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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsSRR396520_R1.good.fq3,300,600214,539,000100.0%65.0 bases65 bases87.4%
total3,300,600214,539,000100.0%65.0 bases65 bases87.4%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,65240.34.4100.0%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≤ 1000001556
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 ≤ 500022
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.001

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.83243

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 input20:48:39 23 Nov 202020:49:31 23 Nov 202052 seconds
Read alignment to reference genome20:49:31 23 Nov 202020:55:48 23 Nov 20206 minutes 17 seconds
Preprocessing alignments for candidate junction identification20:55:48 23 Nov 202020:56:22 23 Nov 202034 seconds
Preliminary analysis of coverage distribution20:56:22 23 Nov 202020:57:29 23 Nov 20201 minute 7 seconds
Identifying junction candidates20:57:29 23 Nov 202020:57:29 23 Nov 20200 seconds
Re-alignment to junction candidates20:57:29 23 Nov 202020:58:12 23 Nov 202043 seconds
Resolving best read alignments20:58:12 23 Nov 202020:59:01 23 Nov 202049 seconds
Creating BAM files20:59:01 23 Nov 202021:00:16 23 Nov 20201 minute 15 seconds
Tabulating error counts21:00:16 23 Nov 202021:00:33 23 Nov 202017 seconds
Re-calibrating base error rates21:00:33 23 Nov 202021:00:34 23 Nov 20201 second
Examining read alignment evidence21:00:34 23 Nov 202021:03:43 23 Nov 20203 minutes 9 seconds
Polymorphism statistics21:03:43 23 Nov 202021:03:43 23 Nov 20200 seconds
Output21:03:43 23 Nov 202021:03:53 23 Nov 202010 seconds
Total 15 minutes 14 seconds