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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsPAL090_S88_L001_R1_001.good.fq1,167,643158,573,607100.0%135.8 bases140 bases99.1%
errorsPAL090_S88_L001_R2_001.good.fq1,167,643158,573,607100.0%135.8 bases140 bases98.7%
total2,335,286317,147,214100.0%135.8 bases140 bases98.9%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionCP0092734,631,46967.54.4100.0%Escherichia coli BW25113, complete genome.
total4,631,469100.0%

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≤ 1000003930
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 ≤ 5000184
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.011

Junction Skew Score Calculation

reference sequencepr(no read start)
CP0092730.86672

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 input22:46:22 16 Jun 202222:47:13 16 Jun 202251 seconds
Read alignment to reference genome22:47:14 16 Jun 202222:52:33 16 Jun 20225 minutes 19 seconds
Preprocessing alignments for candidate junction identification22:52:33 16 Jun 202222:53:02 16 Jun 202229 seconds
Preliminary analysis of coverage distribution22:53:02 16 Jun 202222:54:02 16 Jun 20221 minute 0 seconds
Identifying junction candidates22:54:02 16 Jun 202222:54:03 16 Jun 20221 second
Re-alignment to junction candidates22:54:03 16 Jun 202222:55:17 16 Jun 20221 minute 14 seconds
Resolving best read alignments22:55:17 16 Jun 202222:55:57 16 Jun 202240 seconds
Creating BAM files22:55:57 16 Jun 202222:56:50 16 Jun 202253 seconds
Tabulating error counts22:56:50 16 Jun 202222:57:16 16 Jun 202226 seconds
Re-calibrating base error rates22:57:16 16 Jun 202222:57:17 16 Jun 20221 second
Examining read alignment evidence22:57:17 16 Jun 202223:02:59 16 Jun 20225 minutes 42 seconds
Polymorphism statistics23:02:59 16 Jun 202223:02:59 16 Jun 20220 seconds
Output23:02:59 16 Jun 202223:03:05 16 Jun 20226 seconds
Total 16 minutes 42 seconds