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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsCV23_S3_L001_R1_001269,00666,080,202100.0%245.6 bases251 bases95.8%
errorsCV23_S3_L001_R2_001269,65866,469,678100.0%246.5 bases251 bases88.8%
total538,664132,549,880100.0%246.1 bases251 bases92.3%

Reference Sequence Information

seq idlengthfit meanfit relative_variance% mapped readsdescription
coveragedistributionNC_0009134,641,65226.44.6100.0%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≤ 1000003138
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 ≤ 500097
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.011

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.95332

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 input13:07:56 28 Nov 202413:08:05 28 Nov 20249 seconds
Read alignment to reference genome13:08:05 28 Nov 202413:08:33 28 Nov 202428 seconds
Preprocessing alignments for candidate junction identification13:08:33 28 Nov 202413:08:41 28 Nov 20248 seconds
Preliminary analysis of coverage distribution13:08:41 28 Nov 202413:09:06 28 Nov 202425 seconds
Identifying junction candidates13:09:06 28 Nov 202413:09:07 28 Nov 20241 second
Re-alignment to junction candidates13:09:07 28 Nov 202413:09:11 28 Nov 20244 seconds
Resolving best read alignments13:09:11 28 Nov 202413:09:25 28 Nov 202414 seconds
Creating BAM files13:09:25 28 Nov 202413:09:46 28 Nov 202421 seconds
Tabulating error counts13:09:46 28 Nov 202413:09:58 28 Nov 202412 seconds
Re-calibrating base error rates13:09:58 28 Nov 202413:09:59 28 Nov 20241 second
Examining read alignment evidence13:09:59 28 Nov 202413:11:50 28 Nov 20241 minute 51 seconds
Polymorphism statistics13:11:50 28 Nov 202413:11:51 28 Nov 20241 second
Output13:11:51 28 Nov 202413:12:07 28 Nov 202416 seconds
Output :: Mutation Prediction13:11:51 28 Nov 202413:11:54 28 Nov 20243 seconds
Output :: Mutation Annotation13:11:54 28 Nov 202413:11:54 28 Nov 20240 seconds
Total 4 minutes 14 seconds