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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsERR3687423_R1.good.fq4,768,785324,277,380100.0%68.0 bases68 bases94.4%
total4,768,785324,277,380100.0%68.0 bases68 bases94.4%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionCP0092734,631,46955.13.185.7%Escherichia coli BW25113, complete genome.
coveragedistributionKX0775368,1871751.2170.04.1%Vector pCBB, complete sequence.
coveragedistributionExported3,34410024.5556.610.2%pZS2M_pseudoFDH_strepR_2genes.
total4,643,000100.0%

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≤ 10000033518
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 ≤ 5000120
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.004

Junction Skew Score Calculation

reference sequencepr(no read start)
CP0092730.77934
KX0775360.25572
Exported0.08553

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 input20:49:46 20 Feb 202120:50:51 20 Feb 20211 minute 5 seconds
Read alignment to reference genome20:50:51 20 Feb 202120:58:52 20 Feb 20218 minutes 1 second
Preprocessing alignments for candidate junction identification20:58:52 20 Feb 202120:59:44 20 Feb 202152 seconds
Preliminary analysis of coverage distribution20:59:44 20 Feb 202121:01:37 20 Feb 20211 minute 53 seconds
Identifying junction candidates21:01:37 20 Feb 202121:01:39 20 Feb 20212 seconds
Re-alignment to junction candidates21:01:39 20 Feb 202121:03:26 20 Feb 20211 minute 47 seconds
Resolving best read alignments21:03:26 20 Feb 202121:04:38 20 Feb 20211 minute 12 seconds
Creating BAM files21:04:38 20 Feb 202121:06:20 20 Feb 20211 minute 42 seconds
Tabulating error counts21:06:20 20 Feb 202121:06:49 20 Feb 202129 seconds
Re-calibrating base error rates21:06:49 20 Feb 202121:06:51 20 Feb 20212 seconds
Examining read alignment evidence21:06:51 20 Feb 202121:12:28 20 Feb 20215 minutes 37 seconds
Polymorphism statistics21:12:28 20 Feb 202121:12:29 20 Feb 20211 second
Output21:12:29 20 Feb 202121:12:50 20 Feb 202121 seconds
Total 23 minutes 4 seconds