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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsSRR9016682_R1.good.fq7,192,6091,077,258,017100.0%149.8 bases150 bases95.6%
errorsSRR9016682_R2.good.fq7,192,6091,077,258,017100.0%149.8 bases150 bases94.4%
total14,385,2182,154,516,034100.0%149.8 bases150 bases95.0%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionCP0092734,631,469441.55.0100.0%Escherichia coli BW25113, 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≤ 10000017941
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 ≤ 5000500
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.033

Junction Skew Score Calculation

reference sequencepr(no read start)
CP0092730.33659

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 input02:22:38 01 Jan 202302:26:05 01 Jan 20233 minutes 27 seconds
Read alignment to reference genome02:26:05 01 Jan 202302:53:48 01 Jan 202327 minutes 43 seconds
Preprocessing alignments for candidate junction identification02:53:48 01 Jan 202302:56:52 01 Jan 20233 minutes 4 seconds
Preliminary analysis of coverage distribution02:56:52 01 Jan 202303:04:02 01 Jan 20237 minutes 10 seconds
Identifying junction candidates03:04:02 01 Jan 202303:04:12 01 Jan 202310 seconds
Re-alignment to junction candidates03:04:12 01 Jan 202303:12:05 01 Jan 20237 minutes 53 seconds
Resolving best read alignments03:12:05 01 Jan 202303:17:03 01 Jan 20234 minutes 58 seconds
Creating BAM files03:17:03 01 Jan 202303:22:59 01 Jan 20235 minutes 56 seconds
Tabulating error counts03:22:59 01 Jan 202303:25:58 01 Jan 20232 minutes 59 seconds
Re-calibrating base error rates03:25:58 01 Jan 202303:25:59 01 Jan 20231 second
Examining read alignment evidence03:25:59 01 Jan 202304:03:25 01 Jan 202337 minutes 26 seconds
Polymorphism statistics04:03:25 01 Jan 202304:03:26 01 Jan 20231 second
Output04:03:26 01 Jan 202304:04:06 01 Jan 202340 seconds
Total 1 hour 41 minutes 28 seconds