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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsJ21-A2_S127_R1_001.good.fq1,975,068132,737,581100.0%67.2 bases71 bases96.7%
total1,975,068132,737,581100.0%67.2 bases71 bases96.7%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionW3110S.gb4,646,33427.98.7100.0%Escherichia coli str. K-12 substr. W3110 DNA, complete genome.
total4,646,334100.0%

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≤ 1000005243
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 ≤ 500035
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.001

Junction Skew Score Calculation

reference sequencepr(no read start)
W3110S.gb0.94109

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≤ 0
Number of bases that at least one read must overlap each uniquely aligned side of a predicted junction≥ 6

Read Alignment Evidence

optionvalue
ModeFull Polymorphism
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 cutoff2
Polymorphism frequency cutoff0.05
Polymorphism minimum variant coverage each strand2
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 of ≥3 bases
Skip base substitutions when they create a homopolymer flanked on each side by ≥5 bases

Software Versions

programversion
bowtie22.3.4.1
R3.4.4

Execution Times

stepstartendelapsed
Read and reference sequence file input09:46:33 10 Dec 201909:46:53 10 Dec 201920 seconds
Read alignment to reference genome09:46:54 10 Dec 201909:49:21 10 Dec 20192 minutes 27 seconds
Preprocessing alignments for candidate junction identification09:49:21 10 Dec 201909:49:48 10 Dec 201927 seconds
Preliminary analysis of coverage distribution09:49:48 10 Dec 201909:50:22 10 Dec 201934 seconds
Identifying junction candidates09:50:22 10 Dec 201909:50:22 10 Dec 20190 seconds
Re-alignment to junction candidates09:50:22 10 Dec 201909:51:00 10 Dec 201938 seconds
Resolving best read alignments09:51:00 10 Dec 201909:51:39 10 Dec 201939 seconds
Creating BAM files09:51:39 10 Dec 201909:52:09 10 Dec 201930 seconds
Tabulating error counts09:52:09 10 Dec 201909:52:20 10 Dec 201911 seconds
Re-calibrating base error rates09:52:20 10 Dec 201909:52:21 10 Dec 20191 second
Examining read alignment evidence09:52:21 10 Dec 201909:55:22 10 Dec 20193 minutes 1 second
Polymorphism statistics09:55:22 10 Dec 201909:55:23 10 Dec 20191 second
Output09:55:23 10 Dec 201910:00:36 10 Dec 20195 minutes 13 seconds
Total 14 minutes 2 seconds