mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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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-BOP27-SUCB-END-4_S20_L001_R1_001.good.fq | 375,176 | 54,155,028 | 100.0% | 144.3 bases | 149 bases | 98.4% |
| errors | Plate-1-BOP27-SUCB-END-4_S20_L001_R2_001.good.fq | 375,176 | 54,006,112 | 100.0% | 143.9 bases | 149 bases | 98.0% |
| errors | Plate-1-BOP27-SUCB-END-4_S20_L002_R1_001.good.fq | 350,002 | 50,547,196 | 100.0% | 144.4 bases | 149 bases | 98.5% |
| errors | Plate-1-BOP27-SUCB-END-4_S20_L002_R2_001.good.fq | 350,002 | 50,433,683 | 100.0% | 144.1 bases | 149 bases | 97.7% |
| errors | Plate-1-BOP27-SUCB-END-4_S20_L003_R1_001.good.fq | 363,066 | 52,375,782 | 100.0% | 144.3 bases | 149 bases | 98.3% |
| errors | Plate-1-BOP27-SUCB-END-4_S20_L003_R2_001.good.fq | 363,066 | 52,236,332 | 100.0% | 143.9 bases | 149 bases | 97.9% |
| errors | Plate-1-BOP27-SUCB-END-4_S20_L004_R1_001.good.fq | 369,371 | 53,264,640 | 100.0% | 144.2 bases | 149 bases | 98.5% |
| errors | Plate-1-BOP27-SUCB-END-4_S20_L004_R2_001.good.fq | 369,371 | 53,137,638 | 100.0% | 143.9 bases | 149 bases | 97.8% |
| total | 2,915,230 | 420,156,411 | 100.0% | 144.1 bases | 149 bases | 98.1% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_000913 | 4,641,652 | 89.5 | 10.5 | 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 | 11369 |
| 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 | 839 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.054 |
| reference sequence | pr(no read start) |
|---|---|
| NC_000913 | 0.76875 |
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 | 2.2.6 |
| R | 3.4.4 |
| step | start | end | elapsed |
|---|---|---|---|
| Read and reference sequence file input | 13:11:26 12 Sep 2020 | 13:12:10 12 Sep 2020 | 44 seconds |
| Read alignment to reference genome | 13:12:11 12 Sep 2020 | 13:17:50 12 Sep 2020 | 5 minutes 39 seconds |
| Preprocessing alignments for candidate junction identification | 13:17:50 12 Sep 2020 | 13:18:35 12 Sep 2020 | 45 seconds |
| Preliminary analysis of coverage distribution | 13:18:35 12 Sep 2020 | 13:20:21 12 Sep 2020 | 1 minute 46 seconds |
| Identifying junction candidates | 13:20:21 12 Sep 2020 | 13:20:28 12 Sep 2020 | 7 seconds |
| Re-alignment to junction candidates | 13:20:28 12 Sep 2020 | 13:22:31 12 Sep 2020 | 2 minutes 3 seconds |
| Resolving best read alignments | 13:22:31 12 Sep 2020 | 13:23:42 12 Sep 2020 | 1 minute 11 seconds |
| Creating BAM files | 13:23:42 12 Sep 2020 | 13:25:20 12 Sep 2020 | 1 minute 38 seconds |
| Tabulating error counts | 13:25:20 12 Sep 2020 | 13:25:52 12 Sep 2020 | 32 seconds |
| Re-calibrating base error rates | 13:25:52 12 Sep 2020 | 13:25:55 12 Sep 2020 | 3 seconds |
| Examining read alignment evidence | 13:25:55 12 Sep 2020 | 13:32:34 12 Sep 2020 | 6 minutes 39 seconds |
| Polymorphism statistics | 13:32:34 12 Sep 2020 | 13:32:34 12 Sep 2020 | 0 seconds |
| Output | 13:32:34 12 Sep 2020 | 13:32:50 12 Sep 2020 | 16 seconds |
| Total | 21 minutes 23 seconds | ||
