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_D40_I0_S2130_L001_R1_001.good.fq731,795108,930,090100.0%148.9 bases149 bases98.2%
errorsGlyE_D40_I0_S2130_L001_R2_001.good.fq731,795108,930,090100.0%148.9 bases149 bases90.9%
total1,463,590217,860,180100.0%148.9 bases149 bases94.5%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,65344.11.5100.0%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≤ 1000005331
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 ≤ 500046
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_0009130.87881

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≤ 0
Number of bases that at least one read must overlap each uniquely aligned side of a predicted junction≥ 6

Read Alignment Evidence

optionvalue
ModeFull Polymorphism
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 cutoff2
Polymorphism frequency cutoff0.05
Polymorphism minimum variant coverage each strand2
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 of ≥3 bases
Skip base substitutions when they create a homopolymer flanked on each side by ≥5 bases

Software Versions

programversion
bowtie22.3.4.3
R3.5.1

Execution Times

stepstartendelapsed
Read and reference sequence file input00:36:57 30 Oct 201800:37:17 30 Oct 201820 seconds
Read alignment to reference genome00:37:17 30 Oct 201800:40:59 30 Oct 20183 minutes 42 seconds
Preprocessing alignments for candidate junction identification00:40:59 30 Oct 201800:41:16 30 Oct 201817 seconds
Preliminary analysis of coverage distribution00:41:16 30 Oct 201800:42:07 30 Oct 201851 seconds
Identifying junction candidates00:42:07 30 Oct 201800:42:07 30 Oct 20180 seconds
Re-alignment to junction candidates00:42:07 30 Oct 201800:42:46 30 Oct 201839 seconds
Resolving best read alignments00:42:46 30 Oct 201800:43:15 30 Oct 201829 seconds
Creating BAM files00:43:15 30 Oct 201800:44:09 30 Oct 201854 seconds
Tabulating error counts00:44:09 30 Oct 201800:44:26 30 Oct 201817 seconds
Re-calibrating base error rates00:44:26 30 Oct 201800:44:26 30 Oct 20180 seconds
Examining read alignment evidence00:44:26 30 Oct 201801:01:16 30 Oct 201816 minutes 50 seconds
Polymorphism statistics01:01:16 30 Oct 201801:01:16 30 Oct 20180 seconds
Output01:01:16 30 Oct 201801:01:23 30 Oct 20187 seconds
Total 24 minutes 26 seconds