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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsME5114_S12_L001_R1_001563,036138,546,599100.0%246.1 bases251 bases95.7%
errorsME5114_S12_L001_R2_001563,001138,526,288100.0%246.0 bases251 bases92.9%
total1,126,037277,072,887100.0%246.1 bases251 bases94.3%

Reference Sequence Information

seq idlengthfit meanfit relative_variance% mapped readsdescription
coveragedistributionNC_0009134,641,65261.93.4100.0%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≤ 10000015869
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 ≤ 5000847
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.092

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.90107

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 input18:42:27 20 Nov 202418:42:45 20 Nov 202418 seconds
Read alignment to reference genome18:42:45 20 Nov 202418:43:33 20 Nov 202448 seconds
Preprocessing alignments for candidate junction identification18:43:33 20 Nov 202418:43:49 20 Nov 202416 seconds
Preliminary analysis of coverage distribution18:43:49 20 Nov 202418:44:40 20 Nov 202451 seconds
Identifying junction candidates18:44:40 20 Nov 202418:44:46 20 Nov 20246 seconds
Re-alignment to junction candidates18:44:46 20 Nov 202418:44:58 20 Nov 202412 seconds
Resolving best read alignments18:44:58 20 Nov 202418:45:27 20 Nov 202429 seconds
Creating BAM files18:45:27 20 Nov 202418:46:12 20 Nov 202445 seconds
Tabulating error counts18:46:12 20 Nov 202418:46:37 20 Nov 202425 seconds
Re-calibrating base error rates18:46:37 20 Nov 202418:46:38 20 Nov 20241 second
Examining read alignment evidence18:46:38 20 Nov 202418:50:05 20 Nov 20243 minutes 27 seconds
Polymorphism statistics18:50:05 20 Nov 202418:50:05 20 Nov 20240 seconds
Output18:50:05 20 Nov 202418:50:10 20 Nov 20245 seconds
Output :: Mutation Prediction18:50:05 20 Nov 202418:50:05 20 Nov 20240 seconds
Output :: Mutation Annotation18:50:05 20 Nov 202418:50:05 20 Nov 20240 seconds
Total 7 minutes 43 seconds