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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsERR1473751_R1.good.fq3,958,414391,858,622100.0%99.0 bases99 bases99.9%
errorsERR1473751_R2.good.fq3,958,414391,858,622100.0%99.0 bases99 bases99.3%
total7,916,828783,717,244100.0%99.0 bases99 bases99.6%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652167.32.7100.0%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≤ 1000001607
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 ≤ 500029
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.001

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.48815

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≤ 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
bowtie22.2.6
R3.4.4

Execution Times

stepstartendelapsed
Read and reference sequence file input14:01:42 25 Nov 202014:08:25 25 Nov 20206 minutes 43 seconds
Read alignment to reference genome14:08:26 25 Nov 202014:51:42 25 Nov 202043 minutes 16 seconds
Preprocessing alignments for candidate junction identification14:51:42 25 Nov 202014:57:47 25 Nov 20206 minutes 5 seconds
Preliminary analysis of coverage distribution14:57:47 25 Nov 202015:08:26 25 Nov 202010 minutes 39 seconds
Identifying junction candidates15:08:26 25 Nov 202015:08:27 25 Nov 20201 second
Re-alignment to junction candidates15:08:27 25 Nov 202015:19:25 25 Nov 202010 minutes 58 seconds
Resolving best read alignments15:19:25 25 Nov 202015:27:08 25 Nov 20207 minutes 43 seconds
Creating BAM files15:27:08 25 Nov 202015:36:50 25 Nov 20209 minutes 42 seconds
Tabulating error counts15:36:50 25 Nov 202015:40:34 25 Nov 20203 minutes 44 seconds
Re-calibrating base error rates15:40:34 25 Nov 202015:40:37 25 Nov 20203 seconds
Examining read alignment evidence15:40:37 25 Nov 202017:05:58 25 Nov 20201 hour 25 minutes 21 seconds
Polymorphism statistics17:05:58 25 Nov 202017:05:59 25 Nov 20201 second
Output17:05:59 25 Nov 202017:06:58 25 Nov 202059 seconds
Total 3 hours 5 minutes 15 seconds