breseq  version 0.35.4  revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsSRR3722227_R1.good.fq10,579839,844100.0%79.4 bases90 bases11.0%
errorsSRR3722227_R2.good.fq10,579839,844100.0%79.4 bases90 bases10.1%
total21,1581,679,688100.0%79.4 bases90 bases10.6%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNZ_CP0092734,631,469NANA100.0%Escherichia coli BW25113 strain K-12 chromosome, complete genome.
total4,631,469100.0%

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.

Insufficient coverage Reference sequence counted as entirely deleted due to low coverage. Try either the -t,--targeted-sequencing or the -c,--contig-reference option if you want mutations called for these reference sequences.

New Junction Evidence

Junction Candidates Tested

optionlimitactual
Number of alignment pairs examined for constructing junction candidates≤ 10000080
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 ≤ 500027
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.001

Junction Skew Score Calculation

reference sequencepr(no read start)
NZ_CP0092730.99978

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
Minimum probablilty assigned that no mapped read will start at a given position and strand for junction prediction0.1
Junction allow suboptimal matchesFALSE
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
bowtie22.2.6
R3.4.4

Execution Times

stepstartendelapsed
Read and reference sequence file input15:10:49 25 Jan 202315:10:51 25 Jan 20232 seconds
Read alignment to reference genome15:10:52 25 Jan 202315:11:01 25 Jan 20239 seconds
Preprocessing alignments for candidate junction identification15:11:01 25 Jan 202315:11:01 25 Jan 20230 seconds
Preliminary analysis of coverage distribution15:11:01 25 Jan 202315:11:02 25 Jan 20231 second
Identifying junction candidates15:11:02 25 Jan 202315:11:02 25 Jan 20230 seconds
Re-alignment to junction candidates15:11:02 25 Jan 202315:11:03 25 Jan 20231 second
Resolving best read alignments15:11:03 25 Jan 202315:11:03 25 Jan 20230 seconds
Creating BAM files15:11:03 25 Jan 202315:11:03 25 Jan 20230 seconds
Tabulating error counts15:11:03 25 Jan 202315:11:03 25 Jan 20230 seconds
Re-calibrating base error rates15:11:03 25 Jan 202315:11:05 25 Jan 20232 seconds
Examining read alignment evidence15:11:05 25 Jan 202315:11:09 25 Jan 20234 seconds
Polymorphism statistics15:11:09 25 Jan 202315:11:09 25 Jan 20230 seconds
Output15:11:09 25 Jan 202315:11:10 25 Jan 20231 second
Total 20 seconds