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_gndEvo01EP_Isolate_1_S1625_L005_R2_001.good.fq1,355,649191,684,988100.0%141.4 bases143 bases92.7%
errorsCCK_gndEvo01EP_Isolate_1_S1625_L005_R1_001.good.fq1,355,649191,684,988100.0%141.4 bases143 bases97.6%
total2,711,298383,369,976100.0%141.4 bases143 bases95.1%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,65378.01.7100.0%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≤ 10000018137
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 ≤ 5000666
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.042

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.79925

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 input16:31:14 17 Mar 201816:31:44 17 Mar 201830 seconds
Read alignment to reference genome16:31:44 17 Mar 201816:34:17 17 Mar 20182 minutes 33 seconds
Preprocessing alignments for candidate junction identification16:34:17 17 Mar 201816:34:53 17 Mar 201836 seconds
Preliminary analysis of coverage distribution16:34:53 17 Mar 201816:36:04 17 Mar 20181 minute 11 seconds
Identifying junction candidates16:36:04 17 Mar 201816:36:14 17 Mar 201810 seconds
Re-alignment to junction candidates16:36:14 17 Mar 201816:36:46 17 Mar 201832 seconds
Resolving best read alignments16:36:46 17 Mar 201816:37:47 17 Mar 20181 minute 1 second
Creating BAM files16:37:47 17 Mar 201816:38:49 17 Mar 20181 minute 2 seconds
Tabulating error counts16:38:49 17 Mar 201816:39:20 17 Mar 201831 seconds
Re-calibrating base error rates16:39:20 17 Mar 201816:39:21 17 Mar 20181 second
Examining read alignment evidence16:39:21 17 Mar 201816:46:10 17 Mar 20186 minutes 49 seconds
Polymorphism statistics16:46:10 17 Mar 201816:46:10 17 Mar 20180 seconds
Output16:46:10 17 Mar 201816:46:24 17 Mar 201814 seconds
Total 15 minutes 10 seconds