mutation predictions | marginal predictions | summary statistics | genome diff | command line log
STRAIN: SE8R1A |
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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 | SE8R1A_1_sequence.txt | 9,202,410 | 929,443,410 | 100.0% | 101.0 bases | 101 bases | 95.1% |
| errors | SE8R1A_2_sequence.txt | 9,201,988 | 929,400,788 | 100.0% | 101.0 bases | 101 bases | 94.1% |
| total | 18,404,398 | 1,858,844,198 | 100.0% | 101.0 bases | 101 bases | 94.6% |
| seq id | length | fit mean | fit dispersion | description | ||
|---|---|---|---|---|---|---|
| coverage | distribution | NC_014034 | 3,738,958 | 459.9 | 7.4 | Rhodobacter capsulatus SB 1003 chromosome, complete genome. |
| coverage | distribution | NC_014035 | 132,962 | 273.4 | 4.4 | 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 | 0.19280 |
| NC_014035 | 0.33612 |
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 | 23:39:24 20 Mar 2013 | 23:47:56 20 Mar 2013 | 8 minutes 32 seconds |
| Read alignment to reference genome | 23:47:57 20 Mar 2013 | 01:12:27 21 Mar 2013 | 1 hour 24 minutes 30 seconds |
| Preprocessing alignments for candidate junction identification | 01:12:27 21 Mar 2013 | 01:27:51 21 Mar 2013 | 15 minutes 24 seconds |
| Preliminary analysis of coverage distribution | 01:27:51 21 Mar 2013 | 01:47:55 21 Mar 2013 | 20 minutes 4 seconds |
| Identifying junction candidates | 01:47:55 21 Mar 2013 | 01:48:13 21 Mar 2013 | 18 seconds |
| Re-alignment to junction candidates | 01:48:13 21 Mar 2013 | 02:09:56 21 Mar 2013 | 21 minutes 43 seconds |
| Resolving alignments with junction candidates | 02:09:56 21 Mar 2013 | 02:35:55 21 Mar 2013 | 25 minutes 59 seconds |
| Creating BAM files | 02:35:55 21 Mar 2013 | 02:53:23 21 Mar 2013 | 17 minutes 28 seconds |
| Tabulating error counts | 02:53:23 21 Mar 2013 | 03:00:03 21 Mar 2013 | 6 minutes 40 seconds |
| Re-calibrating base error rates | 03:00:03 21 Mar 2013 | 03:00:07 21 Mar 2013 | 4 seconds |
| Examining read alignment evidence | 03:00:07 21 Mar 2013 | 04:10:06 21 Mar 2013 | 1 hour 9 minutes 59 seconds |
| Polymorphism statistics | 04:10:06 21 Mar 2013 | 04:10:24 21 Mar 2013 | 18 seconds |
| Output | 04:10:24 21 Mar 2013 | 04:25:13 21 Mar 2013 | 14 minutes 49 seconds |
| Total | 4 hours 45 minutes 48 seconds | ||
