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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsCCK_sdhCBEvo01EP_Isolate_1_S1607_L005_R2_001.good.fq994,834142,114,230100.0%142.9 bases143 bases91.3%
errorsCCK_sdhCBEvo01EP_Isolate_1_S1607_L005_R1_001.good.fq994,834142,114,230100.0%142.9 bases143 bases97.4%
total1,989,668284,228,460100.0%142.9 bases143 bases94.4%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,65356.82.1100.0%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≤ 10000010599
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 ≤ 5000333
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.021

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.85458

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≤ 3
Number of bases that at least one read must overlap each uniquely aligned side of a predicted junction≥ 1

Read Alignment Evidence

optionvalue
ModeConsensus/Mixed Base
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 cutoff10
Polymorphism frequency cutoff0.2
Polymorphism minimum variant coverage each strandOFF
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 ofOFF
Skip base substitutions when they create a homopolymer flanked on each side byOFF

Software Versions

programversion
bowtie22.2.8
R3.3.1

Execution Times

stepstartendelapsed
Read and reference sequence file input15:13:04 17 Mar 201815:13:26 17 Mar 201822 seconds
Read alignment to reference genome15:13:26 17 Mar 201815:15:30 17 Mar 20182 minutes 4 seconds
Preprocessing alignments for candidate junction identification15:15:30 17 Mar 201815:15:56 17 Mar 201826 seconds
Preliminary analysis of coverage distribution15:15:56 17 Mar 201815:16:50 17 Mar 201854 seconds
Identifying junction candidates15:16:50 17 Mar 201815:16:54 17 Mar 20184 seconds
Re-alignment to junction candidates15:16:54 17 Mar 201815:17:16 17 Mar 201822 seconds
Resolving best read alignments15:17:16 17 Mar 201815:18:03 17 Mar 201847 seconds
Creating BAM files15:18:03 17 Mar 201815:18:49 17 Mar 201846 seconds
Tabulating error counts15:18:49 17 Mar 201815:19:12 17 Mar 201823 seconds
Re-calibrating base error rates15:19:12 17 Mar 201815:19:12 17 Mar 20180 seconds
Examining read alignment evidence15:19:12 17 Mar 201815:24:13 17 Mar 20185 minutes 1 second
Polymorphism statistics15:24:13 17 Mar 201815:24:14 17 Mar 20181 second
Output15:24:14 17 Mar 201815:24:24 17 Mar 201810 seconds
Total 11 minutes 20 seconds