breseq  version 0.32.0  revision 6ff6de7d1b87
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsEvo04pgiEvo01EP_S1_L001_R1_001.good.fq1,240,107325,653,346100.0%262.6 bases289 bases99.8%
errorsEvo04pgiEvo01EP_S1_L001_R2_001.good.fq1,240,107325,898,637100.0%262.8 bases289 bases97.5%
total2,480,214651,551,983100.0%262.7 bases289 bases98.7%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,653141.05.4100.0%Escherichia coli str. K-12 sbstr. MG1655, complete genome. Live strain from Systems Biology Research Group
total4,641,653100.0%

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≤ 1000007761
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 ≤ 5000517
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.065

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.83599

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 cutoffOFF
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 cutoff0.025
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
bowtie22.2.8
R3.3.1

Execution Times

stepstartendelapsed
Read and reference sequence file input23:32:10 17 Mar 201823:32:47 17 Mar 201837 seconds
Read alignment to reference genome23:32:47 17 Mar 201823:35:43 17 Mar 20182 minutes 56 seconds
Preprocessing alignments for candidate junction identification23:35:43 17 Mar 201823:36:31 17 Mar 201848 seconds
Preliminary analysis of coverage distribution23:36:31 17 Mar 201823:38:00 17 Mar 20181 minute 29 seconds
Identifying junction candidates23:38:00 17 Mar 201823:38:12 17 Mar 201812 seconds
Re-alignment to junction candidates23:38:12 17 Mar 201823:38:53 17 Mar 201841 seconds
Resolving best read alignments23:38:53 17 Mar 201823:40:13 17 Mar 20181 minute 20 seconds
Creating BAM files23:40:13 17 Mar 201823:41:23 17 Mar 20181 minute 10 seconds
Tabulating error counts23:41:23 17 Mar 201823:42:18 17 Mar 201855 seconds
Re-calibrating base error rates23:42:18 17 Mar 201823:42:18 17 Mar 20180 seconds
Examining read alignment evidence23:42:18 17 Mar 201800:39:01 18 Mar 201856 minutes 43 seconds
Polymorphism statistics00:39:01 18 Mar 201800:39:02 18 Mar 20181 second
Output00:39:02 18 Mar 201800:39:28 18 Mar 201826 seconds
Total 1 hour 7 minutes 18 seconds