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-3-BOP-1000-ACNB-END-4_S47_L001_R1_001.good.fq | 429,649 | 60,629,237 | 100.0% | 141.1 bases | 149 bases | 97.9% |
| errors | Plate-3-BOP-1000-ACNB-END-4_S47_L001_R2_001.good.fq | 429,649 | 60,429,751 | 100.0% | 140.6 bases | 149 bases | 98.1% |
| errors | Plate-3-BOP-1000-ACNB-END-4_S47_L002_R1_001.good.fq | 402,278 | 56,809,681 | 100.0% | 141.2 bases | 149 bases | 97.9% |
| errors | Plate-3-BOP-1000-ACNB-END-4_S47_L002_R2_001.good.fq | 402,278 | 56,638,193 | 100.0% | 140.8 bases | 149 bases | 97.7% |
| errors | Plate-3-BOP-1000-ACNB-END-4_S47_L003_R1_001.good.fq | 417,798 | 58,898,931 | 100.0% | 141.0 bases | 149 bases | 97.7% |
| errors | Plate-3-BOP-1000-ACNB-END-4_S47_L003_R2_001.good.fq | 417,798 | 58,702,046 | 100.0% | 140.5 bases | 149 bases | 97.9% |
| errors | Plate-3-BOP-1000-ACNB-END-4_S47_L004_R1_001.good.fq | 439,441 | 61,983,131 | 100.0% | 141.0 bases | 149 bases | 97.9% |
| errors | Plate-3-BOP-1000-ACNB-END-4_S47_L004_R2_001.good.fq | 439,441 | 61,795,458 | 100.0% | 140.6 bases | 149 bases | 97.9% |
| total | 3,378,332 | 475,886,428 | 100.0% | 140.9 bases | 149 bases | 97.9% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_000913 | 4,641,652 | 99.6 | 3.6 | 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 | 19155 |
| 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 | 57 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.004 |
| reference sequence | pr(no read start) |
|---|---|
| NC_000913 | 0.73353 |
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 | ≤ 0 |
| Number of bases that at least one read must overlap each uniquely aligned side of a predicted junction | ≥ 6 |
| option | value |
|---|---|
| Mode | Full Polymorphism |
| 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 | 2 |
| Polymorphism frequency cutoff | 0.05 |
| Polymorphism minimum variant coverage each strand | 2 |
| 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 | ≥3 bases |
| Skip base substitutions when they create a homopolymer flanked on each side by | ≥5 bases |
| program | version |
|---|---|
| bowtie2 | 2.2.6 |
| R | 3.4.4 |
| step | start | end | elapsed |
|---|---|---|---|
| Read and reference sequence file input | 02:28:07 13 Sep 2020 | 02:28:58 13 Sep 2020 | 51 seconds |
| Read alignment to reference genome | 02:28:58 13 Sep 2020 | 02:35:19 13 Sep 2020 | 6 minutes 21 seconds |
| Preprocessing alignments for candidate junction identification | 02:35:19 13 Sep 2020 | 02:36:10 13 Sep 2020 | 51 seconds |
| Preliminary analysis of coverage distribution | 02:36:10 13 Sep 2020 | 02:38:06 13 Sep 2020 | 1 minute 56 seconds |
| Identifying junction candidates | 02:38:06 13 Sep 2020 | 02:38:33 13 Sep 2020 | 27 seconds |
| Re-alignment to junction candidates | 02:38:33 13 Sep 2020 | 02:40:27 13 Sep 2020 | 1 minute 54 seconds |
| Resolving best read alignments | 02:40:27 13 Sep 2020 | 02:41:47 13 Sep 2020 | 1 minute 20 seconds |
| Creating BAM files | 02:41:47 13 Sep 2020 | 02:43:33 13 Sep 2020 | 1 minute 46 seconds |
| Tabulating error counts | 02:43:33 13 Sep 2020 | 02:44:10 13 Sep 2020 | 37 seconds |
| Re-calibrating base error rates | 02:44:10 13 Sep 2020 | 02:44:12 13 Sep 2020 | 2 seconds |
| Examining read alignment evidence | 02:44:12 13 Sep 2020 | 03:14:18 13 Sep 2020 | 30 minutes 6 seconds |
| Polymorphism statistics | 03:14:18 13 Sep 2020 | 03:14:19 13 Sep 2020 | 1 second |
| Output | 03:14:19 13 Sep 2020 | 03:14:45 13 Sep 2020 | 26 seconds |
| Total | 46 minutes 38 seconds | ||
