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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsSRR18439434_R1.good.fq20,651,9532,085,711,149100.0%101.0 bases101 bases99.5%
errorsSRR18439434_R2.good.fq20,651,9532,085,711,149100.0%101.0 bases101 bases99.5%
total41,303,9064,171,422,298100.0%101.0 bases101 bases99.5%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652897.95.1100.0%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≤ 10000075446
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 ≤ 5000206
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_0009130.05131

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 input19:40:28 27 Apr 202319:49:07 27 Apr 20238 minutes 39 seconds
Read alignment to reference genome19:49:08 27 Apr 202320:23:49 27 Apr 202334 minutes 41 seconds
Preprocessing alignments for candidate junction identification20:23:49 27 Apr 202320:31:58 27 Apr 20238 minutes 9 seconds
Preliminary analysis of coverage distribution20:31:58 27 Apr 202320:48:37 27 Apr 202316 minutes 39 seconds
Identifying junction candidates20:48:37 27 Apr 202320:48:42 27 Apr 20235 seconds
Re-alignment to junction candidates20:48:42 27 Apr 202320:57:27 27 Apr 20238 minutes 45 seconds
Resolving best read alignments20:57:27 27 Apr 202321:08:22 27 Apr 202310 minutes 55 seconds
Creating BAM files21:08:22 27 Apr 202321:23:24 27 Apr 202315 minutes 2 seconds
Tabulating error counts21:23:24 27 Apr 202321:29:30 27 Apr 20236 minutes 6 seconds
Re-calibrating base error rates21:29:30 27 Apr 202321:29:32 27 Apr 20232 seconds
Examining read alignment evidence21:29:32 27 Apr 202322:37:08 27 Apr 20231 hour 7 minutes 36 seconds
Polymorphism statistics22:37:08 27 Apr 202322:37:09 27 Apr 20231 second
Output22:37:09 27 Apr 202322:38:27 27 Apr 20231 minute 18 seconds
Total 2 hours 57 minutes 58 seconds