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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsME9772_S44_R1_RMDUP_RM-R2-DUP.cutadapt798,782235,499,160100.0%294.8 bases300 bases92.1%
errorsME9772_S44_R2_RMDUP_RM-R1-DUP.cutadapt799,019233,430,291100.0%292.1 bases300 bases94.8%
total1,597,801468,929,451100.0%293.5 bases300 bases93.5%

Reference Sequence Information

seq idlengthfit meanfit relative_variance% mapped readsdescription
coveragedistributionNC_0009134,641,65293.24.5100.0%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≤ 1000004050
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 ≤ 5000169
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.022

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.89880

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 input03:43:14 11 Oct 202503:43:38 11 Oct 202524 seconds
Read alignment to reference genome03:43:38 11 Oct 202503:44:58 11 Oct 20251 minute 20 seconds
Preprocessing alignments for candidate junction identification03:44:58 11 Oct 202503:45:21 11 Oct 202523 seconds
Preliminary analysis of coverage distribution03:45:21 11 Oct 202503:46:24 11 Oct 20251 minute 3 seconds
Identifying junction candidates03:46:24 11 Oct 202503:46:27 11 Oct 20253 seconds
Re-alignment to junction candidates03:46:27 11 Oct 202503:46:41 11 Oct 202514 seconds
Resolving best read alignments03:46:41 11 Oct 202503:47:25 11 Oct 202544 seconds
Creating BAM files03:47:25 11 Oct 202503:48:18 11 Oct 202553 seconds
Tabulating error counts03:48:18 11 Oct 202503:48:57 11 Oct 202539 seconds
Re-calibrating base error rates03:48:57 11 Oct 202503:48:58 11 Oct 20251 second
Examining read alignment evidence03:48:58 11 Oct 202503:54:35 11 Oct 20255 minutes 37 seconds
Polymorphism statistics03:54:35 11 Oct 202503:54:35 11 Oct 20250 seconds
Output03:54:35 11 Oct 202503:54:41 11 Oct 20256 seconds
Output :: Mutation Prediction03:54:35 11 Oct 202503:54:36 11 Oct 20251 second
Output :: Mutation Annotation03:54:36 11 Oct 202503:54:36 11 Oct 20250 seconds
Total 11 minutes 28 seconds