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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsSRR9723031_R1.good.fq974,899242,851,252100.0%249.1 bases250 bases99.7%
errorsSRR9723031_R2.good.fq974,899242,891,332100.0%249.1 bases250 bases94.3%
total1,949,798485,742,584100.0%249.1 bases250 bases97.0%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNZ_CP0092734,631,469102.71.8100.0%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.

New Junction Evidence

Junction Candidates Tested

optionlimitactual
Number of alignment pairs examined for constructing junction candidates≤ 100000982
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 ≤ 500032
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.004

Junction Skew Score Calculation

reference sequencepr(no read start)
NZ_CP0092730.82553

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 input16:50:56 16 Mar 202316:51:40 16 Mar 202344 seconds
Read alignment to reference genome16:51:40 16 Mar 202316:58:34 16 Mar 20236 minutes 54 seconds
Preprocessing alignments for candidate junction identification16:58:34 16 Mar 202316:59:02 16 Mar 202328 seconds
Preliminary analysis of coverage distribution16:59:02 16 Mar 202317:00:43 16 Mar 20231 minute 41 seconds
Identifying junction candidates17:00:43 16 Mar 202317:00:44 16 Mar 20231 second
Re-alignment to junction candidates17:00:44 16 Mar 202317:02:19 16 Mar 20231 minute 35 seconds
Resolving best read alignments17:02:19 16 Mar 202317:03:02 16 Mar 202343 seconds
Creating BAM files17:03:02 16 Mar 202317:04:29 16 Mar 20231 minute 27 seconds
Tabulating error counts17:04:29 16 Mar 202317:05:14 16 Mar 202345 seconds
Re-calibrating base error rates17:05:14 16 Mar 202317:05:15 16 Mar 20231 second
Examining read alignment evidence17:05:15 16 Mar 202317:14:03 16 Mar 20238 minutes 48 seconds
Polymorphism statistics17:14:03 16 Mar 202317:14:04 16 Mar 20231 second
Output17:14:04 16 Mar 202317:14:13 16 Mar 20239 seconds
Total 23 minutes 17 seconds