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 | 4-END_S3_L001_R1_001_150407.good.fq | 156,919 | 31,823,867 | 100.0% | 202.8 bases | 275 bases | 97.1% |
| errors | 4-END_S3_L001_R1_001_150520.good.fq | 551,148 | 121,041,658 | 100.0% | 219.6 bases | 275 bases | 98.4% |
| errors | 4-END_S3_L001_R2_001_150407.good.fq | 156,919 | 33,387,855 | 100.0% | 212.8 bases | 275 bases | 55.4% |
| errors | 4-END_S3_L001_R2_001_150520.good.fq | 551,143 | 124,674,961 | 100.0% | 226.2 bases | 275 bases | 65.4% |
| errors | GLY_04_195_S314_L001_R1_001.good.fq | 477,915 | 66,122,815 | 100.0% | 138.4 bases | 149 bases | 98.2% |
| errors | GLY_04_195_S314_L001_R2_001.good.fq | 477,915 | 66,122,815 | 100.0% | 138.4 bases | 149 bases | 98.0% |
| errors | GLY_04_195_S314_L002_R1_001.good.fq | 476,387 | 65,772,995 | 100.0% | 138.1 bases | 149 bases | 98.1% |
| errors | GLY_04_195_S314_L002_R2_001.good.fq | 476,387 | 65,772,995 | 100.0% | 138.1 bases | 149 bases | 97.9% |
| total | 3,324,733 | 574,719,961 | 100.0% | 172.9 bases | 275 bases | 90.7% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_000913 | 4,641,652 | 100.4 | 3.6 | 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 | 14320 |
| 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 | 60 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.007 |
| reference sequence | pr(no read start) |
|---|---|
| NC_000913 | 0.76283 |
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 | 23:19:49 02 Jan 2019 | 23:20:41 02 Jan 2019 | 52 seconds |
| Read alignment to reference genome | 23:20:41 02 Jan 2019 | 23:31:28 02 Jan 2019 | 10 minutes 47 seconds |
| Preprocessing alignments for candidate junction identification | 23:31:28 02 Jan 2019 | 23:32:12 02 Jan 2019 | 44 seconds |
| Preliminary analysis of coverage distribution | 23:32:12 02 Jan 2019 | 23:34:25 02 Jan 2019 | 2 minutes 13 seconds |
| Identifying junction candidates | 23:34:25 02 Jan 2019 | 23:35:05 02 Jan 2019 | 40 seconds |
| Re-alignment to junction candidates | 23:35:05 02 Jan 2019 | 23:37:33 02 Jan 2019 | 2 minutes 28 seconds |
| Resolving best read alignments | 23:37:33 02 Jan 2019 | 23:38:49 02 Jan 2019 | 1 minute 16 seconds |
| Creating BAM files | 23:38:49 02 Jan 2019 | 23:40:47 02 Jan 2019 | 1 minute 58 seconds |
| Tabulating error counts | 23:40:47 02 Jan 2019 | 23:41:32 02 Jan 2019 | 45 seconds |
| Re-calibrating base error rates | 23:41:32 02 Jan 2019 | 23:41:34 02 Jan 2019 | 2 seconds |
| Examining read alignment evidence | 23:41:34 02 Jan 2019 | 00:26:46 03 Jan 2019 | 45 minutes 12 seconds |
| Polymorphism statistics | 00:26:46 03 Jan 2019 | 00:26:47 03 Jan 2019 | 1 second |
| Output | 00:26:47 03 Jan 2019 | 00:27:23 03 Jan 2019 | 36 seconds |
| Total | 1 hour 7 minutes 34 seconds | ||
