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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsSRR3098254_R1.good.fq6,907,472684,118,453100.0%99.0 bases101 bases99.7%
errorsSRR3098254_R2.good.fq6,907,472675,114,279100.0%97.7 bases101 bases99.6%
total13,814,9441,359,232,732100.0%98.4 bases101 bases99.7%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652290.23.8100.0%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≤ 1000003697
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 ≤ 500015
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_0009130.25641

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 input16:21:20 16 Feb 202116:24:22 16 Feb 20213 minutes 2 seconds
Read alignment to reference genome16:24:22 16 Feb 202116:41:49 16 Feb 202117 minutes 27 seconds
Preprocessing alignments for candidate junction identification16:41:49 16 Feb 202116:44:14 16 Feb 20212 minutes 25 seconds
Preliminary analysis of coverage distribution16:44:14 16 Feb 202116:50:05 16 Feb 20215 minutes 51 seconds
Identifying junction candidates16:50:05 16 Feb 202116:50:05 16 Feb 20210 seconds
Re-alignment to junction candidates16:50:05 16 Feb 202116:54:51 16 Feb 20214 minutes 46 seconds
Resolving best read alignments16:54:51 16 Feb 202116:58:02 16 Feb 20213 minutes 11 seconds
Creating BAM files16:58:02 16 Feb 202117:03:23 16 Feb 20215 minutes 21 seconds
Tabulating error counts17:03:23 16 Feb 202117:05:17 16 Feb 20211 minute 54 seconds
Re-calibrating base error rates17:05:17 16 Feb 202117:05:17 16 Feb 20210 seconds
Examining read alignment evidence17:05:17 16 Feb 202117:25:58 16 Feb 202120 minutes 41 seconds
Polymorphism statistics17:25:58 16 Feb 202117:25:59 16 Feb 20211 second
Output17:25:59 16 Feb 202117:26:30 16 Feb 202131 seconds
Total 1 hour 5 minutes 10 seconds