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 | JADR33_R3_A3_F57_I1_R1_S87_L001_R1_001.good.fq | 403,921 | 50,085,637 | 100.0% | 124.0 bases | 136 bases | 95.9% |
| errors | JADR33_R3_A3_F57_I1_R1_S87_L001_R2_001.good.fq | 403,921 | 50,087,358 | 100.0% | 124.0 bases | 136 bases | 92.9% |
| errors | JADR33_R3_A3_F57_I1_R1_S87_L002_R1_001.good.fq | 409,830 | 52,299,578 | 100.0% | 127.6 bases | 139 bases | 96.8% |
| errors | JADR33_R3_A3_F57_I1_R1_S87_L002_R2_001.good.fq | 409,830 | 52,302,181 | 100.0% | 127.6 bases | 139 bases | 94.8% |
| errors | JADR33_R3_A3_F57_I1_R1_S87_L003_R1_001.good.fq | 407,644 | 51,905,786 | 100.0% | 127.3 bases | 139 bases | 96.8% |
| errors | JADR33_R3_A3_F57_I1_R1_S87_L003_R2_001.good.fq | 407,644 | 51,908,497 | 100.0% | 127.3 bases | 139 bases | 94.7% |
| errors | JADR33_R3_A3_F57_I1_R1_S87_L004_R1_001.good.fq | 408,078 | 51,803,888 | 100.0% | 126.9 bases | 139 bases | 97.2% |
| errors | JADR33_R3_A3_F57_I1_R1_S87_L004_R2_001.good.fq | 408,078 | 51,805,321 | 100.0% | 126.9 bases | 139 bases | 95.8% |
| total | 3,258,946 | 412,198,246 | 100.0% | 126.5 bases | 139 bases | 95.6% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | BS168_reference_genome | 4,215,606 | 91.7 | 7.2 | 99.9% | Bacillus subtilis subsp. subtilis str. 168 complete genome. |
| coverage | distribution | pSIJ663_pHT315_araE_xy | 11,568 | [33.1] | [16.5] | 0.1% | . |
| total | 4,227,174 | 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.
Fit failed Negative binomial fit failed for this reference sequence. It may have an unusual coverage depth distribution. JC and MC predictions may be less accurate.
| option | limit | actual |
|---|---|---|
| Number of alignment pairs examined for constructing junction candidates | ≤ 100000 | 874 |
| 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 | 77 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.005 |
| reference sequence | pr(no read start) |
|---|---|
| BS168_reference_genome | 0.78839 |
| pSIJ663_pHT315_araE_xy | NA |
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 | 10:17:23 04 Jun 2021 | 10:18:18 04 Jun 2021 | 55 seconds |
| Read alignment to reference genome | 10:18:18 04 Jun 2021 | 10:24:58 04 Jun 2021 | 6 minutes 40 seconds |
| Preprocessing alignments for candidate junction identification | 10:24:58 04 Jun 2021 | 10:25:43 04 Jun 2021 | 45 seconds |
| Preliminary analysis of coverage distribution | 10:25:43 04 Jun 2021 | 10:27:37 04 Jun 2021 | 1 minute 54 seconds |
| Identifying junction candidates | 10:27:37 04 Jun 2021 | 10:27:37 04 Jun 2021 | 0 seconds |
| Re-alignment to junction candidates | 10:27:37 04 Jun 2021 | 10:29:13 04 Jun 2021 | 1 minute 36 seconds |
| Resolving best read alignments | 10:29:13 04 Jun 2021 | 10:30:11 04 Jun 2021 | 58 seconds |
| Creating BAM files | 10:30:11 04 Jun 2021 | 10:31:53 04 Jun 2021 | 1 minute 42 seconds |
| Tabulating error counts | 10:31:53 04 Jun 2021 | 10:32:29 04 Jun 2021 | 36 seconds |
| Re-calibrating base error rates | 10:32:29 04 Jun 2021 | 10:32:33 04 Jun 2021 | 4 seconds |
| Examining read alignment evidence | 10:32:33 04 Jun 2021 | 10:40:01 04 Jun 2021 | 7 minutes 28 seconds |
| Polymorphism statistics | 10:40:01 04 Jun 2021 | 10:40:02 04 Jun 2021 | 1 second |
| Output | 10:40:02 04 Jun 2021 | 10:40:14 04 Jun 2021 | 12 seconds |
| Total | 22 minutes 51 seconds | ||
