breseq  version 0.37.1  
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsLL1211-AGCCS2,711,192409,389,992100.0%151.0 bases151 bases99.0%
total2,711,192409,389,992100.0%151.0 bases151 bases99.0%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionCP0024163,561,619112.32.8100.0%Acetivibrio thermocellus DSM 1313 chromosome, complete genome.
total3,561,619100.0%

fit dispersion 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≤ 10000013144
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 ≤ 5000139
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.012

Junction Skew Score Calculation

reference sequencepr(no read start)
CP0024160.69419

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
bowtie22.4.5
R4.2.1

Execution Times

stepstartendelapsed
Read and reference sequence file input20:54:07 29 Jan 202320:54:54 29 Jan 202347 seconds
Read alignment to reference genome20:54:55 29 Jan 202321:02:58 29 Jan 20238 minutes 3 seconds
Preprocessing alignments for candidate junction identification21:02:58 29 Jan 202321:03:45 29 Jan 202347 seconds
Preliminary analysis of coverage distribution21:03:45 29 Jan 202321:06:08 29 Jan 20232 minutes 23 seconds
Identifying junction candidates21:06:08 29 Jan 202321:06:11 29 Jan 20233 seconds
Re-alignment to junction candidates21:06:11 29 Jan 202321:08:27 29 Jan 20232 minutes 16 seconds
Resolving best read alignments21:08:27 29 Jan 202321:09:32 29 Jan 20231 minute 5 seconds
Creating BAM files21:09:32 29 Jan 202321:11:43 29 Jan 20232 minutes 11 seconds
Tabulating error counts21:11:43 29 Jan 202321:12:32 29 Jan 202349 seconds
Re-calibrating base error rates21:12:32 29 Jan 202321:12:32 29 Jan 20230 seconds
Examining read alignment evidence21:12:32 29 Jan 202321:18:26 29 Jan 20235 minutes 54 seconds
Polymorphism statistics21:18:26 29 Jan 202321:18:26 29 Jan 20230 seconds
Output21:18:26 29 Jan 202321:18:46 29 Jan 202320 seconds
Output :: Mutation Prediction21:18:26 29 Jan 202321:18:27 29 Jan 20231 second
Output :: Mutation Annotation21:18:27 29 Jan 202321:18:27 29 Jan 20230 seconds
Total 24 minutes 39 seconds