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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsERR1638197_R1.good.fq886,066261,590,423100.0%295.2 bases296 bases98.9%
errorsERR1638197_R2.good.fq886,066261,590,423100.0%295.2 bases296 bases82.4%
total1,772,132523,180,846100.0%295.2 bases296 bases90.6%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNZ_LN8324044,638,126100.63.0100.0%Escherichia coli K-12 genome assembly EcoliK12AG100, chromosome :
total4,638,126100.0%

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≤ 1000007067
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 ≤ 500082
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.011

Junction Skew Score Calculation

reference sequencepr(no read start)
NZ_LN8324040.86269

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 input03:46:17 09 Apr 202003:46:53 09 Apr 202036 seconds
Read alignment to reference genome03:46:54 09 Apr 202003:58:25 09 Apr 202011 minutes 31 seconds
Preprocessing alignments for candidate junction identification03:58:25 09 Apr 202003:58:59 09 Apr 202034 seconds
Preliminary analysis of coverage distribution03:58:59 09 Apr 202004:00:33 09 Apr 20201 minute 34 seconds
Identifying junction candidates04:00:33 09 Apr 202004:00:37 09 Apr 20204 seconds
Re-alignment to junction candidates04:00:37 09 Apr 202004:02:09 09 Apr 20201 minute 32 seconds
Resolving best read alignments04:02:09 09 Apr 202004:03:08 09 Apr 202059 seconds
Creating BAM files04:03:08 09 Apr 202004:04:32 09 Apr 20201 minute 24 seconds
Tabulating error counts04:04:32 09 Apr 202004:05:21 09 Apr 202049 seconds
Re-calibrating base error rates04:05:21 09 Apr 202004:05:22 09 Apr 20201 second
Examining read alignment evidence04:05:22 09 Apr 202004:36:45 09 Apr 202031 minutes 23 seconds
Polymorphism statistics04:36:45 09 Apr 202004:36:46 09 Apr 20201 second
Output04:36:46 09 Apr 202004:37:09 09 Apr 202023 seconds
Total 50 minutes 51 seconds