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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsEvo04Evo02EP_S24_L001_R1_001.good.fq767,026200,324,719100.0%261.2 bases289 bases99.7%
errorsEvo04Evo02EP_S24_L001_R2_001.good.fq767,026200,560,687100.0%261.5 bases289 bases94.9%
total1,534,052400,885,406100.0%261.3 bases289 bases97.3%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,65288.34.5100.0%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≤ 1000003754
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 ≤ 5000184
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.023

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.88579

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 input06:34:11 26 Feb 202006:34:35 26 Feb 202024 seconds
Read alignment to reference genome06:34:35 26 Feb 202006:41:09 26 Feb 20206 minutes 34 seconds
Preprocessing alignments for candidate junction identification06:41:09 26 Feb 202006:41:35 26 Feb 202026 seconds
Preliminary analysis of coverage distribution06:41:35 26 Feb 202006:42:49 26 Feb 20201 minute 14 seconds
Identifying junction candidates06:42:49 26 Feb 202006:42:53 26 Feb 20204 seconds
Re-alignment to junction candidates06:42:53 26 Feb 202006:44:41 26 Feb 20201 minute 48 seconds
Resolving best read alignments06:44:41 26 Feb 202006:45:24 26 Feb 202043 seconds
Creating BAM files06:45:24 26 Feb 202006:46:29 26 Feb 20201 minute 5 seconds
Tabulating error counts06:46:29 26 Feb 202006:47:07 26 Feb 202038 seconds
Re-calibrating base error rates06:47:07 26 Feb 202006:47:08 26 Feb 20201 second
Examining read alignment evidence06:47:08 26 Feb 202007:14:52 26 Feb 202027 minutes 44 seconds
Polymorphism statistics07:14:52 26 Feb 202007:14:53 26 Feb 20201 second
Output07:14:53 26 Feb 202007:15:17 26 Feb 202024 seconds
Total 41 minutes 6 seconds