breseq  version 0.35.4  revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsALEevo04-pgi-kan_S2_L001_R1_001.good.fq1,072,533280,702,672100.0%261.7 bases275 bases98.0%
errorsALEevo04-pgi-kan_S2_L001_R2_001.good.fq1,072,532280,778,444100.0%261.8 bases275 bases91.6%
total2,145,065561,481,116100.0%261.8 bases275 bases94.8%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652114.95.0100.0%Escherichia coli str. K-12 substr. MG1655, complete genome.
total4,641,652100.0%

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≤ 10000016703
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 ≤ 500056
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.007

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.86257

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 cutoff0.75
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
bowtie22.2.6
R3.4.4

Execution Times

stepstartendelapsed
Read and reference sequence file input10:31:21 06 Apr 202210:32:06 06 Apr 202245 seconds
Read alignment to reference genome10:32:06 06 Apr 202210:42:38 06 Apr 202210 minutes 32 seconds
Preprocessing alignments for candidate junction identification10:42:38 06 Apr 202210:43:13 06 Apr 202235 seconds
Preliminary analysis of coverage distribution10:43:13 06 Apr 202210:45:11 06 Apr 20221 minute 58 seconds
Identifying junction candidates10:45:11 06 Apr 202210:45:35 06 Apr 202224 seconds
Re-alignment to junction candidates10:45:35 06 Apr 202210:47:16 06 Apr 20221 minute 41 seconds
Resolving best read alignments10:47:16 06 Apr 202210:48:07 06 Apr 202251 seconds
Creating BAM files10:48:07 06 Apr 202210:49:47 06 Apr 20221 minute 40 seconds
Tabulating error counts10:49:47 06 Apr 202210:50:45 06 Apr 202258 seconds
Re-calibrating base error rates10:50:45 06 Apr 202210:50:46 06 Apr 20221 second
Examining read alignment evidence10:50:46 06 Apr 202211:01:57 06 Apr 202211 minutes 11 seconds
Polymorphism statistics11:01:57 06 Apr 202211:01:57 06 Apr 20220 seconds
Output11:01:57 06 Apr 202211:02:11 06 Apr 202214 seconds
Total 30 minutes 50 seconds