breseq  version 0.35.4  revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsPAL056_S80_L003_R1_001.good.fq3,215,162321,410,722100.0%100.0 bases100 bases94.3%
errorsPAL056_S80_L003_R2_001.good.fq3,215,161321,410,622100.0%100.0 bases100 bases93.7%
total6,430,323642,821,344100.0%100.0 bases100 bases94.0%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652129.81.9100.0%Escherichia coli str. K-12 substr. MG1655, complete genome.
total4,641,652100.0%

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≤ 100000100000
Coverage evenness (position-hash) score of junction candidates≥ 2≥ 3
Test this many junction candidates (n). May be smaller if not enough passed the coverage evenness threshold100 ≤ n ≤ 50001620
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.072

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.61204

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 cutoff0.75
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
bowtie22.2.6
R3.4.4

Execution Times

stepstartendelapsed
Read and reference sequence file input02:24:03 17 Apr 202102:25:38 17 Apr 20211 minute 35 seconds
Read alignment to reference genome02:25:38 17 Apr 202102:37:25 17 Apr 202111 minutes 47 seconds
Preprocessing alignments for candidate junction identification02:37:25 17 Apr 202102:38:42 17 Apr 20211 minute 17 seconds
Preliminary analysis of coverage distribution02:38:42 17 Apr 202102:41:09 17 Apr 20212 minutes 27 seconds
Identifying junction candidates02:41:09 17 Apr 202102:49:55 17 Apr 20218 minutes 46 seconds
Re-alignment to junction candidates02:49:55 17 Apr 202102:53:38 17 Apr 20213 minutes 43 seconds
Resolving best read alignments02:53:38 17 Apr 202102:55:20 17 Apr 20211 minute 42 seconds
Creating BAM files02:55:20 17 Apr 202102:57:34 17 Apr 20212 minutes 14 seconds
Tabulating error counts02:57:34 17 Apr 202102:58:29 17 Apr 202155 seconds
Re-calibrating base error rates02:58:29 17 Apr 202102:58:30 17 Apr 20211 second
Examining read alignment evidence02:58:30 17 Apr 202103:09:08 17 Apr 202110 minutes 38 seconds
Polymorphism statistics03:09:08 17 Apr 202103:09:11 17 Apr 20213 seconds
Output03:09:11 17 Apr 202103:09:43 17 Apr 202132 seconds
Total 45 minutes 40 seconds