breseq  version 0.35.4  revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsPAL212_S210_L001_R1_001.good.fq7,686,2431,044,749,297100.0%135.9 bases140 bases98.6%
errorsPAL212_S210_L001_R2_001.good.fq7,686,2431,044,749,297100.0%135.9 bases140 bases97.9%
total15,372,4862,089,498,594100.0%135.9 bases140 bases98.2%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionCP0092734,631,469438.922.5100.0%Escherichia coli BW25113, complete genome.
total4,631,469100.0%

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≤ 10000029949
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 ≤ 50001131
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.070

Junction Skew Score Calculation

reference sequencepr(no read start)
CP0092730.66404

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
Minimum probablilty assigned that no mapped read will start at a given position and strand for junction prediction0.1
Junction allow suboptimal matchesFALSE
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
bowtie22.2.6
R3.4.4

Execution Times

stepstartendelapsed
Read and reference sequence file input23:17:55 16 Jun 202223:22:14 16 Jun 20224 minutes 19 seconds
Read alignment to reference genome23:22:14 16 Jun 202223:55:23 16 Jun 202233 minutes 9 seconds
Preprocessing alignments for candidate junction identification23:55:23 16 Jun 202223:59:12 16 Jun 20223 minutes 49 seconds
Preliminary analysis of coverage distribution23:59:12 16 Jun 202200:06:38 17 Jun 20227 minutes 26 seconds
Identifying junction candidates00:06:38 17 Jun 202200:06:47 17 Jun 20229 seconds
Re-alignment to junction candidates00:06:47 17 Jun 202200:17:34 17 Jun 202210 minutes 47 seconds
Resolving best read alignments00:17:34 17 Jun 202200:22:47 17 Jun 20225 minutes 13 seconds
Creating BAM files00:22:47 17 Jun 202200:29:22 17 Jun 20226 minutes 35 seconds
Tabulating error counts00:29:22 17 Jun 202200:32:20 17 Jun 20222 minutes 58 seconds
Re-calibrating base error rates00:32:20 17 Jun 202200:32:21 17 Jun 20221 second
Examining read alignment evidence00:32:21 17 Jun 202205:34:38 17 Jun 20225 hours 2 minutes 17 seconds
Polymorphism statistics05:34:38 17 Jun 202205:34:40 17 Jun 20222 seconds
Output05:34:40 17 Jun 202205:35:16 17 Jun 202236 seconds
Total 6 hours 17 minutes 21 seconds