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-2_S49_L001_R1_001.good.fq | 448,484 | 59,583,761 | 100.0% | 132.9 bases | 148 bases | 98.9% |
| errors | Plate-3-BOP-1000-ACNB-END-2_S49_L001_R2_001.good.fq | 448,484 | 59,634,010 | 100.0% | 133.0 bases | 148 bases | 98.0% |
| errors | Plate-3-BOP-1000-ACNB-END-2_S49_L002_R1_001.good.fq | 415,953 | 55,334,206 | 100.0% | 133.0 bases | 148 bases | 98.9% |
| errors | Plate-3-BOP-1000-ACNB-END-2_S49_L002_R2_001.good.fq | 415,953 | 55,397,738 | 100.0% | 133.2 bases | 148 bases | 97.7% |
| errors | Plate-3-BOP-1000-ACNB-END-2_S49_L003_R1_001.good.fq | 438,663 | 58,226,265 | 100.0% | 132.7 bases | 148 bases | 98.8% |
| errors | Plate-3-BOP-1000-ACNB-END-2_S49_L003_R2_001.good.fq | 438,663 | 58,287,892 | 100.0% | 132.9 bases | 148 bases | 97.8% |
| errors | Plate-3-BOP-1000-ACNB-END-2_S49_L004_R1_001.good.fq | 456,613 | 60,657,004 | 100.0% | 132.8 bases | 148 bases | 99.0% |
| errors | Plate-3-BOP-1000-ACNB-END-2_S49_L004_R2_001.good.fq | 456,613 | 60,731,777 | 100.0% | 133.0 bases | 148 bases | 97.8% |
| total | 3,519,426 | 467,852,653 | 100.0% | 132.9 bases | 148 bases | 98.4% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_000913 | 4,641,652 | 98.6 | 4.9 | 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 | 24638 |
| 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 | 68 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.004 |
| reference sequence | pr(no read start) |
|---|---|
| NC_000913 | 0.72655 |
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 | 2.3.4.1 |
| R | 3.4.4 |
| step | start | end | elapsed |
|---|---|---|---|
| Read and reference sequence file input | 09:30:01 29 Feb 2020 | 09:30:51 29 Feb 2020 | 50 seconds |
| Read alignment to reference genome | 09:30:52 29 Feb 2020 | 09:37:30 29 Feb 2020 | 6 minutes 38 seconds |
| Preprocessing alignments for candidate junction identification | 09:37:30 29 Feb 2020 | 09:38:19 29 Feb 2020 | 49 seconds |
| Preliminary analysis of coverage distribution | 09:38:19 29 Feb 2020 | 09:40:16 29 Feb 2020 | 1 minute 57 seconds |
| Identifying junction candidates | 09:40:16 29 Feb 2020 | 09:41:11 29 Feb 2020 | 55 seconds |
| Re-alignment to junction candidates | 09:41:11 29 Feb 2020 | 09:43:17 29 Feb 2020 | 2 minutes 6 seconds |
| Resolving best read alignments | 09:43:17 29 Feb 2020 | 09:44:31 29 Feb 2020 | 1 minute 14 seconds |
| Creating BAM files | 09:44:31 29 Feb 2020 | 09:46:18 29 Feb 2020 | 1 minute 47 seconds |
| Tabulating error counts | 09:46:18 29 Feb 2020 | 09:46:55 29 Feb 2020 | 37 seconds |
| Re-calibrating base error rates | 09:46:55 29 Feb 2020 | 09:46:58 29 Feb 2020 | 3 seconds |
| Examining read alignment evidence | 09:46:58 29 Feb 2020 | 10:11:06 29 Feb 2020 | 24 minutes 8 seconds |
| Polymorphism statistics | 10:11:06 29 Feb 2020 | 10:11:07 29 Feb 2020 | 1 second |
| Output | 10:11:07 29 Feb 2020 | 10:11:36 29 Feb 2020 | 29 seconds |
| Total | 41 minutes 34 seconds | ||
