mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.31.0 revision 69e7c3c0fa11
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| read file | reads | bases | passed filters | average | longest | mapped | |
|---|---|---|---|---|---|---|---|
| errors | PAL038_S38_R1_001.good.fq | 6,865,396 | 867,307,759 | 100.0% | 126.3 bases | 128 bases | 99.2% |
| errors | PAL038_S38_R2_001.good.fq | 6,865,396 | 867,307,759 | 100.0% | 126.3 bases | 128 bases | 98.3% |
| total | 13,730,792 | 1,734,615,518 | 100.0% | 126.3 bases | 128 bases | 98.7% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | CP016816 | 543,379 | 3186.4 | 29.6 | 100.0% | Synthetic bacterium JCVI-Syn3.0 strain 6d, complete genome. |
| total | 543,379 | 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 | 42996 |
| Coverage evenness (position-hash) score of junction candidates | ≥ 2 | ≥ 8 |
| Test this many junction candidates (n). May be smaller if not enough passed the coverage evenness threshold | 100 ≤ n ≤ 5000 | 194 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.095 |
| reference sequence | pr(no read start) |
|---|---|
| CP016816 | 0.01035 |
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 | ≤ 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 | 0.8 |
| Consensus minimum coverage each strand | OFF |
| Polymorphism E-value cutoff | 10 |
| Polymorphism frequency cutoff | 0.2 |
| Polymorphism minimum coverage each strand | 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 | 2.2.8 |
| R | 3.3.1 |
| step | start | end | elapsed |
|---|---|---|---|
| Read and reference sequence file input | 17:06:42 17 Nov 2017 | 17:09:29 17 Nov 2017 | 2 minutes 47 seconds |
| Read alignment to reference genome | 17:09:29 17 Nov 2017 | 17:17:41 17 Nov 2017 | 8 minutes 12 seconds |
| Preprocessing alignments for candidate junction identification | 17:17:41 17 Nov 2017 | 17:22:38 17 Nov 2017 | 4 minutes 57 seconds |
| Preliminary analysis of coverage distribution | 17:22:38 17 Nov 2017 | 17:30:16 17 Nov 2017 | 7 minutes 38 seconds |
| Identifying junction candidates | 17:30:16 17 Nov 2017 | 17:30:27 17 Nov 2017 | 11 seconds |
| Re-alignment to junction candidates | 17:30:27 17 Nov 2017 | 17:32:44 17 Nov 2017 | 2 minutes 17 seconds |
| Resolving alignments with junction candidates | 17:32:44 17 Nov 2017 | 17:42:05 17 Nov 2017 | 9 minutes 21 seconds |
| Creating BAM files | 17:42:05 17 Nov 2017 | 17:46:31 17 Nov 2017 | 4 minutes 26 seconds |
| Tabulating error counts | 17:46:31 17 Nov 2017 | 17:54:13 17 Nov 2017 | 7 minutes 42 seconds |
| Re-calibrating base error rates | 17:54:13 17 Nov 2017 | 17:54:15 17 Nov 2017 | 2 seconds |
| Examining read alignment evidence | 17:54:15 17 Nov 2017 | 18:50:25 17 Nov 2017 | 56 minutes 10 seconds |
| Polymorphism statistics | 18:50:25 17 Nov 2017 | 18:50:31 17 Nov 2017 | 6 seconds |
| Output | 18:50:31 17 Nov 2017 | 18:52:22 17 Nov 2017 | 1 minute 51 seconds |
| Total | 1 hour 45 minutes 40 seconds | ||
