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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorspgi-1-2_S2_L001_R1_001.good.fq1,327,664299,483,743100.0%225.6 bases239 bases97.2%
errorspgi-1-2_S2_L001_R2_001.good.fq1,327,664302,300,014100.0%227.7 bases239 bases61.5%
total2,655,328601,783,757100.0%226.6 bases239 bases79.3%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652105.78.4100.0%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≤ 1000003374
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 ≤ 5000164
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.017

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.86890

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 input21:50:25 26 Feb 202021:51:03 26 Feb 202038 seconds
Read alignment to reference genome21:51:04 26 Feb 202022:06:18 26 Feb 202015 minutes 14 seconds
Preprocessing alignments for candidate junction identification22:06:18 26 Feb 202022:06:59 26 Feb 202041 seconds
Preliminary analysis of coverage distribution22:06:59 26 Feb 202022:08:54 26 Feb 20201 minute 55 seconds
Identifying junction candidates22:08:54 26 Feb 202022:08:58 26 Feb 20204 seconds
Re-alignment to junction candidates22:08:58 26 Feb 202022:11:48 26 Feb 20202 minutes 50 seconds
Resolving best read alignments22:11:48 26 Feb 202022:12:53 26 Feb 20201 minute 5 seconds
Creating BAM files22:12:53 26 Feb 202022:14:38 26 Feb 20201 minute 45 seconds
Tabulating error counts22:14:38 26 Feb 202022:15:15 26 Feb 202037 seconds
Re-calibrating base error rates22:15:15 26 Feb 202022:15:16 26 Feb 20201 second
Examining read alignment evidence22:15:16 26 Feb 202023:14:28 26 Feb 202059 minutes 12 seconds
Polymorphism statistics23:14:28 26 Feb 202023:14:29 26 Feb 20201 second
Output23:14:29 26 Feb 202023:15:03 26 Feb 202034 seconds
Total 1 hour 24 minutes 37 seconds