breseq  version 0.39.0  
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsME9795_S46_R1_RMDUP_RM-R2-DUP.cutadapt924,552273,975,778100.0%296.3 bases300 bases94.4%
errorsME9795_S46_R2_RMDUP_RM-R1-DUP.cutadapt924,857272,066,015100.0%294.2 bases300 bases97.6%
total1,849,409546,041,793100.0%295.3 bases300 bases96.0%

Reference Sequence Information

seq idlengthfit meanfit relative_variance% mapped readsdescription
coveragedistributionNC_0009134,641,652111.46.0100.0%Escherichia coli str. K-12 substr. MG1655, complete genome.
total4,641,652100.0%

fit relative_variance 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≤ 10000010475
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 ≤ 5000182
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.024

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.88559

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≤ 3
Number of bases that at least one read must overlap each uniquely aligned side of a predicted junction≥ 1

Read Alignment Evidence

optionvalue
ModeConsensus/Mixed Base
Ploidy1 (haploid)
Consensus mutation E-value cutoff10
Consensus frequency cutoff0.8
Consensus minimum variant coverage each strandOFF
Consensus minimum total coverage each strandOFF
Consensus minimum variant coverageOFF
Consensus minimum total coverageOFF
Polymorphism E-value cutoff10
Polymorphism frequency cutoff0.2
Polymorphism minimum variant coverage each strandOFF
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 ofOFF
Skip base substitutions when they create a homopolymer flanked on each side byOFF

Software Versions

programversion
bowtie22.5.1
R4.0.3

Execution Times

stepstartendelapsed
Read and reference sequence file input04:07:05 11 Oct 202504:07:33 11 Oct 202528 seconds
Read alignment to reference genome04:07:33 11 Oct 202504:09:06 11 Oct 20251 minute 33 seconds
Preprocessing alignments for candidate junction identification04:09:06 11 Oct 202504:09:35 11 Oct 202529 seconds
Preliminary analysis of coverage distribution04:09:35 11 Oct 202504:10:50 11 Oct 20251 minute 15 seconds
Identifying junction candidates04:10:50 11 Oct 202504:10:55 11 Oct 20255 seconds
Re-alignment to junction candidates04:10:55 11 Oct 202504:11:12 11 Oct 202517 seconds
Resolving best read alignments04:11:12 11 Oct 202504:12:05 11 Oct 202553 seconds
Creating BAM files04:12:05 11 Oct 202504:13:07 11 Oct 20251 minute 2 seconds
Tabulating error counts04:13:07 11 Oct 202504:13:56 11 Oct 202549 seconds
Re-calibrating base error rates04:13:56 11 Oct 202504:13:57 11 Oct 20251 second
Examining read alignment evidence04:13:57 11 Oct 202504:21:22 11 Oct 20257 minutes 25 seconds
Polymorphism statistics04:21:22 11 Oct 202504:21:22 11 Oct 20250 seconds
Output04:21:22 11 Oct 202504:21:32 11 Oct 202510 seconds
Output :: Mutation Prediction04:21:22 11 Oct 202504:21:23 11 Oct 20251 second
Output :: Mutation Annotation04:21:23 11 Oct 202504:21:23 11 Oct 20250 seconds
Total 14 minutes 28 seconds