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 | 6-END_S5_L001_R1_001_150407.good.fq | 247,403 | 57,601,335 | 100.0% | 232.8 bases | 279 bases | 97.4% |
| errors | 6-END_S5_L001_R1_001_150520.good.fq | 785,208 | 188,723,774 | 100.0% | 240.3 bases | 275 bases | 99.0% |
| errors | 6-END_S5_L001_R2_001_150407.good.fq | 247,403 | 58,765,565 | 100.0% | 237.5 bases | 279 bases | 54.9% |
| errors | 6-END_S5_L001_R2_001_150520.good.fq | 785,208 | 189,127,666 | 100.0% | 240.9 bases | 275 bases | 89.7% |
| errors | GLY_06_187_S330_L001_R1_001.good.fq | 1,078,780 | 152,656,544 | 100.0% | 141.5 bases | 149 bases | 98.3% |
| errors | GLY_06_187_S330_L001_R2_001.good.fq | 1,078,780 | 152,656,544 | 100.0% | 141.5 bases | 149 bases | 97.9% |
| errors | GLY_06_187_S330_L002_R1_001.good.fq | 1,059,127 | 148,381,212 | 100.0% | 140.1 bases | 148 bases | 98.2% |
| errors | GLY_06_187_S330_L002_R2_001.good.fq | 1,059,127 | 148,381,212 | 100.0% | 140.1 bases | 148 bases | 97.8% |
| total | 6,341,036 | 1,096,293,852 | 100.0% | 172.9 bases | 279 bases | 95.4% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_000913 | 4,641,652 | 206.4 | 4.5 | 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 | 24343 |
| 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 | 181 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.022 |
| reference sequence | pr(no read start) |
|---|---|
| NC_000913 | 0.59497 |
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 | 02:46:25 03 Jan 2019 | 02:48:04 03 Jan 2019 | 1 minute 39 seconds |
| Read alignment to reference genome | 02:48:04 03 Jan 2019 | 03:07:17 03 Jan 2019 | 19 minutes 13 seconds |
| Preprocessing alignments for candidate junction identification | 03:07:17 03 Jan 2019 | 03:08:40 03 Jan 2019 | 1 minute 23 seconds |
| Preliminary analysis of coverage distribution | 03:08:40 03 Jan 2019 | 03:13:23 03 Jan 2019 | 4 minutes 43 seconds |
| Identifying junction candidates | 03:13:23 03 Jan 2019 | 03:14:36 03 Jan 2019 | 1 minute 13 seconds |
| Re-alignment to junction candidates | 03:14:36 03 Jan 2019 | 03:19:44 03 Jan 2019 | 5 minutes 8 seconds |
| Resolving best read alignments | 03:19:44 03 Jan 2019 | 03:22:09 03 Jan 2019 | 2 minutes 25 seconds |
| Creating BAM files | 03:22:09 03 Jan 2019 | 03:26:16 03 Jan 2019 | 4 minutes 7 seconds |
| Tabulating error counts | 03:26:16 03 Jan 2019 | 03:27:53 03 Jan 2019 | 1 minute 37 seconds |
| Re-calibrating base error rates | 03:27:53 03 Jan 2019 | 03:27:56 03 Jan 2019 | 3 seconds |
| Examining read alignment evidence | 03:27:56 03 Jan 2019 | 05:17:56 03 Jan 2019 | 1 hour 50 minutes 0 seconds |
| Polymorphism statistics | 05:17:56 03 Jan 2019 | 05:17:58 03 Jan 2019 | 2 seconds |
| Output | 05:17:58 03 Jan 2019 | 05:18:40 03 Jan 2019 | 42 seconds |
| Total | 2 hours 32 minutes 15 seconds | ||
