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-3-BOP-27-ACEF-END-1_S71_L001_R1_001.good.fq | 472,283 | 66,367,476 | 100.0% | 140.5 bases | 149 bases | 97.2% |
| errors | Plate-3-BOP-27-ACEF-END-1_S71_L001_R2_001.good.fq | 472,283 | 66,147,187 | 100.0% | 140.1 bases | 149 bases | 97.5% |
| errors | Plate-3-BOP-27-ACEF-END-1_S71_L002_R1_001.good.fq | 432,475 | 60,810,063 | 100.0% | 140.6 bases | 149 bases | 97.3% |
| errors | Plate-3-BOP-27-ACEF-END-1_S71_L002_R2_001.good.fq | 432,475 | 60,636,293 | 100.0% | 140.2 bases | 149 bases | 97.0% |
| errors | Plate-3-BOP-27-ACEF-END-1_S71_L003_R1_001.good.fq | 457,901 | 64,292,374 | 100.0% | 140.4 bases | 149 bases | 97.1% |
| errors | Plate-3-BOP-27-ACEF-END-1_S71_L003_R2_001.good.fq | 457,901 | 64,083,823 | 100.0% | 140.0 bases | 149 bases | 97.3% |
| errors | Plate-3-BOP-27-ACEF-END-1_S71_L004_R1_001.good.fq | 471,359 | 66,190,096 | 100.0% | 140.4 bases | 149 bases | 97.4% |
| errors | Plate-3-BOP-27-ACEF-END-1_S71_L004_R2_001.good.fq | 471,359 | 66,006,527 | 100.0% | 140.0 bases | 149 bases | 97.2% |
| total | 3,668,036 | 514,533,839 | 100.0% | 140.3 bases | 149 bases | 97.3% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_000913 | 4,641,652 | 95.2 | 3.3 | 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 | 35767 |
| 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 | 112 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.007 |
| reference sequence | pr(no read start) |
|---|---|
| NC_000913 | 0.72693 |
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 | 01:26:13 11 Sep 2020 | 01:27:08 11 Sep 2020 | 55 seconds |
| Read alignment to reference genome | 01:27:09 11 Sep 2020 | 01:34:05 11 Sep 2020 | 6 minutes 56 seconds |
| Preprocessing alignments for candidate junction identification | 01:34:05 11 Sep 2020 | 01:35:01 11 Sep 2020 | 56 seconds |
| Preliminary analysis of coverage distribution | 01:35:01 11 Sep 2020 | 01:37:05 11 Sep 2020 | 2 minutes 4 seconds |
| Identifying junction candidates | 01:37:05 11 Sep 2020 | 01:37:47 11 Sep 2020 | 42 seconds |
| Re-alignment to junction candidates | 01:37:47 11 Sep 2020 | 01:39:54 11 Sep 2020 | 2 minutes 7 seconds |
| Resolving best read alignments | 01:39:54 11 Sep 2020 | 01:41:22 11 Sep 2020 | 1 minute 28 seconds |
| Creating BAM files | 01:41:22 11 Sep 2020 | 01:43:17 11 Sep 2020 | 1 minute 55 seconds |
| Tabulating error counts | 01:43:17 11 Sep 2020 | 01:43:56 11 Sep 2020 | 39 seconds |
| Re-calibrating base error rates | 01:43:56 11 Sep 2020 | 01:43:59 11 Sep 2020 | 3 seconds |
| Examining read alignment evidence | 01:43:59 11 Sep 2020 | 02:17:03 11 Sep 2020 | 33 minutes 4 seconds |
| Polymorphism statistics | 02:17:03 11 Sep 2020 | 02:17:04 11 Sep 2020 | 1 second |
| Output | 02:17:04 11 Sep 2020 | 02:17:49 11 Sep 2020 | 45 seconds |
| Total | 51 minutes 35 seconds | ||
