breseq  version 0.24rc1  revision 83e50355436e
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsSRR030257_13,739,210134,611,56098.4%36.0 bases36 bases95.1%
errorsSRR030257_23,752,181135,078,51698.7%36.0 bases36 bases93.9%
total7,491,391269,690,07698.6%36.0 bases36 bases94.5%

Reference Sequence Information

seq idlengthfit meanfit dispersiondescription
coveragedistributionREL6064,629,81255.23.0Escherichia coli strain REL606.
total4,629,812

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.

Junction Evidence

reference sequencepr(no read start)
REL6060.51817

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.

Read Alignment Evidence

optionvalue
ModeConsensus/Mixed Base
Ploidy1 (haploid)
Consensus mutation E-value cutoff10
Polymorphism E-value cutoff10
Polymorphism frequency cutoff0.1
Polymorphism minimum coverage each strand2
Polymorphism bias cutoff0.05
Predict indel polymorphismsYES
Skip indel polymorphisms in homopolymers runs ≥3 bases

Execution Times

stepstartendelapsed
Read and reference sequence file input22:43:45 01 Sep 201322:45:37 01 Sep 20131 minute 52 seconds
Read alignment to reference genome22:45:37 01 Sep 201302:18:31 02 Sep 20133 hours 32 minutes 54 seconds
Preprocessing alignments for candidate junction identification02:18:31 02 Sep 201302:28:28 02 Sep 20139 minutes 57 seconds
Preliminary analysis of coverage distribution02:28:28 02 Sep 201302:33:26 02 Sep 20134 minutes 58 seconds
Identifying junction candidates02:33:26 02 Sep 201302:34:02 02 Sep 201336 seconds
Re-alignment to junction candidates02:34:02 02 Sep 201302:36:25 02 Sep 20132 minutes 23 seconds
Resolving alignments with junction candidates02:36:26 02 Sep 201302:45:11 02 Sep 20138 minutes 45 seconds
Creating BAM files02:45:11 02 Sep 201302:49:41 02 Sep 20134 minutes 30 seconds
Tabulating error counts02:49:41 02 Sep 201302:51:10 02 Sep 20131 minute 29 seconds
Re-calibrating base error rates02:51:10 02 Sep 201302:51:12 02 Sep 20132 seconds
Examining read alignment evidence02:51:12 02 Sep 201303:05:55 02 Sep 201314 minutes 43 seconds
Output03:05:55 02 Sep 201303:07:32 02 Sep 20131 minute 37 seconds
Total 4 hours 23 minutes 46 seconds