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 | ALE-4_S4_L001_R1_001.good.fq | 341,384 | 49,184,699 | 100.0% | 144.1 bases | 149 bases | 92.9% |
| errors | ALE-4_S4_L001_R2_001.good.fq | 341,384 | 48,895,845 | 100.0% | 143.2 bases | 149 bases | 94.2% |
| errors | ALE-4_S4_L002_R1_001.good.fq | 329,781 | 47,430,696 | 100.0% | 143.8 bases | 149 bases | 94.3% |
| errors | ALE-4_S4_L002_R2_001.good.fq | 329,781 | 47,180,814 | 100.0% | 143.1 bases | 149 bases | 94.9% |
| errors | ALE-4_S4_L003_R1_001.good.fq | 348,024 | 50,042,810 | 100.0% | 143.8 bases | 149 bases | 94.0% |
| errors | ALE-4_S4_L003_R2_001.good.fq | 348,024 | 49,749,791 | 100.0% | 142.9 bases | 149 bases | 95.1% |
| errors | ALE-4_S4_L004_R1_001.good.fq | 317,635 | 45,677,100 | 100.0% | 143.8 bases | 149 bases | 94.1% |
| errors | ALE-4_S4_L004_R2_001.good.fq | 317,635 | 45,425,664 | 100.0% | 143.0 bases | 149 bases | 94.5% |
| total | 2,673,648 | 383,587,419 | 100.0% | 143.5 bases | 149 bases | 94.2% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_002947 | 6,181,873 | 58.8 | 2.3 | 100.0% | Pseudomonas putida KT2440 chromosome, complete genome. |
| total | 6,181,873 | 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 | 61054 |
| 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 | 540 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.027 |
| reference sequence | pr(no read start) |
|---|---|
| NC_002947 | 0.83077 |
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 | 16:33:58 18 Feb 2020 | 16:34:39 18 Feb 2020 | 41 seconds |
| Read alignment to reference genome | 16:34:39 18 Feb 2020 | 16:40:33 18 Feb 2020 | 5 minutes 54 seconds |
| Preprocessing alignments for candidate junction identification | 16:40:33 18 Feb 2020 | 16:41:11 18 Feb 2020 | 38 seconds |
| Preliminary analysis of coverage distribution | 16:41:11 18 Feb 2020 | 16:42:41 18 Feb 2020 | 1 minute 30 seconds |
| Identifying junction candidates | 16:42:41 18 Feb 2020 | 16:49:08 18 Feb 2020 | 6 minutes 27 seconds |
| Re-alignment to junction candidates | 16:49:08 18 Feb 2020 | 16:51:00 18 Feb 2020 | 1 minute 52 seconds |
| Resolving best read alignments | 16:51:00 18 Feb 2020 | 16:51:58 18 Feb 2020 | 58 seconds |
| Creating BAM files | 16:51:58 18 Feb 2020 | 16:53:23 18 Feb 2020 | 1 minute 25 seconds |
| Tabulating error counts | 16:53:23 18 Feb 2020 | 16:53:50 18 Feb 2020 | 27 seconds |
| Re-calibrating base error rates | 16:53:50 18 Feb 2020 | 16:53:53 18 Feb 2020 | 3 seconds |
| Examining read alignment evidence | 16:53:53 18 Feb 2020 | 17:07:56 18 Feb 2020 | 14 minutes 3 seconds |
| Polymorphism statistics | 17:07:56 18 Feb 2020 | 17:07:58 18 Feb 2020 | 2 seconds |
| Output | 17:07:58 18 Feb 2020 | 17:11:34 18 Feb 2020 | 3 minutes 36 seconds |
| Total | 37 minutes 36 seconds | ||
