mutation predictions | marginal predictions | summary statistics | genome diff | command line log
STRAIN: SE8R1B |
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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 | SE8R1B_1_sequence.txt | 5,800,386 | 585,838,986 | 100.0% | 101.0 bases | 101 bases | 95.9% |
| errors | SE8R1B_2_sequence.txt | 5,800,091 | 585,809,191 | 100.0% | 101.0 bases | 101 bases | 95.0% |
| total | 11,600,477 | 1,171,648,177 | 100.0% | 101.0 bases | 101 bases | 95.5% |
| seq id | length | fit mean | fit dispersion | description | ||
|---|---|---|---|---|---|---|
| coverage | distribution | NC_014034 | 3,738,958 | 294.3 | 3.2 | Rhodobacter capsulatus SB 1003 chromosome, complete genome. |
| coverage | distribution | NC_014035 | 132,962 | 183.0 | 2.1 | 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 | 0.28950 |
| NC_014035 | 0.44609 |
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 | 12:37:30 21 Mar 2013 | 12:42:02 21 Mar 2013 | 4 minutes 32 seconds |
| Read alignment to reference genome | 12:42:03 21 Mar 2013 | 13:34:53 21 Mar 2013 | 52 minutes 50 seconds |
| Preprocessing alignments for candidate junction identification | 13:34:53 21 Mar 2013 | 13:44:37 21 Mar 2013 | 9 minutes 44 seconds |
| Preliminary analysis of coverage distribution | 13:44:37 21 Mar 2013 | 13:57:16 21 Mar 2013 | 12 minutes 39 seconds |
| Identifying junction candidates | 13:57:16 21 Mar 2013 | 13:57:27 21 Mar 2013 | 11 seconds |
| Re-alignment to junction candidates | 13:57:27 21 Mar 2013 | 14:10:34 21 Mar 2013 | 13 minutes 7 seconds |
| Resolving alignments with junction candidates | 14:10:34 21 Mar 2013 | 14:25:51 21 Mar 2013 | 15 minutes 17 seconds |
| Creating BAM files | 14:25:51 21 Mar 2013 | 14:37:28 21 Mar 2013 | 11 minutes 37 seconds |
| Tabulating error counts | 14:37:28 21 Mar 2013 | 14:41:40 21 Mar 2013 | 4 minutes 12 seconds |
| Re-calibrating base error rates | 14:41:40 21 Mar 2013 | 14:41:43 21 Mar 2013 | 3 seconds |
| Examining read alignment evidence | 14:41:43 21 Mar 2013 | 15:26:01 21 Mar 2013 | 44 minutes 18 seconds |
| Polymorphism statistics | 15:26:01 21 Mar 2013 | 15:26:16 21 Mar 2013 | 15 seconds |
| Output | 15:26:16 21 Mar 2013 | 15:37:47 21 Mar 2013 | 11 minutes 31 seconds |
| Total | 3 hours 16 seconds | ||
