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_Lane2_BC03_R1.good.fq2,048,244155,529,425100.0%75.9 bases76 bases95.7%
errorsR2_Lane2_BC03_R2.good.fq2,048,243155,529,349100.0%75.9 bases76 bases93.3%
total4,096,487311,058,774100.0%75.9 bases76 bases94.5%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionREL6064,629,81261.93.6100.0%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≤ 1000005478
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 ≤ 500096
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.003

Junction Skew Score Calculation

reference sequencepr(no read start)
REL6060.69998

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 input20:37:45 31 Jan 201920:38:28 31 Jan 201943 seconds
Read alignment to reference genome20:38:28 31 Jan 201920:45:11 31 Jan 20196 minutes 43 seconds
Preprocessing alignments for candidate junction identification20:45:11 31 Jan 201920:45:57 31 Jan 201946 seconds
Preliminary analysis of coverage distribution20:45:57 31 Jan 201920:47:36 31 Jan 20191 minute 39 seconds
Identifying junction candidates20:47:36 31 Jan 201920:47:37 31 Jan 20191 second
Re-alignment to junction candidates20:47:37 31 Jan 201920:49:04 31 Jan 20191 minute 27 seconds
Resolving best read alignments20:49:04 31 Jan 201920:50:16 31 Jan 20191 minute 12 seconds
Creating BAM files20:50:16 31 Jan 201920:51:46 31 Jan 20191 minute 30 seconds
Tabulating error counts20:51:46 31 Jan 201920:52:12 31 Jan 201926 seconds
Re-calibrating base error rates20:52:12 31 Jan 201920:52:14 31 Jan 20192 seconds
Examining read alignment evidence20:52:14 31 Jan 201920:56:36 31 Jan 20194 minutes 22 seconds
Polymorphism statistics20:56:36 31 Jan 201920:56:37 31 Jan 20191 second
Output20:56:37 31 Jan 201920:56:46 31 Jan 20199 seconds
Total 19 minutes 1 second