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 | Glu_KHP_A5_F417_I2_R1_S25_L008_R1_001.good.fq | 5,576,727 | 557,672,700 | 100.0% | 100.0 bases | 100 bases | 94.3% |
| errors | Glu_KHP_A5_F417_I2_R1_S25_L008_R2_001.good.fq | 5,502,470 | 550,247,000 | 100.0% | 100.0 bases | 100 bases | 92.0% |
| total | 11,079,197 | 1,107,919,700 | 100.0% | 100.0 bases | 100 bases | 93.2% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_000913 | 4,641,652 | 220.4 | 2.7 | 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 | 100097 |
| 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 | 1070 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.048 |
| reference sequence | pr(no read start) |
|---|---|
| NC_000913 | 0.41749 |
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 | 23:14:36 22 May 2019 | 23:16:24 22 May 2019 | 1 minute 48 seconds |
| Read alignment to reference genome | 23:16:24 22 May 2019 | 23:35:42 22 May 2019 | 19 minutes 18 seconds |
| Preprocessing alignments for candidate junction identification | 23:35:42 22 May 2019 | 23:37:52 22 May 2019 | 2 minutes 10 seconds |
| Preliminary analysis of coverage distribution | 23:37:52 22 May 2019 | 23:41:58 22 May 2019 | 4 minutes 6 seconds |
| Identifying junction candidates | 23:41:58 22 May 2019 | 23:46:41 22 May 2019 | 4 minutes 43 seconds |
| Re-alignment to junction candidates | 23:46:41 22 May 2019 | 23:53:13 22 May 2019 | 6 minutes 32 seconds |
| Resolving best read alignments | 23:53:13 22 May 2019 | 23:56:39 22 May 2019 | 3 minutes 26 seconds |
| Creating BAM files | 23:56:39 22 May 2019 | 00:00:19 23 May 2019 | 3 minutes 40 seconds |
| Tabulating error counts | 00:00:19 23 May 2019 | 00:01:51 23 May 2019 | 1 minute 32 seconds |
| Re-calibrating base error rates | 00:01:51 23 May 2019 | 00:01:52 23 May 2019 | 1 second |
| Examining read alignment evidence | 00:01:52 23 May 2019 | 00:17:28 23 May 2019 | 15 minutes 36 seconds |
| Polymorphism statistics | 00:17:28 23 May 2019 | 00:17:30 23 May 2019 | 2 seconds |
| Output | 00:17:30 23 May 2019 | 00:18:46 23 May 2019 | 1 minute 16 seconds |
| Total | 1 hour 4 minutes 10 seconds | ||
