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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsR3_Lane1_BC08_R1.good.fq6,958,744528,780,895100.0%76.0 bases76 bases96.7%
errorsR3_Lane1_BC08_R2.good.fq6,958,744528,780,895100.0%76.0 bases76 bases94.6%
total13,917,4881,057,561,790100.0%76.0 bases76 bases95.6%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionREL6064,629,812220.56.5100.0%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≤ 10000011082
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 ≤ 5000211
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.007

Junction Skew Score Calculation

reference sequencepr(no read start)
REL6060.32045

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 input03:46:02 31 Jan 201903:48:28 31 Jan 20192 minutes 26 seconds
Read alignment to reference genome03:48:28 31 Jan 201904:07:37 31 Jan 201919 minutes 9 seconds
Preprocessing alignments for candidate junction identification04:07:37 31 Jan 201904:10:10 31 Jan 20192 minutes 33 seconds
Preliminary analysis of coverage distribution04:10:10 31 Jan 201904:15:26 31 Jan 20195 minutes 16 seconds
Identifying junction candidates04:15:26 31 Jan 201904:15:28 31 Jan 20192 seconds
Re-alignment to junction candidates04:15:28 31 Jan 201904:20:08 31 Jan 20194 minutes 40 seconds
Resolving best read alignments04:20:08 31 Jan 201904:24:15 31 Jan 20194 minutes 7 seconds
Creating BAM files04:24:15 31 Jan 201904:29:02 31 Jan 20194 minutes 47 seconds
Tabulating error counts04:29:02 31 Jan 201904:30:33 31 Jan 20191 minute 31 seconds
Re-calibrating base error rates04:30:33 31 Jan 201904:30:34 31 Jan 20191 second
Examining read alignment evidence04:30:34 31 Jan 201904:44:01 31 Jan 201913 minutes 27 seconds
Polymorphism statistics04:44:01 31 Jan 201904:44:02 31 Jan 20191 second
Output04:44:02 31 Jan 201904:44:26 31 Jan 201924 seconds
Total 58 minutes 24 seconds