mutation predictions | marginal predictions | summary statistics | genome diff | command line log
STRAIN: SE8E |
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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 | SE8-E_1_sequence.txt | 5,054,872 | 510,542,072 | 100.0% | 101.0 bases | 101 bases | 92.7% |
| errors | SE8-E_2_sequence.txt | 5,054,542 | 510,508,742 | 100.0% | 101.0 bases | 101 bases | 91.4% |
| total | 10,109,414 | 1,021,050,814 | 100.0% | 101.0 bases | 101 bases | 92.0% |
| seq id | length | fit mean | fit dispersion | description | ||
|---|---|---|---|---|---|---|
| coverage | distribution | NC_014034 | 3,738,958 | 246.4 | 4.7 | Rhodobacter capsulatus SB 1003 chromosome, complete genome. |
| coverage | distribution | NC_014035 | 132,962 | 138.0 | 3.0 | 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 | 0.36800 |
| NC_014035 | 0.54986 |
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 | 15:52:43 20 Mar 2013 | 15:57:16 20 Mar 2013 | 4 minutes 33 seconds |
| Read alignment to reference genome | 15:57:17 20 Mar 2013 | 16:51:28 20 Mar 2013 | 54 minutes 11 seconds |
| Preprocessing alignments for candidate junction identification | 16:51:28 20 Mar 2013 | 17:01:07 20 Mar 2013 | 9 minutes 39 seconds |
| Preliminary analysis of coverage distribution | 17:01:07 20 Mar 2013 | 17:12:22 20 Mar 2013 | 11 minutes 15 seconds |
| Identifying junction candidates | 17:12:22 20 Mar 2013 | 17:12:32 20 Mar 2013 | 10 seconds |
| Re-alignment to junction candidates | 17:12:32 20 Mar 2013 | 17:26:51 20 Mar 2013 | 14 minutes 19 seconds |
| Resolving alignments with junction candidates | 17:26:51 20 Mar 2013 | 17:40:16 20 Mar 2013 | 13 minutes 25 seconds |
| Creating BAM files | 17:40:16 20 Mar 2013 | 17:50:00 20 Mar 2013 | 9 minutes 44 seconds |
| Tabulating error counts | 17:50:00 20 Mar 2013 | 17:53:31 20 Mar 2013 | 3 minutes 31 seconds |
| Re-calibrating base error rates | 17:53:31 20 Mar 2013 | 17:53:35 20 Mar 2013 | 4 seconds |
| Examining read alignment evidence | 17:53:35 20 Mar 2013 | 18:30:41 20 Mar 2013 | 37 minutes 6 seconds |
| Polymorphism statistics | 18:30:41 20 Mar 2013 | 18:30:53 20 Mar 2013 | 12 seconds |
| Output | 18:30:53 20 Mar 2013 | 18:47:48 20 Mar 2013 | 16 minutes 55 seconds |
| Total | 2 hours 55 minutes 4 seconds | ||
