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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsC13-Redo-Population-2-23_S11_L001_R1_001.good.fq1,213,402298,657,378100.0%246.1 bases281 bases98.2%
errorsC13-Redo-Population-2-23_S11_L001_R2_001.good.fq1,213,402301,184,537100.0%248.2 bases281 bases89.1%
total2,426,804599,841,915100.0%247.2 bases281 bases93.6%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652118.68.5100.0%Escherichia coli str. K-12 substr. MG1655, complete genome.
total4,641,652100.0%

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≤ 1000003075
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 ≤ 5000478
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.058

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.84430

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
bowtie22.3.4.1
R3.4.4

Execution Times

stepstartendelapsed
Read and reference sequence file input01:53:39 16 May 201901:54:17 16 May 201938 seconds
Read alignment to reference genome01:54:17 16 May 201902:07:16 16 May 201912 minutes 59 seconds
Preprocessing alignments for candidate junction identification02:07:16 16 May 201902:07:55 16 May 201939 seconds
Preliminary analysis of coverage distribution02:07:55 16 May 201902:10:13 16 May 20192 minutes 18 seconds
Identifying junction candidates02:10:13 16 May 201902:10:17 16 May 20194 seconds
Re-alignment to junction candidates02:10:17 16 May 201902:13:31 16 May 20193 minutes 14 seconds
Resolving best read alignments02:13:31 16 May 201902:14:42 16 May 20191 minute 11 seconds
Creating BAM files02:14:42 16 May 201902:16:45 16 May 20192 minutes 3 seconds
Tabulating error counts02:16:45 16 May 201902:17:38 16 May 201953 seconds
Re-calibrating base error rates02:17:38 16 May 201902:17:39 16 May 20191 second
Examining read alignment evidence02:17:39 16 May 201903:20:33 16 May 20191 hour 2 minutes 54 seconds
Polymorphism statistics03:20:33 16 May 201903:20:34 16 May 20191 second
Output03:20:34 16 May 201903:20:47 16 May 201913 seconds
Total 1 hour 27 minutes 8 seconds