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-27-ACEF-END-2_S2_L001_R1_001.good.fq | 409,182 | 57,402,824 | 100.0% | 140.3 bases | 149 bases | 97.7% |
| errors | Plate-1-BOP-27-ACEF-END-2_S2_L001_R2_001.good.fq | 409,182 | 57,234,687 | 100.0% | 139.9 bases | 149 bases | 97.8% |
| errors | Plate-1-BOP-27-ACEF-END-2_S2_L002_R1_001.good.fq | 374,871 | 52,600,263 | 100.0% | 140.3 bases | 149 bases | 97.8% |
| errors | Plate-1-BOP-27-ACEF-END-2_S2_L002_R2_001.good.fq | 374,871 | 52,467,722 | 100.0% | 140.0 bases | 149 bases | 97.5% |
| errors | Plate-1-BOP-27-ACEF-END-2_S2_L003_R1_001.good.fq | 397,124 | 55,671,944 | 100.0% | 140.2 bases | 149 bases | 97.6% |
| errors | Plate-1-BOP-27-ACEF-END-2_S2_L003_R2_001.good.fq | 397,124 | 55,514,849 | 100.0% | 139.8 bases | 149 bases | 97.7% |
| errors | Plate-1-BOP-27-ACEF-END-2_S2_L004_R1_001.good.fq | 406,156 | 56,933,497 | 100.0% | 140.2 bases | 149 bases | 97.9% |
| errors | Plate-1-BOP-27-ACEF-END-2_S2_L004_R2_001.good.fq | 406,156 | 56,798,904 | 100.0% | 139.8 bases | 149 bases | 97.6% |
| total | 3,174,666 | 444,624,690 | 100.0% | 140.1 bases | 149 bases | 97.7% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_000913 | 4,641,652 | 95.2 | 6.2 | 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 | 21807 |
| 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 | 65 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.004 |
| reference sequence | pr(no read start) |
|---|---|
| NC_000913 | 0.74667 |
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 | 03:57:11 28 Feb 2020 | 03:57:58 28 Feb 2020 | 47 seconds |
| Read alignment to reference genome | 03:57:58 28 Feb 2020 | 04:04:13 28 Feb 2020 | 6 minutes 15 seconds |
| Preprocessing alignments for candidate junction identification | 04:04:13 28 Feb 2020 | 04:04:57 28 Feb 2020 | 44 seconds |
| Preliminary analysis of coverage distribution | 04:04:57 28 Feb 2020 | 04:06:48 28 Feb 2020 | 1 minute 51 seconds |
| Identifying junction candidates | 04:06:48 28 Feb 2020 | 04:07:13 28 Feb 2020 | 25 seconds |
| Re-alignment to junction candidates | 04:07:13 28 Feb 2020 | 04:09:08 28 Feb 2020 | 1 minute 55 seconds |
| Resolving best read alignments | 04:09:08 28 Feb 2020 | 04:10:16 28 Feb 2020 | 1 minute 8 seconds |
| Creating BAM files | 04:10:16 28 Feb 2020 | 04:11:58 28 Feb 2020 | 1 minute 42 seconds |
| Tabulating error counts | 04:11:58 28 Feb 2020 | 04:12:32 28 Feb 2020 | 34 seconds |
| Re-calibrating base error rates | 04:12:32 28 Feb 2020 | 04:12:34 28 Feb 2020 | 2 seconds |
| Examining read alignment evidence | 04:12:34 28 Feb 2020 | 04:19:01 28 Feb 2020 | 6 minutes 27 seconds |
| Polymorphism statistics | 04:19:01 28 Feb 2020 | 04:19:01 28 Feb 2020 | 0 seconds |
| Output | 04:19:01 28 Feb 2020 | 04:19:17 28 Feb 2020 | 16 seconds |
| Total | 22 minutes 6 seconds | ||
