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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsSRR12717899_R1.good.fq3,010,858439,345,451100.0%145.9 bases149 bases97.6%
errorsSRR12717899_R2.good.fq3,010,858447,277,951100.0%148.6 bases149 bases97.1%
total6,021,716886,623,402100.0%147.2 bases149 bases97.3%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652182.83.5100.0%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≤ 10000077926
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 ≤ 5000912
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.059

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.56203

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 input20:21:21 01 Feb 202120:27:03 01 Feb 20215 minutes 42 seconds
Read alignment to reference genome20:27:04 01 Feb 202121:11:36 01 Feb 202144 minutes 32 seconds
Preprocessing alignments for candidate junction identification21:11:36 01 Feb 202121:17:09 01 Feb 20215 minutes 33 seconds
Preliminary analysis of coverage distribution21:17:09 01 Feb 202121:28:14 01 Feb 202111 minutes 5 seconds
Identifying junction candidates21:28:14 01 Feb 202121:28:42 01 Feb 202128 seconds
Re-alignment to junction candidates21:28:42 01 Feb 202121:42:31 01 Feb 202113 minutes 49 seconds
Resolving best read alignments21:42:31 01 Feb 202121:50:19 01 Feb 20217 minutes 48 seconds
Creating BAM files21:50:19 01 Feb 202122:00:11 01 Feb 20219 minutes 52 seconds
Tabulating error counts22:00:11 01 Feb 202122:04:39 01 Feb 20214 minutes 28 seconds
Re-calibrating base error rates22:04:39 01 Feb 202122:04:42 01 Feb 20213 seconds
Examining read alignment evidence22:04:42 01 Feb 202122:55:31 01 Feb 202150 minutes 49 seconds
Polymorphism statistics22:55:31 01 Feb 202122:55:33 01 Feb 20212 seconds
Output22:55:33 01 Feb 202122:56:40 01 Feb 20211 minute 7 seconds
Total 2 hours 35 minutes 18 seconds