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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsJ0-D2_S85_R1_001.good.fq518,98733,488,210100.0%64.5 bases71 bases97.1%
total518,98733,488,210100.0%64.5 bases71 bases97.1%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionminE2,987,94211.01.7100.0%Escherichia coli str. K-12 substr. W3110 DNA, complete genome.
total2,987,942100.0%

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≤ 1000002575
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 ≤ 50005
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.000

Junction Skew Score Calculation

reference sequencepr(no read start)
minE0.92408

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 input18:46:41 10 Dec 201918:46:47 10 Dec 20196 seconds
Read alignment to reference genome18:46:47 10 Dec 201918:47:22 10 Dec 201935 seconds
Preprocessing alignments for candidate junction identification18:47:22 10 Dec 201918:47:29 10 Dec 20197 seconds
Preliminary analysis of coverage distribution18:47:29 10 Dec 201918:47:39 10 Dec 201910 seconds
Identifying junction candidates18:47:39 10 Dec 201918:47:39 10 Dec 20190 seconds
Re-alignment to junction candidates18:47:39 10 Dec 201918:47:49 10 Dec 201910 seconds
Resolving best read alignments18:47:49 10 Dec 201918:47:58 10 Dec 20199 seconds
Creating BAM files18:47:58 10 Dec 201918:48:07 10 Dec 20199 seconds
Tabulating error counts18:48:07 10 Dec 201918:48:10 10 Dec 20193 seconds
Re-calibrating base error rates18:48:10 10 Dec 201918:48:10 10 Dec 20190 seconds
Examining read alignment evidence18:48:10 10 Dec 201918:49:03 10 Dec 201953 seconds
Polymorphism statistics18:49:03 10 Dec 201918:49:05 10 Dec 20192 seconds
Output18:49:05 10 Dec 201918:49:49 10 Dec 201944 seconds
Total 3 minutes 8 seconds