breseq  version 0.33.1  revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsPputida_HGL_3_S381_L002_R1_001.good.fq820,255109,937,400100.0%134.0 bases150 bases94.2%
errorsPputida_HGL_3_S381_L002_R2_001.good.fq820,255109,937,400100.0%134.0 bases150 bases92.4%
total1,640,510219,874,800100.0%134.0 bases150 bases93.3%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0029476,181,92933.22.3100.0%Pseudomonas putida KT2440 chromosome, complete genome.
total6,181,929100.0%

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≤ 10000031369
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 ≤ 5000419
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.021

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0029470.89022

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
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
bowtie22.3.4.1
R3.4.4

Execution Times

stepstartendelapsed
Read and reference sequence file input09:51:08 06 Apr 202009:51:34 06 Apr 202026 seconds
Read alignment to reference genome09:51:34 06 Apr 202009:55:17 06 Apr 20203 minutes 43 seconds
Preprocessing alignments for candidate junction identification09:55:17 06 Apr 202009:55:38 06 Apr 202021 seconds
Preliminary analysis of coverage distribution09:55:38 06 Apr 202009:56:24 06 Apr 202046 seconds
Identifying junction candidates09:56:24 06 Apr 202009:58:43 06 Apr 20202 minutes 19 seconds
Re-alignment to junction candidates09:58:43 06 Apr 202009:59:37 06 Apr 202054 seconds
Resolving best read alignments09:59:37 06 Apr 202010:00:14 06 Apr 202037 seconds
Creating BAM files10:00:14 06 Apr 202010:00:58 06 Apr 202044 seconds
Tabulating error counts10:00:58 06 Apr 202010:01:15 06 Apr 202017 seconds
Re-calibrating base error rates10:01:15 06 Apr 202010:01:17 06 Apr 20202 seconds
Examining read alignment evidence10:01:17 06 Apr 202010:04:55 06 Apr 20203 minutes 38 seconds
Polymorphism statistics10:04:55 06 Apr 202010:04:56 06 Apr 20201 second
Output10:04:56 06 Apr 202010:05:15 06 Apr 202019 seconds
Total 14 minutes 7 seconds