mutation predictions | marginal predictions | summary statistics | genome diff | command line log
STRAIN: SE8R5 |
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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 | SE8R5_1_sequence.txt | 4,672,899 | 471,962,799 | 100.0% | 101.0 bases | 101 bases | 96.8% |
| errors | SE8R5_2_sequence.txt | 4,672,598 | 471,932,398 | 100.0% | 101.0 bases | 101 bases | 95.9% |
| total | 9,345,497 | 943,895,197 | 100.0% | 101.0 bases | 101 bases | 96.4% |
| seq id | length | fit mean | fit dispersion | description | ||
|---|---|---|---|---|---|---|
| coverage | distribution | NC_014034 | 3,738,958 | 239.9 | 2.7 | Rhodobacter capsulatus SB 1003 chromosome, complete genome. |
| coverage | distribution | NC_014035 | 132,962 | 137.3 | 1.8 | 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 | 0.35518 |
| NC_014035 | 0.53920 |
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 | 08:55:54 22 Mar 2013 | 08:59:50 22 Mar 2013 | 3 minutes 56 seconds |
| Read alignment to reference genome | 08:59:51 22 Mar 2013 | 09:41:42 22 Mar 2013 | 41 minutes 51 seconds |
| Preprocessing alignments for candidate junction identification | 09:41:42 22 Mar 2013 | 09:49:37 22 Mar 2013 | 7 minutes 55 seconds |
| Preliminary analysis of coverage distribution | 09:49:37 22 Mar 2013 | 10:00:10 22 Mar 2013 | 10 minutes 33 seconds |
| Identifying junction candidates | 10:00:10 22 Mar 2013 | 10:00:19 22 Mar 2013 | 9 seconds |
| Re-alignment to junction candidates | 10:00:19 22 Mar 2013 | 10:13:57 22 Mar 2013 | 13 minutes 38 seconds |
| Resolving alignments with junction candidates | 10:13:57 22 Mar 2013 | 10:26:41 22 Mar 2013 | 12 minutes 44 seconds |
| Creating BAM files | 10:26:41 22 Mar 2013 | 10:36:10 22 Mar 2013 | 9 minutes 29 seconds |
| Tabulating error counts | 10:36:10 22 Mar 2013 | 10:39:33 22 Mar 2013 | 3 minutes 23 seconds |
| Re-calibrating base error rates | 10:39:33 22 Mar 2013 | 10:39:37 22 Mar 2013 | 4 seconds |
| Examining read alignment evidence | 10:39:37 22 Mar 2013 | 11:16:04 22 Mar 2013 | 36 minutes 27 seconds |
| Polymorphism statistics | 11:16:04 22 Mar 2013 | 11:16:17 22 Mar 2013 | 13 seconds |
| Output | 11:16:17 22 Mar 2013 | 11:33:36 22 Mar 2013 | 17 minutes 19 seconds |
| Total | 2 hours 37 minutes 41 seconds | ||
