breseq  version 0.33.1  revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsR2_Lane7_BC06_R1.good.fq1,592,116120,947,305100.0%76.0 bases76 bases97.5%
errorsR2_Lane7_BC06_R2.good.fq1,592,116120,947,305100.0%76.0 bases76 bases94.1%
total3,184,232241,894,610100.0%76.0 bases76 bases95.8%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionREL6064,629,81249.72.6100.0%Escherichia coli strain REL606.
total4,629,812100.0%

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≤ 1000007624
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 ≤ 5000143
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.005

Junction Skew Score Calculation

reference sequencepr(no read start)
REL6060.74595

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
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
bowtie22.3.4.1
R3.4.4

Execution Times

stepstartendelapsed
Read and reference sequence file input23:48:44 01 Feb 201923:49:17 01 Feb 201933 seconds
Read alignment to reference genome23:49:17 01 Feb 201923:53:59 01 Feb 20194 minutes 42 seconds
Preprocessing alignments for candidate junction identification23:53:59 01 Feb 201923:54:36 01 Feb 201937 seconds
Preliminary analysis of coverage distribution23:54:36 01 Feb 201923:55:55 01 Feb 20191 minute 19 seconds
Identifying junction candidates23:55:55 01 Feb 201923:55:56 01 Feb 20191 second
Re-alignment to junction candidates23:55:56 01 Feb 201923:57:07 01 Feb 20191 minute 11 seconds
Resolving best read alignments23:57:07 01 Feb 201923:58:03 01 Feb 201956 seconds
Creating BAM files23:58:03 01 Feb 201923:59:17 01 Feb 20191 minute 14 seconds
Tabulating error counts23:59:17 01 Feb 201923:59:38 01 Feb 201921 seconds
Re-calibrating base error rates23:59:38 01 Feb 201923:59:39 01 Feb 20191 second
Examining read alignment evidence23:59:39 01 Feb 201900:03:01 02 Feb 20193 minutes 22 seconds
Polymorphism statistics00:03:01 02 Feb 201900:03:02 02 Feb 20191 second
Output00:03:02 02 Feb 201900:03:12 02 Feb 201910 seconds
Total 14 minutes 28 seconds