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 | ACB143VanA13_F91_I0_R1_S6_L001_R1_001.good.fq | 300,806 | 39,523,426 | 100.0% | 131.4 bases | 136 bases | 97.1% |
| errors | ACB143VanA13_F91_I0_R1_S6_L001_R2_001.good.fq | 300,806 | 39,525,166 | 100.0% | 131.4 bases | 136 bases | 95.4% |
| errors | ACB143VanA13_F91_I0_R1_S6_L002_R1_001.good.fq | 298,171 | 39,245,701 | 100.0% | 131.6 bases | 136 bases | 97.1% |
| errors | ACB143VanA13_F91_I0_R1_S6_L002_R2_001.good.fq | 298,171 | 39,247,311 | 100.0% | 131.6 bases | 136 bases | 95.3% |
| errors | ACB143VanA13_F91_I0_R1_S6_L003_R1_001.good.fq | 293,767 | 38,646,305 | 100.0% | 131.6 bases | 136 bases | 97.2% |
| errors | ACB143VanA13_F91_I0_R1_S6_L003_R2_001.good.fq | 293,767 | 38,648,009 | 100.0% | 131.6 bases | 136 bases | 95.4% |
| errors | ACB143VanA13_F91_I0_R1_S6_L004_R1_001.good.fq | 284,593 | 37,401,311 | 100.0% | 131.4 bases | 136 bases | 97.2% |
| errors | ACB143VanA13_F91_I0_R1_S6_L004_R2_001.good.fq | 284,593 | 37,402,898 | 100.0% | 131.4 bases | 136 bases | 95.5% |
| total | 2,354,674 | 309,640,127 | 100.0% | 131.5 bases | 136 bases | 96.3% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | ACB143 | 6,188,635 | 45.3 | 3.2 | 100.0% | tig00000001_arrow. |
| total | 6,188,635 | 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 | 1059 |
| 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 | 39 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.002 |
| reference sequence | pr(no read start) |
|---|---|
| ACB143 | 0.88346 |
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 | ≤ 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 | 2.2.6 |
| R | 3.4.4 |
| step | start | end | elapsed |
|---|---|---|---|
| Read and reference sequence file input | 22:01:57 01 May 2023 | 22:02:53 01 May 2023 | 56 seconds |
| Read alignment to reference genome | 22:02:54 01 May 2023 | 22:10:38 01 May 2023 | 7 minutes 44 seconds |
| Preprocessing alignments for candidate junction identification | 22:10:38 01 May 2023 | 22:11:07 01 May 2023 | 29 seconds |
| Preliminary analysis of coverage distribution | 22:11:07 01 May 2023 | 22:12:32 01 May 2023 | 1 minute 25 seconds |
| Identifying junction candidates | 22:12:32 01 May 2023 | 22:12:33 01 May 2023 | 1 second |
| Re-alignment to junction candidates | 22:12:33 01 May 2023 | 22:13:47 01 May 2023 | 1 minute 14 seconds |
| Resolving best read alignments | 22:13:47 01 May 2023 | 22:14:30 01 May 2023 | 43 seconds |
| Creating BAM files | 22:14:30 01 May 2023 | 22:15:45 01 May 2023 | 1 minute 15 seconds |
| Tabulating error counts | 22:15:45 01 May 2023 | 22:16:12 01 May 2023 | 27 seconds |
| Re-calibrating base error rates | 22:16:12 01 May 2023 | 22:16:15 01 May 2023 | 3 seconds |
| Examining read alignment evidence | 22:16:15 01 May 2023 | 22:33:45 01 May 2023 | 17 minutes 30 seconds |
| Polymorphism statistics | 22:33:45 01 May 2023 | 22:33:46 01 May 2023 | 1 second |
| Output | 22:33:46 01 May 2023 | 22:34:14 01 May 2023 | 28 seconds |
| Total | 32 minutes 16 seconds | ||
