mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.29.0 revision 8f9c342918e4
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| read file | reads | bases | passed filters | average | longest | mapped | |
|---|---|---|---|---|---|---|---|
| errors | qtrim-IND_KHP_HOT_A3_F228_I1_R1_S58_L004_R1_001 | 3,268,274 | 326,730,587 | 100.0% | 100.0 bases | 100 bases | 94.0% |
| errors | qtrim-IND_KHP_HOT_A3_F228_I1_R1_S58_L004_R2_001 | 3,268,235 | 326,240,557 | 100.0% | 99.8 bases | 100 bases | 94.5% |
| total | 6,536,509 | 652,971,144 | 100.0% | 99.9 bases | 100 bases | 94.2% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_000913 | 4,641,652 | 128.3 | 2.6 | 98.1% | Escherichia coli str. K-12 substr. MG1655, complete genome. |
| total | 4,641,652 | 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 | 100039 |
| 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 | 1284 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.057 |
| reference sequence | pr(no read start) |
|---|---|
| NC_000913 | 0.56884 |
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 |
| step | start | end | elapsed |
|---|---|---|---|
| Read and reference sequence file input | 20:41:36 04 Jan 2017 | 20:42:43 04 Jan 2017 | 1 minute 7 seconds |
| Read alignment to reference genome | 20:42:43 04 Jan 2017 | 20:46:35 04 Jan 2017 | 3 minutes 52 seconds |
| Preprocessing alignments for candidate junction identification | 20:46:35 04 Jan 2017 | 20:48:59 04 Jan 2017 | 2 minutes 24 seconds |
| Preliminary analysis of coverage distribution | 20:48:59 04 Jan 2017 | 20:51:29 04 Jan 2017 | 2 minutes 30 seconds |
| Identifying junction candidates | 20:51:29 04 Jan 2017 | 21:01:53 04 Jan 2017 | 10 minutes 24 seconds |
| Re-alignment to junction candidates | 21:01:53 04 Jan 2017 | 21:03:21 04 Jan 2017 | 1 minute 28 seconds |
| Resolving alignments with junction candidates | 21:03:21 04 Jan 2017 | 21:08:17 04 Jan 2017 | 4 minutes 56 seconds |
| Creating BAM files | 21:08:18 04 Jan 2017 | 21:09:45 04 Jan 2017 | 1 minute 27 seconds |
| Tabulating error counts | 21:09:45 04 Jan 2017 | 21:12:33 04 Jan 2017 | 2 minutes 48 seconds |
| Re-calibrating base error rates | 21:12:33 04 Jan 2017 | 21:12:34 04 Jan 2017 | 1 second |
| Examining read alignment evidence | 21:12:34 04 Jan 2017 | 21:32:26 04 Jan 2017 | 19 minutes 52 seconds |
| Polymorphism statistics | 21:32:26 04 Jan 2017 | 21:32:29 04 Jan 2017 | 3 seconds |
| Output | 21:32:29 04 Jan 2017 | 21:33:47 04 Jan 2017 | 1 minute 18 seconds |
| Total | 52 minutes 10 seconds | ||
