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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsERR1473728_R1.good.fq2,364,430234,068,121100.0%99.0 bases99 bases99.8%
errorsERR1473728_R2.good.fq2,364,430234,068,121100.0%99.0 bases99 bases98.7%
total4,728,860468,136,242100.0%99.0 bases99 bases99.2%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652100.11.9100.0%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≤ 1000002458
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 ≤ 500028
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_0009130.63352

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 input13:41:45 25 Nov 202013:45:36 25 Nov 20203 minutes 51 seconds
Read alignment to reference genome13:45:37 25 Nov 202014:12:17 25 Nov 202026 minutes 40 seconds
Preprocessing alignments for candidate junction identification14:12:17 25 Nov 202014:15:58 25 Nov 20203 minutes 41 seconds
Preliminary analysis of coverage distribution14:15:58 25 Nov 202014:22:38 25 Nov 20206 minutes 40 seconds
Identifying junction candidates14:22:38 25 Nov 202014:22:39 25 Nov 20201 second
Re-alignment to junction candidates14:22:39 25 Nov 202014:29:19 25 Nov 20206 minutes 40 seconds
Resolving best read alignments14:29:19 25 Nov 202014:34:04 25 Nov 20204 minutes 45 seconds
Creating BAM files14:34:04 25 Nov 202014:40:01 25 Nov 20205 minutes 57 seconds
Tabulating error counts14:40:01 25 Nov 202014:42:11 25 Nov 20202 minutes 10 seconds
Re-calibrating base error rates14:42:11 25 Nov 202014:42:14 25 Nov 20203 seconds
Examining read alignment evidence14:42:14 25 Nov 202015:29:59 25 Nov 202047 minutes 45 seconds
Polymorphism statistics15:29:59 25 Nov 202015:30:00 25 Nov 20201 second
Output15:30:00 25 Nov 202015:30:36 25 Nov 202036 seconds
Total 1 hour 48 minutes 50 seconds