breseq  version 0.33.1  revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsGlyA_D15_I1_S2101_L001_R1_001.good.fq3,025,245444,505,519100.0%146.9 bases149 bases97.4%
errorsGlyA_D15_I1_S2101_L001_R2_001.good.fq3,025,245444,505,519100.0%146.9 bases149 bases92.8%
total6,050,490889,011,038100.0%146.9 bases149 bases95.1%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,653172.82.2100.0%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≤ 10000052091
Coverage evenness (position-hash) score of junction candidates≥ 2≥ 3
Test this many junction candidates (n). May be smaller if not enough passed the coverage evenness threshold100 ≤ n ≤ 5000175
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.011

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.61347

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
bowtie22.3.4.3
R3.5.1

Execution Times

stepstartendelapsed
Read and reference sequence file input02:56:04 30 Oct 201802:57:27 30 Oct 20181 minute 23 seconds
Read alignment to reference genome02:57:27 30 Oct 201803:11:48 30 Oct 201814 minutes 21 seconds
Preprocessing alignments for candidate junction identification03:11:48 30 Oct 201803:13:03 30 Oct 20181 minute 15 seconds
Preliminary analysis of coverage distribution03:13:03 30 Oct 201803:16:47 30 Oct 20183 minutes 44 seconds
Identifying junction candidates03:16:47 30 Oct 201803:17:09 30 Oct 201822 seconds
Re-alignment to junction candidates03:17:09 30 Oct 201803:20:07 30 Oct 20182 minutes 58 seconds
Resolving best read alignments03:20:07 30 Oct 201803:22:06 30 Oct 20181 minute 59 seconds
Creating BAM files03:22:06 30 Oct 201803:25:33 30 Oct 20183 minutes 27 seconds
Tabulating error counts03:25:33 30 Oct 201803:26:46 30 Oct 20181 minute 13 seconds
Re-calibrating base error rates03:26:46 30 Oct 201803:26:47 30 Oct 20181 second
Examining read alignment evidence03:26:47 30 Oct 201803:40:31 30 Oct 201813 minutes 44 seconds
Polymorphism statistics03:40:31 30 Oct 201803:40:32 30 Oct 20181 second
Output03:40:32 30 Oct 201803:40:52 30 Oct 201820 seconds
Total 44 minutes 48 seconds