mutation predictions | marginal predictions | summary statistics | genome diff | command line log
STRAIN: SE8R6 |
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|
breseq version 0.22
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| read file | reads | bases | passed filters | average | longest | mapped | |
|---|---|---|---|---|---|---|---|
| errors | SE8R6_1_sequence.txt | 4,449,891 | 449,438,991 | 100.0% | 101.0 bases | 101 bases | 96.9% |
| errors | SE8R6_2_sequence.txt | 4,449,619 | 449,411,519 | 100.0% | 101.0 bases | 101 bases | 95.9% |
| total | 8,899,510 | 898,850,510 | 100.0% | 101.0 bases | 101 bases | 96.4% |
| seq id | length | fit mean | fit dispersion | description | ||
|---|---|---|---|---|---|---|
| coverage | distribution | NC_014034 | 3,738,958 | 228.0 | 2.8 | Rhodobacter capsulatus SB 1003 chromosome, complete genome. |
| coverage | distribution | NC_014035 | 132,962 | 132.7 | 1.9 | Rhodobacter capsulatus SB 1003 plasmid pRCB133, complete sequence. |
| total | 3,871,920 |
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) |
|---|---|
| NC_014034 | 0.37180 |
| NC_014035 | 0.54998 |
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 | Full Polymorphism |
| Ploidy | 1 (haploid) |
| Consensus mutation E-value cutoff | 10 |
| Polymorphism E-value cutoff | 2 |
| Polymorphism frequency cutoff | OFF |
| Polymorphism minimum coverage each strand | OFF |
| Polymorphism homopolymer length cutoff | OFF |
| Polymorphism bias cutoff | 0 |
| Polymorphism predict indel polymorphisms | OFF |
| step | start | end | elapsed |
|---|---|---|---|
| Read and reference sequence file input | 16:05:34 21 Mar 2013 | 16:09:18 21 Mar 2013 | 3 minutes 44 seconds |
| Read alignment to reference genome | 16:09:19 21 Mar 2013 | 16:50:09 21 Mar 2013 | 40 minutes 50 seconds |
| Preprocessing alignments for candidate junction identification | 16:50:09 21 Mar 2013 | 16:57:53 21 Mar 2013 | 7 minutes 44 seconds |
| Preliminary analysis of coverage distribution | 16:57:54 21 Mar 2013 | 17:07:59 21 Mar 2013 | 10 minutes 5 seconds |
| Identifying junction candidates | 17:07:59 21 Mar 2013 | 17:08:09 21 Mar 2013 | 10 seconds |
| Re-alignment to junction candidates | 17:08:09 21 Mar 2013 | 17:21:04 21 Mar 2013 | 12 minutes 55 seconds |
| Resolving alignments with junction candidates | 17:21:04 21 Mar 2013 | 17:32:41 21 Mar 2013 | 11 minutes 37 seconds |
| Creating BAM files | 17:32:41 21 Mar 2013 | 17:41:35 21 Mar 2013 | 8 minutes 54 seconds |
| Tabulating error counts | 17:41:35 21 Mar 2013 | 17:44:50 21 Mar 2013 | 3 minutes 15 seconds |
| Re-calibrating base error rates | 17:44:50 21 Mar 2013 | 17:44:54 21 Mar 2013 | 4 seconds |
| Examining read alignment evidence | 17:44:54 21 Mar 2013 | 18:19:13 21 Mar 2013 | 34 minutes 19 seconds |
| Polymorphism statistics | 18:19:13 21 Mar 2013 | 18:19:24 21 Mar 2013 | 11 seconds |
| Output | 18:19:24 21 Mar 2013 | 18:36:39 21 Mar 2013 | 17 minutes 15 seconds |
| Total | 2 hours 31 minutes 3 seconds | ||
