mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.35.4 revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| read file | reads | bases | passed filters | average | longest | mapped | |
|---|---|---|---|---|---|---|---|
| errors | JADR49_R4_A16_F57_I1_R1_S71_L001_R1_001.good.fq | 439,434 | 56,118,227 | 100.0% | 127.7 bases | 139 bases | 96.1% |
| errors | JADR49_R4_A16_F57_I1_R1_S71_L001_R2_001.good.fq | 439,434 | 56,122,043 | 100.0% | 127.7 bases | 139 bases | 92.9% |
| errors | JADR49_R4_A16_F57_I1_R1_S71_L002_R1_001.good.fq | 446,281 | 56,998,861 | 100.0% | 127.7 bases | 139 bases | 96.9% |
| errors | JADR49_R4_A16_F57_I1_R1_S71_L002_R2_001.good.fq | 446,281 | 57,001,743 | 100.0% | 127.7 bases | 139 bases | 94.6% |
| errors | JADR49_R4_A16_F57_I1_R1_S71_L003_R1_001.good.fq | 443,527 | 56,634,527 | 100.0% | 127.7 bases | 139 bases | 96.7% |
| errors | JADR49_R4_A16_F57_I1_R1_S71_L003_R2_001.good.fq | 443,527 | 56,637,556 | 100.0% | 127.7 bases | 139 bases | 94.5% |
| errors | JADR49_R4_A16_F57_I1_R1_S71_L004_R1_001.good.fq | 443,258 | 56,386,333 | 100.0% | 127.2 bases | 139 bases | 97.3% |
| errors | JADR49_R4_A16_F57_I1_R1_S71_L004_R2_001.good.fq | 443,258 | 56,388,910 | 100.0% | 127.2 bases | 139 bases | 95.6% |
| total | 3,545,000 | 452,288,200 | 100.0% | 127.6 bases | 139 bases | 95.6% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | CP006881 | 4,033,459 | 90.3 | 5.9 | 86.2% | Bacillus subtilis PY79, complete genome. |
| coverage | distribution | pSIJ663_pHT315_araE_xy | 11,568 | 10065.3 | 565.3 | 13.8% | . |
| total | 4,045,027 | 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 | 19340 |
| 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 | 46 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.003 |
| reference sequence | pr(no read start) |
|---|---|
| CP006881 | 0.80994 |
| pSIJ663_pHT315_araE_xy | 0.44831 |
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 |
| Minimum probablilty assigned that no mapped read will start at a given position and strand for junction prediction | 0.1 |
| Junction allow suboptimal matches | FALSE |
| 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 | 2.2.6 |
| R | 3.4.4 |
| step | start | end | elapsed |
|---|---|---|---|
| Read and reference sequence file input | 10:17:47 04 Jun 2021 | 10:18:46 04 Jun 2021 | 59 seconds |
| Read alignment to reference genome | 10:18:46 04 Jun 2021 | 10:25:54 04 Jun 2021 | 7 minutes 8 seconds |
| Preprocessing alignments for candidate junction identification | 10:25:54 04 Jun 2021 | 10:26:43 04 Jun 2021 | 49 seconds |
| Preliminary analysis of coverage distribution | 10:26:43 04 Jun 2021 | 10:28:46 04 Jun 2021 | 2 minutes 3 seconds |
| Identifying junction candidates | 10:28:46 04 Jun 2021 | 10:28:47 04 Jun 2021 | 1 second |
| Re-alignment to junction candidates | 10:28:47 04 Jun 2021 | 10:30:40 04 Jun 2021 | 1 minute 53 seconds |
| Resolving best read alignments | 10:30:40 04 Jun 2021 | 10:31:48 04 Jun 2021 | 1 minute 8 seconds |
| Creating BAM files | 10:31:48 04 Jun 2021 | 10:33:38 04 Jun 2021 | 1 minute 50 seconds |
| Tabulating error counts | 10:33:38 04 Jun 2021 | 10:34:20 04 Jun 2021 | 42 seconds |
| Re-calibrating base error rates | 10:34:20 04 Jun 2021 | 10:34:23 04 Jun 2021 | 3 seconds |
| Examining read alignment evidence | 10:34:23 04 Jun 2021 | 10:42:42 04 Jun 2021 | 8 minutes 19 seconds |
| Polymorphism statistics | 10:42:42 04 Jun 2021 | 10:42:43 04 Jun 2021 | 1 second |
| Output | 10:42:43 04 Jun 2021 | 10:43:14 04 Jun 2021 | 31 seconds |
| Total | 25 minutes 27 seconds | ||
