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_pgIsolate_Evo02EP_Isolate_2_S1618_L005_R1_001.good.fq486,71069,539,931100.0%142.9 bases143 bases97.5%
errorsCCK_pgIsolate_Evo02EP_Isolate_2_S1618_L005_R2_001.good.fq486,71069,539,931100.0%142.9 bases143 bases91.1%
total973,420139,079,862100.0%142.9 bases143 bases94.3%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,65328.11.3100.0%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≤ 1000004747
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 ≤ 500055
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.003

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.92255

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 input12:17:13 17 Mar 201812:17:25 17 Mar 201812 seconds
Read alignment to reference genome12:17:25 17 Mar 201812:18:24 17 Mar 201859 seconds
Preprocessing alignments for candidate junction identification12:18:24 17 Mar 201812:18:36 17 Mar 201812 seconds
Preliminary analysis of coverage distribution12:18:36 17 Mar 201812:19:05 17 Mar 201829 seconds
Identifying junction candidates12:19:05 17 Mar 201812:19:06 17 Mar 20181 second
Re-alignment to junction candidates12:19:06 17 Mar 201812:19:15 17 Mar 20189 seconds
Resolving best read alignments12:19:15 17 Mar 201812:19:36 17 Mar 201821 seconds
Creating BAM files12:19:36 17 Mar 201812:20:03 17 Mar 201827 seconds
Tabulating error counts12:20:03 17 Mar 201812:20:22 17 Mar 201819 seconds
Re-calibrating base error rates12:20:22 17 Mar 201812:20:26 17 Mar 20184 seconds
Examining read alignment evidence12:20:26 17 Mar 201812:24:47 17 Mar 20184 minutes 21 seconds
Polymorphism statistics12:24:47 17 Mar 201812:24:48 17 Mar 20181 second
Output12:24:48 17 Mar 201812:24:54 17 Mar 20186 seconds
Total 7 minutes 41 seconds