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_75_S160_L001_R1_001.good.fq2,453,806334,526,427100.0%136.3 bases150 bases94.9%
errorsPputida_HGL_75_S160_L001_R2_001.good.fq2,453,806334,526,427100.0%136.3 bases150 bases93.2%
total4,907,612669,052,854100.0%136.3 bases150 bases94.1%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0029476,181,929100.63.2100.0%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≤ 10000066593
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 ≤ 50001345
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.067

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0029470.72444

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≤ 0
Number of bases that at least one read must overlap each uniquely aligned side of a predicted junction≥ 6

Read Alignment Evidence

optionvalue
ModeFull Polymorphism
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 cutoff2
Polymorphism frequency cutoff0.05
Polymorphism minimum variant coverage each strand2
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 of ≥3 bases
Skip base substitutions when they create a homopolymer flanked on each side by ≥5 bases

Software Versions

programversion
bowtie22.3.4.1
R3.4.4

Execution Times

stepstartendelapsed
Read and reference sequence file input08:47:58 27 Mar 202008:49:54 27 Mar 20201 minute 56 seconds
Read alignment to reference genome08:49:55 27 Mar 202009:00:42 27 Mar 202010 minutes 47 seconds
Preprocessing alignments for candidate junction identification09:00:42 27 Mar 202009:02:46 27 Mar 20202 minutes 4 seconds
Preliminary analysis of coverage distribution09:02:46 27 Mar 202009:05:23 27 Mar 20202 minutes 37 seconds
Identifying junction candidates09:05:23 27 Mar 202009:35:55 27 Mar 202030 minutes 32 seconds
Re-alignment to junction candidates09:35:55 27 Mar 202009:39:14 27 Mar 20203 minutes 19 seconds
Resolving best read alignments09:39:14 27 Mar 202009:42:48 27 Mar 20203 minutes 34 seconds
Creating BAM files09:42:48 27 Mar 202009:45:04 27 Mar 20202 minutes 16 seconds
Tabulating error counts09:45:04 27 Mar 202009:46:41 27 Mar 20201 minute 37 seconds
Re-calibrating base error rates09:46:41 27 Mar 202009:46:43 27 Mar 20202 seconds
Examining read alignment evidence09:46:43 27 Mar 202010:46:15 27 Mar 202059 minutes 32 seconds
Polymorphism statistics10:46:15 27 Mar 202010:46:19 27 Mar 20204 seconds
Output10:46:19 27 Mar 202010:59:07 27 Mar 202012 minutes 48 seconds
Total 2 hours 11 minutes 8 seconds