mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.20 revision c633c5005425
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| read file | reads | bases | passed filters | average | longest | mapped | |
|---|---|---|---|---|---|---|---|
| errors | REL8593A | 7,491,391 | 269,690,076 | 98.6% | 36.0 bases | 36 bases | 94.0% |
| total | 7,491,391 | 269,690,076 | 98.6% | 36.0 bases | 36 bases | 94.0% |
| seq id | length | fit mean | fit dispersion | description | ||
|---|---|---|---|---|---|---|
| coverage | distribution | REL606 | 4,629,812 | 55.0 | 3.0 | Escherichia coli strain REL606. |
| total | 4,629,812 |
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.
| reference sequence | pr(no read start) |
|---|---|
| REL606 | 0.52020 |
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 |
|---|---|
| Mode | Consensus/Mixed Base |
| Ploidy | 1 (haploid) |
| Consensus mutation E-value cutoff | 10 |
| Polymorphism E-value cutoff | 10 |
| Polymorphism frequency cutoff | 0 |
| Polymorphism minimum coverage each strand | 2 |
| Polymorphism homopolymer length cutoff | 3 |
| Polymorphism bias cutoff | OFF |
| Polymorphism predict indel polymorphisms | 3 |
| step | start | end | elapsed |
|---|---|---|---|
| Read and reference sequence file input | 07:59:58 24 Sep 2012 | 08:01:31 24 Sep 2012 | 1 minute 33 seconds |
| Read alignment to reference genome | 08:01:31 24 Sep 2012 | 08:23:24 24 Sep 2012 | 21 minutes 53 seconds |
| Preprocessing alignments for candidate junction identification | 08:23:24 24 Sep 2012 | 08:32:52 24 Sep 2012 | 9 minutes 28 seconds |
| Preliminary analysis of coverage distribution | 08:32:52 24 Sep 2012 | 08:37:30 24 Sep 2012 | 4 minutes 38 seconds |
| Identifying junction candidates | 08:37:30 24 Sep 2012 | 08:38:26 24 Sep 2012 | 56 seconds |
| Re-alignment to junction candidates | 08:38:26 24 Sep 2012 | 08:41:39 24 Sep 2012 | 3 minutes 13 seconds |
| Resolving alignments with junction candidates | 08:41:39 24 Sep 2012 | 08:49:38 24 Sep 2012 | 7 minutes 59 seconds |
| Creating BAM files | 08:49:38 24 Sep 2012 | 08:55:29 24 Sep 2012 | 5 minutes 51 seconds |
| Tabulating error counts | 08:55:29 24 Sep 2012 | 08:56:55 24 Sep 2012 | 1 minute 26 seconds |
| Re-calibrating base error rates | 08:56:55 24 Sep 2012 | 08:56:57 24 Sep 2012 | 2 seconds |
| Examining read alignment evidence | 08:56:57 24 Sep 2012 | 09:11:04 24 Sep 2012 | 14 minutes 7 seconds |
| Output | 09:11:04 24 Sep 2012 | 09:12:24 24 Sep 2012 | 1 minute 20 seconds |
| Total | 1 hour 12 minutes 26 seconds | ||
