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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsW_S1_R1.good.fq2,082,774103,286,326100.0%49.6 bases50 bases98.3%
errorsW_S1_R2.good.fq2,082,774103,287,701100.0%49.6 bases50 bases96.4%
total4,165,548206,574,027100.0%49.6 bases50 bases97.4%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0176354,900,96839.07.1100.0%Escherichia coli W, complete sequence.
total4,900,968100.0%

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≤ 10000037762
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 ≤ 500050
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_0176350.71332

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 input17:47:32 15 Jan 202317:48:52 15 Jan 20231 minute 20 seconds
Read alignment to reference genome17:48:52 15 Jan 202318:16:37 15 Jan 202327 minutes 45 seconds
Preprocessing alignments for candidate junction identification18:16:37 15 Jan 202318:17:20 15 Jan 202343 seconds
Preliminary analysis of coverage distribution18:17:20 15 Jan 202318:18:28 15 Jan 20231 minute 8 seconds
Identifying junction candidates18:18:28 15 Jan 202318:18:30 15 Jan 20232 seconds
Re-alignment to junction candidates18:18:30 15 Jan 202318:19:26 15 Jan 202356 seconds
Resolving best read alignments18:19:26 15 Jan 202318:20:18 15 Jan 202352 seconds
Creating BAM files18:20:18 15 Jan 202318:21:20 15 Jan 20231 minute 2 seconds
Tabulating error counts18:21:20 15 Jan 202318:21:41 15 Jan 202321 seconds
Re-calibrating base error rates18:21:41 15 Jan 202318:21:42 15 Jan 20231 second
Examining read alignment evidence18:21:42 15 Jan 202318:25:32 15 Jan 20233 minutes 50 seconds
Polymorphism statistics18:25:32 15 Jan 202318:25:32 15 Jan 20230 seconds
Output18:25:32 15 Jan 202318:25:44 15 Jan 202312 seconds
Total 38 minutes 12 seconds