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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsSRR4302535_R1.good.fq4,688,074435,950,801100.0%93.0 bases93 bases98.7%
errorsSRR4302535_R2.good.fq4,688,074435,950,801100.0%93.0 bases93 bases97.7%
total9,376,148871,901,602100.0%93.0 bases93 bases98.2%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,639,221183.119.1100.0%Escherichia coli K12, complete genome.
total4,639,221100.0%

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≤ 1000003408
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 ≤ 500046
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.002

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.44067

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 input09:59:34 17 Jan 202310:01:44 17 Jan 20232 minutes 10 seconds
Read alignment to reference genome10:01:44 17 Jan 202310:14:29 17 Jan 202312 minutes 45 seconds
Preprocessing alignments for candidate junction identification10:14:29 17 Jan 202310:16:11 17 Jan 20231 minute 42 seconds
Preliminary analysis of coverage distribution10:16:11 17 Jan 202310:20:35 17 Jan 20234 minutes 24 seconds
Identifying junction candidates10:20:35 17 Jan 202310:20:36 17 Jan 20231 second
Re-alignment to junction candidates10:20:36 17 Jan 202310:23:43 17 Jan 20233 minutes 7 seconds
Resolving best read alignments10:23:43 17 Jan 202310:25:59 17 Jan 20232 minutes 16 seconds
Creating BAM files10:25:59 17 Jan 202310:30:00 17 Jan 20234 minutes 1 second
Tabulating error counts10:30:00 17 Jan 202310:31:13 17 Jan 20231 minute 13 seconds
Re-calibrating base error rates10:31:13 17 Jan 202310:31:14 17 Jan 20231 second
Examining read alignment evidence10:31:14 17 Jan 202310:45:44 17 Jan 202314 minutes 30 seconds
Polymorphism statistics10:45:44 17 Jan 202310:45:45 17 Jan 20231 second
Output10:45:45 17 Jan 202310:48:41 17 Jan 20232 minutes 56 seconds
Total 49 minutes 7 seconds