breseq  version 0.33.1  revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsJ3-F1_S100_R1_001.good.fq4,450,826272,545,321100.0%61.2 bases71 bases94.1%
total4,450,826272,545,321100.0%61.2 bases71 bases94.1%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionminE2,987,94286.67.8100.0%Escherichia coli str. K-12 substr. W3110 DNA, complete genome.
total2,987,942100.0%

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≤ 10000022086
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 ≤ 5000343
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.017

Junction Skew Score Calculation

reference sequencepr(no read start)
minE0.67078

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
Skew score of predicted junction (−log10 probability of unusual coverage evenness) must be≤ 0
Number of bases that at least one read must overlap each uniquely aligned side of a predicted junction≥ 6

Read Alignment Evidence

optionvalue
ModeFull Polymorphism
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 cutoff2
Polymorphism frequency cutoff0.05
Polymorphism minimum variant coverage each strand2
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 of ≥3 bases
Skip base substitutions when they create a homopolymer flanked on each side by ≥5 bases

Software Versions

programversion
bowtie22.3.4.1
R3.4.4

Execution Times

stepstartendelapsed
Read and reference sequence file input04:14:49 11 Dec 201904:15:33 11 Dec 201944 seconds
Read alignment to reference genome04:15:33 11 Dec 201904:20:38 11 Dec 20195 minutes 5 seconds
Preprocessing alignments for candidate junction identification04:20:38 11 Dec 201904:21:32 11 Dec 201954 seconds
Preliminary analysis of coverage distribution04:21:32 11 Dec 201904:22:50 11 Dec 20191 minute 18 seconds
Identifying junction candidates04:22:50 11 Dec 201904:22:52 11 Dec 20192 seconds
Re-alignment to junction candidates04:22:52 11 Dec 201904:24:18 11 Dec 20191 minute 26 seconds
Resolving best read alignments04:24:18 11 Dec 201904:25:39 11 Dec 20191 minute 21 seconds
Creating BAM files04:25:39 11 Dec 201904:26:51 11 Dec 20191 minute 12 seconds
Tabulating error counts04:26:51 11 Dec 201904:27:13 11 Dec 201922 seconds
Re-calibrating base error rates04:27:13 11 Dec 201904:27:14 11 Dec 20191 second
Examining read alignment evidence04:27:14 11 Dec 201904:34:32 11 Dec 20197 minutes 18 seconds
Polymorphism statistics04:34:32 11 Dec 201904:34:33 11 Dec 20191 second
Output04:34:33 11 Dec 201904:34:45 11 Dec 201912 seconds
Total 19 minutes 56 seconds