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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsF1C2_S169_R1_001.good.fq3,297,834190,320,843100.0%57.7 bases62 bases97.8%
total3,297,834190,320,843100.0%57.7 bases62 bases97.8%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionminE2,987,942300.6331.0100.0%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≤ 1000001630
Coverage evenness (position-hash) score of junction candidates≥ 2≥ 0
Test this many junction candidates (n). May be smaller if not enough passed the coverage evenness threshold100 ≤ n ≤ 50000
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.000

Junction Skew Score Calculation

reference sequencepr(no read start)
minE0.97100

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≤ 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
bowtie22.3.4.1
R3.4.4

Execution Times

stepstartendelapsed
Read and reference sequence file input21:58:43 10 Dec 201921:59:15 10 Dec 201932 seconds
Read alignment to reference genome21:59:15 10 Dec 201922:03:33 10 Dec 20194 minutes 18 seconds
Preprocessing alignments for candidate junction identification22:03:33 10 Dec 201922:04:14 10 Dec 201941 seconds
Preliminary analysis of coverage distribution22:04:14 10 Dec 201922:05:01 10 Dec 201947 seconds
Identifying junction candidates22:05:01 10 Dec 201922:05:01 10 Dec 20190 seconds
Re-alignment to junction candidates22:05:01 10 Dec 201922:05:01 10 Dec 20190 seconds
Resolving best read alignments22:05:01 10 Dec 201922:05:54 10 Dec 201953 seconds
Creating BAM files22:05:54 10 Dec 201922:06:36 10 Dec 201942 seconds
Tabulating error counts22:06:36 10 Dec 201922:06:51 10 Dec 201915 seconds
Re-calibrating base error rates22:06:51 10 Dec 201922:06:52 10 Dec 20191 second
Examining read alignment evidence22:06:52 10 Dec 201922:09:51 10 Dec 20192 minutes 59 seconds
Polymorphism statistics22:09:51 10 Dec 201922:09:52 10 Dec 20191 second
Output22:09:52 10 Dec 201923:45:07 10 Dec 20191 hour 35 minutes 15 seconds
Total 1 hour 46 minutes 24 seconds