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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsERR1638182_R1.good.fq1,104,700324,373,676100.0%293.6 bases294 bases99.4%
errorsERR1638182_R2.good.fq1,104,700324,373,676100.0%293.6 bases294 bases81.9%
total2,209,400648,747,352100.0%293.6 bases294 bases90.7%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNZ_LN8324044,638,126124.63.1100.0%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≤ 1000007048
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 ≤ 500090
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.012

Junction Skew Score Calculation

reference sequencepr(no read start)
NZ_LN8324040.83267

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 input01:39:11 09 Apr 202001:39:56 09 Apr 202045 seconds
Read alignment to reference genome01:39:56 09 Apr 202001:54:03 09 Apr 202014 minutes 7 seconds
Preprocessing alignments for candidate junction identification01:54:03 09 Apr 202001:54:47 09 Apr 202044 seconds
Preliminary analysis of coverage distribution01:54:47 09 Apr 202001:56:46 09 Apr 20201 minute 59 seconds
Identifying junction candidates01:56:46 09 Apr 202001:56:50 09 Apr 20204 seconds
Re-alignment to junction candidates01:56:50 09 Apr 202001:58:49 09 Apr 20201 minute 59 seconds
Resolving best read alignments01:58:49 09 Apr 202002:00:01 09 Apr 20201 minute 12 seconds
Creating BAM files02:00:01 09 Apr 202002:01:45 09 Apr 20201 minute 44 seconds
Tabulating error counts02:01:45 09 Apr 202002:02:47 09 Apr 20201 minute 2 seconds
Re-calibrating base error rates02:02:47 09 Apr 202002:02:49 09 Apr 20202 seconds
Examining read alignment evidence02:02:49 09 Apr 202002:48:35 09 Apr 202045 minutes 46 seconds
Polymorphism statistics02:48:35 09 Apr 202002:48:35 09 Apr 20200 seconds
Output02:48:35 09 Apr 202002:49:00 09 Apr 202025 seconds
Total 1 hour 9 minutes 49 seconds