breseq  version 0.35.4  
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errors8A_S8_R1_00117,788,1261,334,109,450100.0%75.0 bases75 bases1.6%
total17,788,1261,334,109,450100.0%75.0 bases75 bases1.6%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_00430233,350163.7194.7100.0%Bacteriophage r1t integrase, repressor protein (rro), dUTPase,
total33,350100.0%

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≤ 100000206
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 ≤ 50002
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.009

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0043020.85277

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
Minimum probablilty assigned that no mapped read will start at a given position and strand for junction prediction0.1
Junction allow suboptimal matchesFALSE
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 cutoff0.8
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
bowtie22.4.1
R4.0.0

Execution Times

stepstartendelapsed
Read and reference sequence file input13:36:37 04 May 202113:40:21 04 May 20213 minutes 44 seconds
Read alignment to reference genome13:40:21 04 May 202113:47:51 04 May 20217 minutes 30 seconds
Preprocessing alignments for candidate junction identification13:47:51 04 May 202113:48:39 04 May 202148 seconds
Preliminary analysis of coverage distribution13:48:39 04 May 202113:48:47 04 May 20218 seconds
Identifying junction candidates13:48:47 04 May 202113:48:48 04 May 20211 second
Re-alignment to junction candidates13:48:48 04 May 202113:50:41 04 May 20211 minute 53 seconds
Resolving best read alignments13:50:41 04 May 202113:53:48 04 May 20213 minutes 7 seconds
Creating BAM files13:53:48 04 May 202113:53:52 04 May 20214 seconds
Tabulating error counts13:53:52 04 May 202113:53:55 04 May 20213 seconds
Re-calibrating base error rates13:53:55 04 May 202113:53:58 04 May 20213 seconds
Examining read alignment evidence13:53:58 04 May 202113:54:39 04 May 202141 seconds
Polymorphism statistics13:54:39 04 May 202113:54:41 04 May 20212 seconds
Output13:54:41 04 May 202113:54:44 04 May 20213 seconds
Total 18 minutes 7 seconds