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-BOP27-ACNB-END-1_S54_L001_R1_001.good.fq | 415,111 | 58,364,820 | 100.0% | 140.6 bases | 149 bases | 97.3% |
| errors | Plate-3-BOP27-ACNB-END-1_S54_L001_R2_001.good.fq | 415,111 | 58,066,632 | 100.0% | 139.9 bases | 149 bases | 98.0% |
| errors | Plate-3-BOP27-ACNB-END-1_S54_L002_R1_001.good.fq | 384,076 | 54,037,083 | 100.0% | 140.7 bases | 149 bases | 97.4% |
| errors | Plate-3-BOP27-ACNB-END-1_S54_L002_R2_001.good.fq | 384,076 | 53,797,365 | 100.0% | 140.1 bases | 149 bases | 97.6% |
| errors | Plate-3-BOP27-ACNB-END-1_S54_L003_R1_001.good.fq | 403,762 | 56,731,894 | 100.0% | 140.5 bases | 149 bases | 97.2% |
| errors | Plate-3-BOP27-ACNB-END-1_S54_L003_R2_001.good.fq | 403,762 | 56,447,989 | 100.0% | 139.8 bases | 149 bases | 97.8% |
| errors | Plate-3-BOP27-ACNB-END-1_S54_L004_R1_001.good.fq | 414,126 | 58,173,641 | 100.0% | 140.5 bases | 149 bases | 97.4% |
| errors | Plate-3-BOP27-ACNB-END-1_S54_L004_R2_001.good.fq | 414,126 | 57,911,326 | 100.0% | 139.8 bases | 149 bases | 97.8% |
| total | 3,234,150 | 453,530,750 | 100.0% | 140.2 bases | 149 bases | 97.6% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_000913 | 4,641,652 | 94.3 | 3.4 | 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 | 14450 |
| 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 | 47 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.003 |
| reference sequence | pr(no read start) |
|---|---|
| NC_000913 | 0.74196 |
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 | 07:52:58 11 Sep 2020 | 07:53:47 11 Sep 2020 | 49 seconds |
| Read alignment to reference genome | 07:53:47 11 Sep 2020 | 07:59:54 11 Sep 2020 | 6 minutes 7 seconds |
| Preprocessing alignments for candidate junction identification | 07:59:54 11 Sep 2020 | 08:00:43 11 Sep 2020 | 49 seconds |
| Preliminary analysis of coverage distribution | 08:00:43 11 Sep 2020 | 08:02:34 11 Sep 2020 | 1 minute 51 seconds |
| Identifying junction candidates | 08:02:34 11 Sep 2020 | 08:02:48 11 Sep 2020 | 14 seconds |
| Re-alignment to junction candidates | 08:02:48 11 Sep 2020 | 08:04:37 11 Sep 2020 | 1 minute 49 seconds |
| Resolving best read alignments | 08:04:37 11 Sep 2020 | 08:05:53 11 Sep 2020 | 1 minute 16 seconds |
| Creating BAM files | 08:05:53 11 Sep 2020 | 08:07:35 11 Sep 2020 | 1 minute 42 seconds |
| Tabulating error counts | 08:07:35 11 Sep 2020 | 08:08:10 11 Sep 2020 | 35 seconds |
| Re-calibrating base error rates | 08:08:10 11 Sep 2020 | 08:08:12 11 Sep 2020 | 2 seconds |
| Examining read alignment evidence | 08:08:12 11 Sep 2020 | 08:35:32 11 Sep 2020 | 27 minutes 20 seconds |
| Polymorphism statistics | 08:35:32 11 Sep 2020 | 08:35:33 11 Sep 2020 | 1 second |
| Output | 08:35:33 11 Sep 2020 | 08:36:03 11 Sep 2020 | 30 seconds |
| Total | 43 minutes 5 seconds | ||
