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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsPAL141_S139_L001_R1_001.good.fq2,105,736285,817,791100.0%135.7 bases140 bases98.9%
errorsPAL141_S139_L001_R2_001.good.fq2,105,736285,817,791100.0%135.7 bases140 bases98.1%
total4,211,472571,635,582100.0%135.7 bases140 bases98.5%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNZ_CP0349434,045,538137.38.0100.0%Bacillus subtilis subsp. spizizenii ATCC 6633 = JCM 2499 strain
total4,045,538100.0%

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≤ 1000002249
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 ≤ 5000147
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.010

Junction Skew Score Calculation

reference sequencepr(no read start)
NZ_CP0349430.79286

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 input10:52:10 16 May 202310:53:53 16 May 20231 minute 43 seconds
Read alignment to reference genome10:53:53 16 May 202311:03:54 16 May 202310 minutes 1 second
Preprocessing alignments for candidate junction identification11:03:54 16 May 202311:04:55 16 May 20231 minute 1 second
Preliminary analysis of coverage distribution11:04:55 16 May 202311:06:56 16 May 20232 minutes 1 second
Identifying junction candidates11:06:56 16 May 202311:06:57 16 May 20231 second
Re-alignment to junction candidates11:06:57 16 May 202311:09:12 16 May 20232 minutes 15 seconds
Resolving best read alignments11:09:12 16 May 202311:10:34 16 May 20231 minute 22 seconds
Creating BAM files11:10:34 16 May 202311:12:19 16 May 20231 minute 45 seconds
Tabulating error counts11:12:19 16 May 202311:13:09 16 May 202350 seconds
Re-calibrating base error rates11:13:09 16 May 202311:13:10 16 May 20231 second
Examining read alignment evidence11:13:10 16 May 202311:23:42 16 May 202310 minutes 32 seconds
Polymorphism statistics11:23:42 16 May 202311:23:42 16 May 20230 seconds
Output11:23:42 16 May 202311:23:53 16 May 202311 seconds
Total 31 minutes 43 seconds