mutation predictions | marginal predictions | summary statistics | genome diff | command line log
STRAIN: SE8H |
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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-H_1_sequence.txt | 7,137,451 | 720,882,551 | 100.0% | 101.0 bases | 101 bases | 95.3% |
| errors | SE8-H_2_sequence.txt | 7,137,077 | 720,844,777 | 100.0% | 101.0 bases | 101 bases | 94.3% |
| total | 14,274,528 | 1,441,727,328 | 100.0% | 101.0 bases | 101 bases | 94.8% |
| seq id | length | fit mean | fit dispersion | description | ||
|---|---|---|---|---|---|---|
| coverage | distribution | NC_014034 | 3,738,958 | 359.5 | 5.4 | Rhodobacter capsulatus SB 1003 chromosome, complete genome. |
| coverage | distribution | NC_014035 | 132,962 | 169.2 | 2.9 | 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 | 0.25087 |
| NC_014035 | 0.48503 |
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 | 19:17:28 20 Mar 2013 | 19:25:53 20 Mar 2013 | 8 minutes 25 seconds |
| Read alignment to reference genome | 19:25:54 20 Mar 2013 | 20:37:06 20 Mar 2013 | 1 hour 11 minutes 12 seconds |
| Preprocessing alignments for candidate junction identification | 20:37:06 20 Mar 2013 | 20:51:39 20 Mar 2013 | 14 minutes 33 seconds |
| Preliminary analysis of coverage distribution | 20:51:39 20 Mar 2013 | 21:08:59 20 Mar 2013 | 17 minutes 20 seconds |
| Identifying junction candidates | 21:08:59 20 Mar 2013 | 21:09:12 20 Mar 2013 | 13 seconds |
| Re-alignment to junction candidates | 21:09:12 20 Mar 2013 | 21:27:52 20 Mar 2013 | 18 minutes 40 seconds |
| Resolving alignments with junction candidates | 21:27:52 20 Mar 2013 | 21:49:44 20 Mar 2013 | 21 minutes 52 seconds |
| Creating BAM files | 21:49:44 20 Mar 2013 | 22:05:04 20 Mar 2013 | 15 minutes 20 seconds |
| Tabulating error counts | 22:05:04 20 Mar 2013 | 22:10:13 20 Mar 2013 | 5 minutes 9 seconds |
| Re-calibrating base error rates | 22:10:13 20 Mar 2013 | 22:10:17 20 Mar 2013 | 4 seconds |
| Examining read alignment evidence | 22:10:17 20 Mar 2013 | 23:04:04 20 Mar 2013 | 53 minutes 47 seconds |
| Polymorphism statistics | 23:04:04 20 Mar 2013 | 23:04:18 20 Mar 2013 | 14 seconds |
| Output | 23:04:18 20 Mar 2013 | 23:16:52 20 Mar 2013 | 12 minutes 34 seconds |
| Total | 3 hours 59 minutes 23 seconds | ||
