breseq  version 0.35.5  revision 9f368df52761
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsABF018_S18_L001_R1_001_ptrim.fq975,144277,068,740100.0%284.1 bases301 bases99.3%
errorsABF018_S18_L001_R2_001_ptrim.fq975,118263,244,345100.0%270.0 bases301 bases98.7%
total1,950,262540,313,085100.0%277.0 bases301 bases99.0%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionAE0154516,181,87383.72.6100.0%Pseudomonas putida KT2440 complete genome.
total6,181,873100.0%

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≤ 1000007316
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 ≤ 5000764
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.075

Junction Skew Score Calculation

reference sequencepr(no read start)
AE0154510.86241

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
bowtie22.4.2
R3.6.3

Execution Times

stepstartendelapsed
Read and reference sequence file input12:23:45 29 Apr 202112:24:13 29 Apr 202128 seconds
Read alignment to reference genome12:24:13 29 Apr 202112:34:23 29 Apr 202110 minutes 10 seconds
Preprocessing alignments for candidate junction identification12:34:23 29 Apr 202112:34:48 29 Apr 202125 seconds
Preliminary analysis of coverage distribution12:34:48 29 Apr 202112:36:49 29 Apr 20212 minutes 1 second
Identifying junction candidates12:36:49 29 Apr 202112:37:16 29 Apr 202127 seconds
Re-alignment to junction candidates12:37:16 29 Apr 202112:40:15 29 Apr 20212 minutes 59 seconds
Resolving best read alignments12:40:15 29 Apr 202112:40:55 29 Apr 202140 seconds
Creating BAM files12:40:55 29 Apr 202112:42:39 29 Apr 20211 minute 44 seconds
Tabulating error counts12:42:39 29 Apr 202112:43:30 29 Apr 202151 seconds
Re-calibrating base error rates12:43:30 29 Apr 202112:43:31 29 Apr 20211 second
Examining read alignment evidence12:43:31 29 Apr 202112:50:09 29 Apr 20216 minutes 38 seconds
Polymorphism statistics12:50:09 29 Apr 202112:50:09 29 Apr 20210 seconds
Output12:50:09 29 Apr 202112:50:35 29 Apr 202126 seconds
Total 26 minutes 50 seconds