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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsGlyE_D15_I1_S2109_L001_R1_001.good.fq1,093,913162,374,408100.0%148.4 bases149 bases97.8%
errorsGlyE_D15_I1_S2109_L001_R2_001.good.fq1,093,913162,374,408100.0%148.4 bases149 bases92.1%
total2,187,826324,748,816100.0%148.4 bases149 bases94.9%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,65366.21.6100.0%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≤ 10000012860
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 ≤ 5000461
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.030

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.82471

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 input00:20:41 30 Oct 201800:21:11 30 Oct 201830 seconds
Read alignment to reference genome00:21:11 30 Oct 201800:26:36 30 Oct 20185 minutes 25 seconds
Preprocessing alignments for candidate junction identification00:26:36 30 Oct 201800:27:02 30 Oct 201826 seconds
Preliminary analysis of coverage distribution00:27:02 30 Oct 201800:28:18 30 Oct 20181 minute 16 seconds
Identifying junction candidates00:28:18 30 Oct 201800:28:19 30 Oct 20181 second
Re-alignment to junction candidates00:28:19 30 Oct 201800:29:26 30 Oct 20181 minute 7 seconds
Resolving best read alignments00:29:26 30 Oct 201800:30:09 30 Oct 201843 seconds
Creating BAM files00:30:09 30 Oct 201800:31:28 30 Oct 20181 minute 19 seconds
Tabulating error counts00:31:28 30 Oct 201800:31:53 30 Oct 201825 seconds
Re-calibrating base error rates00:31:53 30 Oct 201800:31:53 30 Oct 20180 seconds
Examining read alignment evidence00:31:53 30 Oct 201800:36:47 30 Oct 20184 minutes 54 seconds
Polymorphism statistics00:36:47 30 Oct 201800:36:47 30 Oct 20180 seconds
Output00:36:47 30 Oct 201800:36:56 30 Oct 20189 seconds
Total 16 minutes 15 seconds