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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsSRR0323738,477,398305,186,328100.0%36.0 bases36 bases93.8%
total8,477,398305,186,328100.0%36.0 bases36 basesNA%

Reference Sequence Information

seq idlengthfit meanfit dispersiondescription
coveragedistributionREL6064,629,81262.52.7Escherichia 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)
REL6060.46539

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.

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 input12:13:36 06 Aug 201312:14:27 06 Aug 201351 seconds
Read alignment to reference genome12:14:27 06 Aug 201313:01:58 06 Aug 201347 minutes 31 seconds
Preprocessing alignments for candidate junction identification13:01:58 06 Aug 201313:06:41 06 Aug 20134 minutes 43 seconds
Preliminary analysis of coverage distribution13:06:41 06 Aug 201313:09:29 06 Aug 20132 minutes 48 seconds
Identifying junction candidates13:09:29 06 Aug 201313:09:40 06 Aug 201311 seconds
Re-alignment to junction candidates13:09:40 06 Aug 201313:10:42 06 Aug 20131 minute 2 seconds
Resolving alignments with junction candidates13:10:42 06 Aug 201313:15:33 06 Aug 20134 minutes 51 seconds
Creating BAM files13:15:33 06 Aug 201313:18:14 06 Aug 20132 minutes 41 seconds
Tabulating error counts13:18:14 06 Aug 201313:18:52 06 Aug 201338 seconds
Re-calibrating base error rates13:18:52 06 Aug 201313:18:54 06 Aug 20132 seconds
Examining read alignment evidence16:07:37 06 Aug 201316:18:53 06 Aug 201311 minutes 16 seconds
Polymorphism statistics16:18:53 06 Aug 201316:18:57 06 Aug 20134 seconds
Output23:29:36 06 Aug 201323:31:10 06 Aug 20131 minute 34 seconds
Total 1 hour 18 minutes 12 seconds