breseq  version 0.38.1  
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsFusobacterium-ATCC-fusnuc_S12_L001_R1_001918,623203,508,046100.0%221.5 bases251 bases99.2%
errorsFusobacterium-ATCC-fusnuc_S12_L001_R2_001918,623203,451,002100.0%221.5 bases251 bases99.1%
total1,837,246406,959,048100.0%221.5 bases251 bases99.2%

Reference Sequence Information

seq idlengthfit meanfit relative_variance% mapped readsdescription
coveragedistributionCP0281012,180,101177.547.5100.0%Fusobacterium nucleatum subsp. nucleatum ATCC 25586 chromosome,
total2,180,101100.0%

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≤ 1000004226
Coverage evenness (position-hash) score of junction candidates≥ 2≥ 3
Test this many junction candidates (n). May be smaller if not enough passed the coverage evenness threshold100 ≤ n ≤ 50008
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.002

Junction Skew Score Calculation

reference sequencepr(no read start)
CP0281010.78510

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
bowtie2s.2023.01/rocky8/x86_64/amd/zen3/software/Bowtie2/2.4.5-GCC-11.3.0/bin/bowtie2-align-s
R4.2.1

Execution Times

stepstartendelapsed
Read and reference sequence file input09:26:30 05 Jul 202409:27:01 05 Jul 202431 seconds
Read alignment to reference genome09:27:01 05 Jul 202409:28:09 05 Jul 20241 minute 8 seconds
Preprocessing alignments for candidate junction identification09:28:09 05 Jul 202409:28:30 05 Jul 202421 seconds
Preliminary analysis of coverage distribution09:28:30 05 Jul 202409:29:47 05 Jul 20241 minute 17 seconds
Identifying junction candidates09:29:47 05 Jul 202409:29:50 05 Jul 20243 seconds
Re-alignment to junction candidates09:29:50 05 Jul 202409:30:06 05 Jul 202416 seconds
Resolving best read alignments09:30:06 05 Jul 202409:30:39 05 Jul 202433 seconds
Creating BAM files09:30:39 05 Jul 202409:31:43 05 Jul 20241 minute 4 seconds
Tabulating error counts09:31:43 05 Jul 202409:32:27 05 Jul 202444 seconds
Re-calibrating base error rates09:32:27 05 Jul 202409:32:29 05 Jul 20242 seconds
Examining read alignment evidence09:32:29 05 Jul 202409:37:33 05 Jul 20245 minutes 4 seconds
Polymorphism statistics09:37:33 05 Jul 202409:37:33 05 Jul 20240 seconds
Output09:37:33 05 Jul 202409:37:41 05 Jul 20248 seconds
Output :: Mutation Prediction09:37:33 05 Jul 202409:37:33 05 Jul 20240 seconds
Output :: Mutation Annotation09:37:33 05 Jul 202409:37:33 05 Jul 20240 seconds
Total 11 minutes 11 seconds