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 | 28-END_S9_L001_R1_001_150407.good.fq | 297,433 | 57,853,897 | 100.0% | 194.5 bases | 279 bases | 97.6% |
| errors | 28-END_S9_L001_R1_001_150520.good.fq | 786,036 | 164,650,532 | 100.0% | 209.5 bases | 275 bases | 98.7% |
| errors | 28-END_S9_L001_R2_001_150407.good.fq | 297,433 | 59,981,123 | 100.0% | 201.7 bases | 279 bases | 65.2% |
| errors | 28-END_S9_L001_R2_001_150520.good.fq | 786,030 | 168,461,452 | 100.0% | 214.3 bases | 275 bases | 75.8% |
| errors | GLY_28_034_S316_L001_R1_001.good.fq | 1,724,216 | 240,131,292 | 100.0% | 139.3 bases | 149 bases | 98.2% |
| errors | GLY_28_034_S316_L001_R2_001.good.fq | 1,724,216 | 240,131,292 | 100.0% | 139.3 bases | 149 bases | 97.8% |
| errors | GLY_28_034_S316_L002_R1_001.good.fq | 1,690,335 | 234,912,276 | 100.0% | 139.0 bases | 149 bases | 98.1% |
| errors | GLY_28_034_S316_L002_R2_001.good.fq | 1,690,335 | 234,912,276 | 100.0% | 139.0 bases | 149 bases | 97.7% |
| total | 8,996,034 | 1,401,034,140 | 100.0% | 155.7 bases | 279 bases | 95.0% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_000913 | 4,641,652 | 258.1 | 4.8 | 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 | 43678 |
| 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 | 567 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.069 |
| reference sequence | pr(no read start) |
|---|---|
| NC_000913 | 0.50724 |
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 | 05:18:40 03 Jan 2019 | 05:20:51 03 Jan 2019 | 2 minutes 11 seconds |
| Read alignment to reference genome | 05:20:52 03 Jan 2019 | 05:44:24 03 Jan 2019 | 23 minutes 32 seconds |
| Preprocessing alignments for candidate junction identification | 05:44:24 03 Jan 2019 | 05:46:19 03 Jan 2019 | 1 minute 55 seconds |
| Preliminary analysis of coverage distribution | 05:46:19 03 Jan 2019 | 05:52:17 03 Jan 2019 | 5 minutes 58 seconds |
| Identifying junction candidates | 05:52:17 03 Jan 2019 | 06:00:35 03 Jan 2019 | 8 minutes 18 seconds |
| Re-alignment to junction candidates | 06:00:35 03 Jan 2019 | 06:09:23 03 Jan 2019 | 8 minutes 48 seconds |
| Resolving best read alignments | 06:09:23 03 Jan 2019 | 06:12:46 03 Jan 2019 | 3 minutes 23 seconds |
| Creating BAM files | 06:12:46 03 Jan 2019 | 06:18:06 03 Jan 2019 | 5 minutes 20 seconds |
| Tabulating error counts | 06:18:06 03 Jan 2019 | 06:20:09 03 Jan 2019 | 2 minutes 3 seconds |
| Re-calibrating base error rates | 06:20:09 03 Jan 2019 | 06:20:11 03 Jan 2019 | 2 seconds |
| Examining read alignment evidence | 06:20:11 03 Jan 2019 | 08:40:57 03 Jan 2019 | 2 hours 20 minutes 46 seconds |
| Polymorphism statistics | 08:40:57 03 Jan 2019 | 08:41:01 03 Jan 2019 | 4 seconds |
| Output | 08:41:01 03 Jan 2019 | 08:42:12 03 Jan 2019 | 1 minute 11 seconds |
| Total | 3 hours 23 minutes 31 seconds | ||
