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breseq version 0.24rc1 revision 83e50355436e
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
read file | reads | bases | passed filters | average | longest | mapped | |
---|---|---|---|---|---|---|---|
errors | SRR030257_1 | 3,739,210 | 134,611,560 | 98.4% | 36.0 bases | 36 bases | 95.1% |
errors | SRR030257_2 | 3,752,181 | 135,078,516 | 98.7% | 36.0 bases | 36 bases | 93.9% |
total | 7,491,391 | 269,690,076 | 98.6% | 36.0 bases | 36 bases | 94.5% |
seq id | length | fit mean | fit dispersion | description | ||
---|---|---|---|---|---|---|
coverage | distribution | REL606 | 4,629,812 | 55.2 | 3.0 | 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 | 0.51817 |
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 | Consensus/Mixed Base |
Ploidy | 1 (haploid) |
Consensus mutation E-value cutoff | 10 |
Polymorphism E-value cutoff | 10 |
Polymorphism frequency cutoff | 0.1 |
Polymorphism minimum coverage each strand | 2 |
Polymorphism bias cutoff | 0.05 |
Predict indel polymorphisms | YES |
Skip indel polymorphisms in homopolymers runs | ≥3 bases |
step | start | end | elapsed |
---|---|---|---|
Read and reference sequence file input | 22:43:45 01 Sep 2013 | 22:45:37 01 Sep 2013 | 1 minute 52 seconds |
Read alignment to reference genome | 22:45:37 01 Sep 2013 | 02:18:31 02 Sep 2013 | 3 hours 32 minutes 54 seconds |
Preprocessing alignments for candidate junction identification | 02:18:31 02 Sep 2013 | 02:28:28 02 Sep 2013 | 9 minutes 57 seconds |
Preliminary analysis of coverage distribution | 02:28:28 02 Sep 2013 | 02:33:26 02 Sep 2013 | 4 minutes 58 seconds |
Identifying junction candidates | 02:33:26 02 Sep 2013 | 02:34:02 02 Sep 2013 | 36 seconds |
Re-alignment to junction candidates | 02:34:02 02 Sep 2013 | 02:36:25 02 Sep 2013 | 2 minutes 23 seconds |
Resolving alignments with junction candidates | 02:36:26 02 Sep 2013 | 02:45:11 02 Sep 2013 | 8 minutes 45 seconds |
Creating BAM files | 02:45:11 02 Sep 2013 | 02:49:41 02 Sep 2013 | 4 minutes 30 seconds |
Tabulating error counts | 02:49:41 02 Sep 2013 | 02:51:10 02 Sep 2013 | 1 minute 29 seconds |
Re-calibrating base error rates | 02:51:10 02 Sep 2013 | 02:51:12 02 Sep 2013 | 2 seconds |
Examining read alignment evidence | 02:51:12 02 Sep 2013 | 03:05:55 02 Sep 2013 | 14 minutes 43 seconds |
Output | 03:05:55 02 Sep 2013 | 03:07:32 02 Sep 2013 | 1 minute 37 seconds |
Total | 4 hours 23 minutes 46 seconds |