mutation predictions | marginal predictions | summary statistics | genome diff | command line log
STRAIN: MT1131 |
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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 | MT1131_1_sequence.txt | 4,755,465 | 480,301,965 | 100.0% | 101.0 bases | 101 bases | 95.1% |
| errors | MT1131_2_sequence.txt | 4,755,209 | 480,276,109 | 100.0% | 101.0 bases | 101 bases | 94.2% |
| total | 9,510,674 | 960,578,074 | 100.0% | 101.0 bases | 101 bases | 94.7% |
| seq id | length | fit mean | fit dispersion | description | ||
|---|---|---|---|---|---|---|
| coverage | distribution | NC_014034 | 3,738,958 | 238.3 | 3.8 | Rhodobacter capsulatus SB 1003 chromosome, complete genome. |
| coverage | distribution | NC_014035 | 132,962 | 138.9 | 2.3 | 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 | 0.36538 |
| NC_014035 | 0.54089 |
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 | 13:08:16 20 Mar 2013 | 13:12:06 20 Mar 2013 | 3 minutes 50 seconds |
| Read alignment to reference genome | 13:12:07 20 Mar 2013 | 13:54:43 20 Mar 2013 | 42 minutes 36 seconds |
| Preprocessing alignments for candidate junction identification | 13:54:43 20 Mar 2013 | 14:02:36 20 Mar 2013 | 7 minutes 53 seconds |
| Preliminary analysis of coverage distribution | 14:02:36 20 Mar 2013 | 14:12:57 20 Mar 2013 | 10 minutes 21 seconds |
| Identifying junction candidates | 14:12:57 20 Mar 2013 | 14:13:06 20 Mar 2013 | 9 seconds |
| Re-alignment to junction candidates | 14:13:06 20 Mar 2013 | 14:25:57 20 Mar 2013 | 12 minutes 51 seconds |
| Resolving alignments with junction candidates | 14:25:57 20 Mar 2013 | 14:38:48 20 Mar 2013 | 12 minutes 51 seconds |
| Creating BAM files | 14:38:48 20 Mar 2013 | 14:48:18 20 Mar 2013 | 9 minutes 30 seconds |
| Tabulating error counts | 14:48:18 20 Mar 2013 | 14:51:42 20 Mar 2013 | 3 minutes 24 seconds |
| Re-calibrating base error rates | 14:51:42 20 Mar 2013 | 14:51:45 20 Mar 2013 | 3 seconds |
| Examining read alignment evidence | 14:51:45 20 Mar 2013 | 15:27:26 20 Mar 2013 | 35 minutes 41 seconds |
| Polymorphism statistics | 15:27:26 20 Mar 2013 | 15:27:37 20 Mar 2013 | 11 seconds |
| Output | 15:27:37 20 Mar 2013 | 15:43:49 20 Mar 2013 | 16 minutes 12 seconds |
| Total | 2 hours 35 minutes 32 seconds | ||
