BRESEQ :: Summary Statistics
breseq  version 0.36.1  
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsSRR030257_1.fq999,82735,993,772100.0%36.0 bases36 bases92.9%
errorsSRR030257_2.fq999,83335,993,988100.0%36.0 bases36 bases85.4%
total1,999,66071,987,760100.0%36.0 bases36 bases89.1%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0129674,629,81213.91.5100.0%Escherichia coli B str. REL606, complete sequence.
total4,629,812100.0%

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.

New Junction Evidence

Junction Candidates Tested

optionlimitactual
Number of alignment pairs examined for constructing junction candidates≤ 10000026358
Coverage evenness (position-hash) score of junction candidates≥ 2≥ 2
Test this many junction candidates (n). May be smaller if not enough passed the coverage evenness threshold100 ≤ n ≤ 500028
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.000

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0129670.84574

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.

Final Junction Predictions

optionvalue
Coverage evenness (position-hash) score of predicted junctions must be≥ 3
Minimum probablilty assigned that no mapped read will start at a given position and strand for junction prediction0.1
Junction allow suboptimal matchesFALSE
Skew score of predicted junction (−log10 probability of unusual coverage evenness) must be≤ 0
Number of bases that at least one read must overlap each uniquely aligned side of a predicted junction≥ 6

Read Alignment Evidence

optionvalue
ModeFull Polymorphism
Ploidy1 (haploid)
Consensus mutation E-value cutoff10
Consensus frequency cutoffOFF
Consensus minimum variant coverage each strandOFF
Consensus minimum total coverage each strandOFF
Consensus minimum variant coverageOFF
Consensus minimum total coverageOFF
Polymorphism E-value cutoff2
Polymorphism frequency cutoff0.05
Polymorphism minimum variant coverage each strand2
Polymorphism minimum total coverage each strandOFF
Polymorphism minimum variant coverageOFF
Polymorphism minimum total coverageOFF
Polymorphism bias cutoffOFF
Predict indel polymorphismsYES
Skip indel polymorphisms in homopolymers runs of ≥3 bases
Skip base substitutions when they create a homopolymer flanked on each side by ≥5 bases

Software Versions

programversion
bowtie22.4.5
R4.1.3

Execution Times

stepstartendelapsed
Read and reference sequence file input09:01:42 01 Apr 202209:02:20 01 Apr 202238 seconds
Read alignment to reference genome09:02:21 01 Apr 202209:11:03 01 Apr 20228 minutes 42 seconds
Preprocessing alignments for candidate junction identification09:11:03 01 Apr 202209:11:47 01 Apr 202244 seconds
Preliminary analysis of coverage distribution09:11:47 01 Apr 202209:12:07 01 Apr 202220 seconds
Identifying junction candidates09:12:07 01 Apr 202209:12:09 01 Apr 20222 seconds
Re-alignment to junction candidates09:12:09 01 Apr 202209:12:15 01 Apr 20226 seconds
Resolving best read alignments09:12:15 01 Apr 202209:13:01 01 Apr 202246 seconds
Creating BAM files09:13:01 01 Apr 202209:13:17 01 Apr 202216 seconds
Tabulating error counts09:13:17 01 Apr 202209:13:23 01 Apr 20226 seconds
Re-calibrating base error rates09:13:23 01 Apr 202209:13:24 01 Apr 20221 second
Examining read alignment evidence09:13:24 01 Apr 202209:14:56 01 Apr 20221 minute 32 seconds
Polymorphism statistics09:14:56 01 Apr 202209:14:58 01 Apr 20222 seconds
Output09:14:58 01 Apr 202209:15:14 01 Apr 202216 seconds
Output :: Mutation Prediction09:14:58 01 Apr 202209:15:02 01 Apr 20224 seconds
Output :: Mutation Annotation09:15:02 01 Apr 202209:15:04 01 Apr 20222 seconds
Total 13 minutes 37 seconds