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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsDRR075739_R1.good.fq2,258,709596,493,246100.0%264.1 bases289 bases99.5%
errorsDRR075739_R2.good.fq2,258,709597,198,022100.0%264.4 bases289 bases94.6%
total4,517,4181,193,691,268100.0%264.2 bases289 bases97.0%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionAP0123063,976,195297.15.8100.0%Escherichia coli str. K-12 substr. MDS42 DNA, complete genome.
total3,976,195100.0%

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≤ 10000010891
Coverage evenness (position-hash) score of junction candidates≥ 2≥ 3
Test this many junction candidates (n). May be smaller if not enough passed the coverage evenness threshold100 ≤ n ≤ 500031
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.005

Junction Skew Score Calculation

reference sequencepr(no read start)
AP0123060.72884

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 input10:41:05 09 Feb 202310:42:25 09 Feb 20231 minute 20 seconds
Read alignment to reference genome10:42:25 09 Feb 202311:00:44 09 Feb 202318 minutes 19 seconds
Preprocessing alignments for candidate junction identification11:00:44 09 Feb 202311:01:58 09 Feb 20231 minute 14 seconds
Preliminary analysis of coverage distribution11:01:58 09 Feb 202311:05:51 09 Feb 20233 minutes 53 seconds
Identifying junction candidates11:05:51 09 Feb 202311:06:02 09 Feb 202311 seconds
Re-alignment to junction candidates11:06:02 09 Feb 202311:09:38 09 Feb 20233 minutes 36 seconds
Resolving best read alignments11:09:38 09 Feb 202311:11:27 09 Feb 20231 minute 49 seconds
Creating BAM files11:11:27 09 Feb 202311:14:44 09 Feb 20233 minutes 17 seconds
Tabulating error counts11:14:44 09 Feb 202311:16:36 09 Feb 20231 minute 52 seconds
Re-calibrating base error rates11:16:36 09 Feb 202311:16:37 09 Feb 20231 second
Examining read alignment evidence11:16:37 09 Feb 202311:39:07 09 Feb 202322 minutes 30 seconds
Polymorphism statistics11:39:07 09 Feb 202311:39:07 09 Feb 20230 seconds
Output11:39:07 09 Feb 202311:39:28 09 Feb 202321 seconds
Total 58 minutes 23 seconds