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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsSRR7212217_R1.good.fq5,883,669728,844,168100.0%123.9 bases125 bases99.9%
errorsSRR7212217_R2.good.fq5,883,669715,080,376100.0%121.5 bases125 bases99.8%
total11,767,3381,443,924,544100.0%122.7 bases125 bases99.9%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0029476,181,873234.45.5100.0%Pseudomonas putida KT2440 chromosome, complete genome.
total6,181,873100.0%

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≤ 1000002013
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 ≤ 5000118
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.005

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0029470.42171

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 input18:41:45 27 Jan 202018:46:47 27 Jan 20205 minutes 2 seconds
Read alignment to reference genome18:46:48 27 Jan 202019:06:37 27 Jan 202019 minutes 49 seconds
Preprocessing alignments for candidate junction identification19:06:37 27 Jan 202019:12:47 27 Jan 20206 minutes 10 seconds
Preliminary analysis of coverage distribution19:12:47 27 Jan 202019:19:09 27 Jan 20206 minutes 22 seconds
Identifying junction candidates19:19:09 27 Jan 202019:19:12 27 Jan 20203 seconds
Re-alignment to junction candidates19:19:12 27 Jan 202019:24:55 27 Jan 20205 minutes 43 seconds
Resolving best read alignments19:24:55 27 Jan 202019:33:20 27 Jan 20208 minutes 25 seconds
Creating BAM files19:33:20 27 Jan 202019:38:07 27 Jan 20204 minutes 47 seconds
Tabulating error counts19:38:07 27 Jan 202019:41:50 27 Jan 20203 minutes 43 seconds
Re-calibrating base error rates19:41:50 27 Jan 202019:41:52 27 Jan 20202 seconds
Examining read alignment evidence19:41:53 27 Jan 202020:13:27 27 Jan 202031 minutes 34 seconds
Polymorphism statistics20:13:27 27 Jan 202020:13:27 27 Jan 20200 seconds
Output20:13:27 27 Jan 202020:14:45 27 Jan 20201 minute 18 seconds
Total 1 hour 32 minutes 58 seconds