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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorspgi-7-3_S10_L001_R2_001.good.fq1,738,764393,610,668100.0%226.4 bases239 bases96.0%
errorspgi-7-3_S10_L001_R1_001.good.fq1,738,764393,047,704100.0%226.1 bases239 bases99.8%
total3,477,528786,658,372100.0%226.2 bases239 bases97.9%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,653172.96.6100.0%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≤ 1000008757
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 ≤ 5000496
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.052

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.79715

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 input02:36:20 18 Mar 201802:37:07 18 Mar 201847 seconds
Read alignment to reference genome02:37:07 18 Mar 201802:40:30 18 Mar 20183 minutes 23 seconds
Preprocessing alignments for candidate junction identification02:40:30 18 Mar 201802:41:28 18 Mar 201858 seconds
Preliminary analysis of coverage distribution02:41:28 18 Mar 201802:43:40 18 Mar 20182 minutes 12 seconds
Identifying junction candidates02:43:40 18 Mar 201802:43:48 18 Mar 20188 seconds
Re-alignment to junction candidates02:43:48 18 Mar 201802:44:39 18 Mar 201851 seconds
Resolving best read alignments02:44:39 18 Mar 201802:46:17 18 Mar 20181 minute 38 seconds
Creating BAM files02:46:17 18 Mar 201802:48:05 18 Mar 20181 minute 48 seconds
Tabulating error counts02:48:05 18 Mar 201802:49:12 18 Mar 20181 minute 7 seconds
Re-calibrating base error rates02:49:12 18 Mar 201802:49:13 18 Mar 20181 second
Examining read alignment evidence02:49:13 18 Mar 201804:00:07 18 Mar 20181 hour 10 minutes 54 seconds
Polymorphism statistics04:00:07 18 Mar 201804:00:10 18 Mar 20183 seconds
Output04:00:10 18 Mar 201804:00:46 18 Mar 201836 seconds
Total 1 hour 24 minutes 26 seconds