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breseq version 0.24 revision cd15a9d216e1
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
read file | reads | bases | passed filters | average | longest | mapped | |
---|---|---|---|---|---|---|---|
errors | SRR032373 | 8,477,398 | 305,186,328 | 100.0% | 36.0 bases | 36 bases | 93.8% |
total | 8,477,398 | 305,186,328 | 100.0% | 36.0 bases | 36 bases | NA% |
seq id | length | fit mean | fit dispersion | description | ||
---|---|---|---|---|---|---|
coverage | distribution | REL606 | 4,629,812 | 62.5 | 2.7 | Escherichia coli strain REL606. |
total | 4,629,812 |
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) |
---|---|
REL606 | 0.46539 |
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 | 2 |
Polymorphism homopolymer length cutoff | OFF |
Polymorphism bias cutoff | 0 |
Predict indel polymorphisms | YES |
Skip indel polymorphisms in homopolymers runs | ALL |
step | start | end | elapsed |
---|---|---|---|
Read and reference sequence file input | 12:13:36 06 Aug 2013 | 12:14:27 06 Aug 2013 | 51 seconds |
Read alignment to reference genome | 12:14:27 06 Aug 2013 | 13:01:58 06 Aug 2013 | 47 minutes 31 seconds |
Preprocessing alignments for candidate junction identification | 13:01:58 06 Aug 2013 | 13:06:41 06 Aug 2013 | 4 minutes 43 seconds |
Preliminary analysis of coverage distribution | 13:06:41 06 Aug 2013 | 13:09:29 06 Aug 2013 | 2 minutes 48 seconds |
Identifying junction candidates | 13:09:29 06 Aug 2013 | 13:09:40 06 Aug 2013 | 11 seconds |
Re-alignment to junction candidates | 13:09:40 06 Aug 2013 | 13:10:42 06 Aug 2013 | 1 minute 2 seconds |
Resolving alignments with junction candidates | 13:10:42 06 Aug 2013 | 13:15:33 06 Aug 2013 | 4 minutes 51 seconds |
Creating BAM files | 13:15:33 06 Aug 2013 | 13:18:14 06 Aug 2013 | 2 minutes 41 seconds |
Tabulating error counts | 13:18:14 06 Aug 2013 | 13:18:52 06 Aug 2013 | 38 seconds |
Re-calibrating base error rates | 13:18:52 06 Aug 2013 | 13:18:54 06 Aug 2013 | 2 seconds |
Examining read alignment evidence | 16:07:37 06 Aug 2013 | 16:18:53 06 Aug 2013 | 11 minutes 16 seconds |
Polymorphism statistics | 16:18:53 06 Aug 2013 | 16:18:57 06 Aug 2013 | 4 seconds |
Output | 23:29:36 06 Aug 2013 | 23:31:10 06 Aug 2013 | 1 minute 34 seconds |
Total | 1 hour 18 minutes 12 seconds |