breseq  version 0.24  revision cd15a9d216e1
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsSRR0323707,513,933270,501,588100.0%36.0 bases36 bases98.5%
total7,513,933270,501,588100.0%36.0 bases36 basesNA%

Reference Sequence Information

seq idlengthfit meanfit dispersiondescription
coveragedistributionREL6064,629,81258.13.9Escherichia 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)
REL6060.48489

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
ModeFull Polymorphism
Ploidy1 (haploid)
Consensus mutation E-value cutoff10
Polymorphism E-value cutoff2
Polymorphism frequency cutoffOFF
Polymorphism minimum coverage each strand2
Polymorphism homopolymer length cutoffOFF
Polymorphism bias cutoff0
Predict indel polymorphismsYES
Skip indel polymorphisms in homopolymers runsALL

Execution Times

stepstartendelapsed
Read and reference sequence file input12:13:35 06 Aug 201312:14:22 06 Aug 201347 seconds
Read alignment to reference genome12:14:22 06 Aug 201312:50:27 06 Aug 201336 minutes 5 seconds
Preprocessing alignments for candidate junction identification12:50:27 06 Aug 201312:54:31 06 Aug 20134 minutes 4 seconds
Preliminary analysis of coverage distribution12:54:31 06 Aug 201312:57:14 06 Aug 20132 minutes 43 seconds
Identifying junction candidates12:57:14 06 Aug 201312:57:22 06 Aug 20138 seconds
Re-alignment to junction candidates12:57:22 06 Aug 201312:58:17 06 Aug 201355 seconds
Resolving alignments with junction candidates12:58:17 06 Aug 201313:02:49 06 Aug 20134 minutes 32 seconds
Creating BAM files13:02:49 06 Aug 201313:05:23 06 Aug 20132 minutes 34 seconds
Tabulating error counts13:05:23 06 Aug 201313:06:00 06 Aug 201337 seconds
Re-calibrating base error rates13:06:00 06 Aug 201313:06:01 06 Aug 20131 second
Examining read alignment evidence16:07:37 06 Aug 201316:18:21 06 Aug 201310 minutes 44 seconds
Polymorphism statistics16:18:21 06 Aug 201316:18:23 06 Aug 20132 seconds
Output23:29:36 06 Aug 201323:30:35 06 Aug 201359 seconds
Total 1 hour 4 minutes 11 seconds