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-6_S6_L001_R1_001.good.fq | 413,380 | 57,326,609 | 100.0% | 138.7 bases | 149 bases | 94.1% |
| errors | ALE-6_S6_L001_R2_001.good.fq | 413,380 | 57,021,623 | 100.0% | 137.9 bases | 149 bases | 95.0% |
| errors | ALE-6_S6_L002_R1_001.good.fq | 408,988 | 56,577,762 | 100.0% | 138.3 bases | 149 bases | 95.3% |
| errors | ALE-6_S6_L002_R2_001.good.fq | 408,988 | 56,349,454 | 100.0% | 137.8 bases | 149 bases | 95.6% |
| errors | ALE-6_S6_L003_R1_001.good.fq | 427,247 | 59,078,409 | 100.0% | 138.3 bases | 149 bases | 95.2% |
| errors | ALE-6_S6_L003_R2_001.good.fq | 427,247 | 58,806,283 | 100.0% | 137.6 bases | 149 bases | 96.1% |
| errors | ALE-6_S6_L004_R1_001.good.fq | 393,862 | 54,453,881 | 100.0% | 138.3 bases | 149 bases | 95.1% |
| errors | ALE-6_S6_L004_R2_001.good.fq | 393,862 | 54,242,225 | 100.0% | 137.7 bases | 149 bases | 95.3% |
| total | 3,286,954 | 453,856,246 | 100.0% | 138.1 bases | 149 bases | 95.2% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_002947 | 6,181,873 | 70.1 | 2.7 | 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 | 64165 |
| 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 | 634 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.031 |
| reference sequence | pr(no read start) |
|---|---|
| NC_002947 | 0.79515 |
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 | 17:44:23 18 Feb 2020 | 17:45:11 18 Feb 2020 | 48 seconds |
| Read alignment to reference genome | 17:45:12 18 Feb 2020 | 17:52:11 18 Feb 2020 | 6 minutes 59 seconds |
| Preprocessing alignments for candidate junction identification | 17:52:11 18 Feb 2020 | 17:52:56 18 Feb 2020 | 45 seconds |
| Preliminary analysis of coverage distribution | 17:52:56 18 Feb 2020 | 17:54:44 18 Feb 2020 | 1 minute 48 seconds |
| Identifying junction candidates | 17:54:44 18 Feb 2020 | 18:03:29 18 Feb 2020 | 8 minutes 45 seconds |
| Re-alignment to junction candidates | 18:03:29 18 Feb 2020 | 18:05:47 18 Feb 2020 | 2 minutes 18 seconds |
| Resolving best read alignments | 18:05:47 18 Feb 2020 | 18:06:58 18 Feb 2020 | 1 minute 11 seconds |
| Creating BAM files | 18:06:58 18 Feb 2020 | 18:08:39 18 Feb 2020 | 1 minute 41 seconds |
| Tabulating error counts | 18:08:39 18 Feb 2020 | 18:09:12 18 Feb 2020 | 33 seconds |
| Re-calibrating base error rates | 18:09:12 18 Feb 2020 | 18:09:15 18 Feb 2020 | 3 seconds |
| Examining read alignment evidence | 18:09:15 18 Feb 2020 | 18:26:42 18 Feb 2020 | 17 minutes 27 seconds |
| Polymorphism statistics | 18:26:42 18 Feb 2020 | 18:26:44 18 Feb 2020 | 2 seconds |
| Output | 18:26:44 18 Feb 2020 | 18:30:57 18 Feb 2020 | 4 minutes 13 seconds |
| Total | 46 minutes 33 seconds | ||
