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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsME6189_rmdup_R1902,116270,634,800100.0%300.0 bases300 bases97.8%
errorsME6189_rmdup_R2878,594263,578,200100.0%300.0 bases300 bases97.0%
total1,780,710534,213,000100.0%300.0 bases300 bases97.4%

Reference Sequence Information

seq idlengthfit meanfit relative_variance% mapped readsdescription
coveragedistributionNC_0009134,641,652112.85.2100.0%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≤ 10000016455
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 ≤ 5000193
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.025

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.88119

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 input05:32:41 04 Jun 202505:33:08 04 Jun 202527 seconds
Read alignment to reference genome05:33:08 04 Jun 202505:34:40 04 Jun 20251 minute 32 seconds
Preprocessing alignments for candidate junction identification05:34:40 04 Jun 202505:35:08 04 Jun 202528 seconds
Preliminary analysis of coverage distribution05:35:08 04 Jun 202505:36:20 04 Jun 20251 minute 12 seconds
Identifying junction candidates05:36:20 04 Jun 202505:36:29 04 Jun 20259 seconds
Re-alignment to junction candidates05:36:29 04 Jun 202505:36:46 04 Jun 202517 seconds
Resolving best read alignments05:36:46 04 Jun 202505:37:39 04 Jun 202553 seconds
Creating BAM files05:37:39 04 Jun 202505:38:38 04 Jun 202559 seconds
Tabulating error counts05:38:38 04 Jun 202505:39:26 04 Jun 202548 seconds
Re-calibrating base error rates05:39:26 04 Jun 202505:39:27 04 Jun 20251 second
Examining read alignment evidence05:39:27 04 Jun 202505:46:03 04 Jun 20256 minutes 36 seconds
Polymorphism statistics05:46:03 04 Jun 202505:46:04 04 Jun 20251 second
Output05:46:04 04 Jun 202505:46:14 04 Jun 202510 seconds
Output :: Mutation Prediction05:46:04 04 Jun 202505:46:04 04 Jun 20250 seconds
Output :: Mutation Annotation05:46:04 04 Jun 202505:46:05 04 Jun 20251 second
Total 13 minutes 34 seconds