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 | 14-68_S14_L001_R1_001_150209.good.fq | 697,967 | 177,230,591 | 100.0% | 253.9 bases | 275 bases | 98.5% |
| errors | 14-68_S14_L001_R1_001_150513.good.fq | 637,920 | 166,726,566 | 100.0% | 261.4 bases | 278 bases | 98.2% |
| errors | 14-68_S14_L001_R2_001_150209.good.fq | 697,967 | 177,569,514 | 100.0% | 254.4 bases | 275 bases | 88.8% |
| errors | 14-68_S14_L001_R2_001_150513.good.fq | 637,920 | 167,508,154 | 100.0% | 262.6 bases | 278 bases | 73.1% |
| total | 2,671,774 | 689,034,825 | 100.0% | 257.9 bases | 278 bases | 89.8% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_000913 | 4,641,652 | 128.3 | 4.3 | 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 | 2976 |
| 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 | 185 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.022 |
| reference sequence | pr(no read start) |
|---|---|
| NC_000913 | 0.84396 |
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 | 2.3.4.1 |
| R | 3.4.4 |
| step | start | end | elapsed |
|---|---|---|---|
| Read and reference sequence file input | 04:43:21 08 Jan 2019 | 04:44:15 08 Jan 2019 | 54 seconds |
| Read alignment to reference genome | 04:44:15 08 Jan 2019 | 05:01:02 08 Jan 2019 | 16 minutes 47 seconds |
| Preprocessing alignments for candidate junction identification | 05:01:02 08 Jan 2019 | 05:01:44 08 Jan 2019 | 42 seconds |
| Preliminary analysis of coverage distribution | 05:01:44 08 Jan 2019 | 05:04:12 08 Jan 2019 | 2 minutes 28 seconds |
| Identifying junction candidates | 05:04:12 08 Jan 2019 | 05:04:16 08 Jan 2019 | 4 seconds |
| Re-alignment to junction candidates | 05:04:16 08 Jan 2019 | 05:07:23 08 Jan 2019 | 3 minutes 7 seconds |
| Resolving best read alignments | 05:07:23 08 Jan 2019 | 05:08:40 08 Jan 2019 | 1 minute 17 seconds |
| Creating BAM files | 05:08:40 08 Jan 2019 | 05:10:47 08 Jan 2019 | 2 minutes 7 seconds |
| Tabulating error counts | 05:10:47 08 Jan 2019 | 05:11:46 08 Jan 2019 | 59 seconds |
| Re-calibrating base error rates | 05:11:46 08 Jan 2019 | 05:11:48 08 Jan 2019 | 2 seconds |
| Examining read alignment evidence | 05:11:48 08 Jan 2019 | 05:22:11 08 Jan 2019 | 10 minutes 23 seconds |
| Polymorphism statistics | 05:22:11 08 Jan 2019 | 05:22:12 08 Jan 2019 | 1 second |
| Output | 05:22:12 08 Jan 2019 | 05:22:27 08 Jan 2019 | 15 seconds |
| Total | 39 minutes 6 seconds | ||
