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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsJADR50_R1.good.fq4,782,048717,196,331100.0%150.0 bases150 bases98.7%
errorsJADR50_R2.good.fq4,782,048717,196,331100.0%150.0 bases150 bases98.3%
total9,564,0961,434,392,662100.0%150.0 bases150 bases98.5%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionCP0068814,033,459306.812.887.4%Bacillus subtilis PY79, complete genome.
coveragedistributionpSIJ663_pHT315_araE_xy11,56816810.8555.212.6%.
total4,045,027100.0%

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≤ 10000029811
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 ≤ 500073
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.005

Junction Skew Score Calculation

reference sequencepr(no read start)
CP0068810.40803
pSIJ663_pHT315_araE_xy0.02086

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 input11:46:19 20 Jan 202111:49:11 20 Jan 20212 minutes 52 seconds
Read alignment to reference genome11:49:11 20 Jan 202112:12:05 20 Jan 202122 minutes 54 seconds
Preprocessing alignments for candidate junction identification12:12:06 20 Jan 202112:14:19 20 Jan 20212 minutes 13 seconds
Preliminary analysis of coverage distribution12:14:19 20 Jan 202112:22:21 20 Jan 20218 minutes 2 seconds
Identifying junction candidates12:22:21 20 Jan 202112:22:23 20 Jan 20212 seconds
Re-alignment to junction candidates12:22:23 20 Jan 202112:28:22 20 Jan 20215 minutes 59 seconds
Resolving best read alignments12:28:22 20 Jan 202112:31:51 20 Jan 20213 minutes 29 seconds
Creating BAM files12:31:51 20 Jan 202112:39:15 20 Jan 20217 minutes 24 seconds
Tabulating error counts12:39:15 20 Jan 202112:41:37 20 Jan 20212 minutes 22 seconds
Re-calibrating base error rates12:41:37 20 Jan 202112:41:39 20 Jan 20212 seconds
Examining read alignment evidence12:41:39 20 Jan 202113:08:44 20 Jan 202127 minutes 5 seconds
Polymorphism statistics13:08:44 20 Jan 202113:08:45 20 Jan 20211 second
Output13:08:45 20 Jan 202113:10:21 20 Jan 20211 minute 36 seconds
Total 1 hour 24 minutes 1 second