mutation predictions | marginal predictions | summary statistics | genome diff | command line log
STRAIN: SE8R2 |
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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 | SE8R2_1_sequence.txt | 4,236,725 | 427,909,225 | 100.0% | 101.0 bases | 101 bases | 95.6% |
| errors | SE8R2_2_sequence.txt | 4,236,463 | 427,882,763 | 100.0% | 101.0 bases | 101 bases | 94.7% |
| total | 8,473,188 | 855,791,988 | 100.0% | 101.0 bases | 101 bases | 95.2% |
| seq id | length | fit mean | fit dispersion | description | ||
|---|---|---|---|---|---|---|
| coverage | distribution | NC_014034 | 3,738,958 | 213.2 | 3.0 | Rhodobacter capsulatus SB 1003 chromosome, complete genome. |
| coverage | distribution | NC_014035 | 132,962 | 142.0 | 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 | 0.39563 |
| NC_014035 | 0.52953 |
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 | 10:35:58 20 Mar 2013 | 10:39:18 20 Mar 2013 | 3 minutes 20 seconds |
| Read alignment to reference genome | 10:39:19 20 Mar 2013 | 11:17:26 20 Mar 2013 | 38 minutes 7 seconds |
| Preprocessing alignments for candidate junction identification | 11:17:26 20 Mar 2013 | 11:24:28 20 Mar 2013 | 7 minutes 2 seconds |
| Preliminary analysis of coverage distribution | 11:24:29 20 Mar 2013 | 11:33:49 20 Mar 2013 | 9 minutes 20 seconds |
| Identifying junction candidates | 11:33:49 20 Mar 2013 | 11:33:58 20 Mar 2013 | 9 seconds |
| Re-alignment to junction candidates | 11:33:58 20 Mar 2013 | 11:46:27 20 Mar 2013 | 12 minutes 29 seconds |
| Resolving alignments with junction candidates | 11:46:27 20 Mar 2013 | 11:57:24 20 Mar 2013 | 10 minutes 57 seconds |
| Creating BAM files | 11:57:24 20 Mar 2013 | 12:05:53 20 Mar 2013 | 8 minutes 29 seconds |
| Tabulating error counts | 12:05:53 20 Mar 2013 | 12:08:55 20 Mar 2013 | 3 minutes 2 seconds |
| Re-calibrating base error rates | 12:08:55 20 Mar 2013 | 12:08:59 20 Mar 2013 | 4 seconds |
| Examining read alignment evidence | 12:08:59 20 Mar 2013 | 12:41:13 20 Mar 2013 | 32 minutes 14 seconds |
| Polymorphism statistics | 12:41:13 20 Mar 2013 | 12:41:24 20 Mar 2013 | 11 seconds |
| Output | 12:41:24 20 Mar 2013 | 12:58:18 20 Mar 2013 | 16 minutes 54 seconds |
| Total | 2 hours 22 minutes 18 seconds | ||
