S39_L001_R1_001.good.fq | 189,822 | 23,530,167 | 100.0% | 124.0 bases | 149 bases | 95.7% |
| errors | Plate-2-BOP-27-SUCB-ALE-4-flask-8_S39_L001_R2_001.good.fq | 189,822 | 23,282,663 | 100.0% | 122.7 bases | 149 bases | 98.0% |
| errors | Plate-2-BOP-27-SUCB-ALE-4-flask-8_S39_L002_R1_001.good.fq | 147,888 | 18,219,323 | 100.0% | 123.2 bases | 149 bases | 95.3% |
| errors | Plate-2-BOP-27-SUCB-ALE-4-flask-8_S39_L002_R2_001.good.fq | 147,888 | 18,028,100 | 100.0% | 121.9 bases | 149 bases | 97.5% |
| errors | Plate-2-BOP-27-SUCB-ALE-4-flask-8_S39_L003_R1_001.good.fq | 170,648 | 21,018,006 | 100.0% | 123.2 bases | 149 bases | 95.6% |
| errors | Plate-2-BOP-27-SUCB-ALE-4-flask-8_S39_L003_R2_001.good.fq | 170,648 | 20,792,022 | 100.0% | 121.8 bases | 149 bases | 97.9% |
| errors | Plate-2-BOP-27-SUCB-ALE-4-flask-8_S39_L004_R1_001.good.fq | 145,022 | 17,806,239 | 100.0% | 122.8 bases | 149 bases | 95.1% |
| errors | Plate-2-BOP-27-SUCB-ALE-4-flask-8_S39_L004_R2_001.good.fq | 145,022 | 17,615,929 | 100.0% | 121.5 bases | 149 bases | 97.3% |
| total | 1,306,760 | 160,292,449 | 100.0% | 122.7 bases | 149 bases | 96.6% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_000913 | 4,641,652 | 33.4 | 2.4 | 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 | 15109 |
| 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 | 129 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.009 |
| reference sequence | pr(no read start) |
|---|---|
| NC_000913 | 0.87975 |
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 | 00:23:20 28 Feb 2020 | 00:23:39 28 Feb 2020 | 19 seconds |
| Read alignment to reference genome | 00:23:39 28 Feb 2020 | 00:26:01 28 Feb 2020 | 2 minutes 22 seconds |
| Preprocessing alignments for candidate junction identification | 00:26:01 28 Feb 2020 | 00:26:18 28 Feb 2020 | 17 seconds |
| Preliminary analysis of coverage distribution | 00:26:18 28 Feb 2020 | 00:26:52 28 Feb 2020 | 34 seconds |
| Identifying junction candidates | 00:26:52 28 Feb 2020 | 00:27:11 28 Feb 2020 | 19 seconds |
| Re-alignment to junction candidates | 00:27:11 28 Feb 2020 | 00:27:56 28 Feb 2020 | 45 seconds |
| Resolving best read alignments | 00:27:56 28 Feb 2020 | 00:28:23 28 Feb 2020 | 27 seconds |
| Creating BAM files | 00:28:23 28 Feb 2020 | 00:28:54 28 Feb 2020 | 31 seconds |
| Tabulating error counts | 00:28:54 28 Feb 2020 | 00:29:06 28 Feb 2020 | 12 seconds |
| Re-calibrating base error rates | 00:29:06 28 Feb 2020 | 00:29:09 28 Feb 2020 | 3 seconds |
| Examining read alignment evidence | 00:29:09 28 Feb 2020 | 00:31:34 28 Feb 2020 | 2 minutes 25 seconds |
| Polymorphism statistics | 00:31:34 28 Feb 2020 | 00:31:34 28 Feb 2020 | 0 seconds |
| Output | 00:31:34 28 Feb 2020 | 00:31:46 28 Feb 2020 | 12 seconds |
| Total | 8 minutes 26 seconds | ||
