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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsPAL050_S49_L007_R1_001.good.fq3,635,323330,241,654100.0%90.8 bases91 bases96.4%
errorsPAL050_S49_L007_R2_001.good.fq3,635,323330,241,654100.0%90.8 bases91 bases96.4%
total7,270,646660,483,308100.0%90.8 bases91 bases96.4%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionUSA300TCH1516_ALE2,872,915208.15.495.8%Staphylococcus species strain strain.
coveragedistributionCP00073127,041982.948.14.0%Staphylococcus aureus subsp. aureus USA300_TCH1516 plasmid
coveragedistributionNC_0124173,125317.93.30.2%Staphylococcus aureus subsp. aureus USA300_TCH1516 plasmid
total2,903,081100.0%

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≤ 100000100044
Coverage evenness (position-hash) score of junction candidates≥ 2≥ 4
Test this many junction candidates (n). May be smaller if not enough passed the coverage evenness threshold100 ≤ n ≤ 50001450
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.095

Junction Skew Score Calculation

reference sequencepr(no read start)
USA300TCH1516_ALE0.42495
CP0007310.07727
NC_0124170.31498

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 input04:29:20 25 May 201904:30:43 25 May 20191 minute 23 seconds
Read alignment to reference genome04:30:43 25 May 201904:40:39 25 May 20199 minutes 56 seconds
Preprocessing alignments for candidate junction identification04:40:39 25 May 201904:42:00 25 May 20191 minute 21 seconds
Preliminary analysis of coverage distribution04:42:00 25 May 201904:44:15 25 May 20192 minutes 15 seconds
Identifying junction candidates04:44:15 25 May 201904:48:03 25 May 20193 minutes 48 seconds
Re-alignment to junction candidates04:48:03 25 May 201904:51:33 25 May 20193 minutes 30 seconds
Resolving best read alignments04:51:33 25 May 201904:53:45 25 May 20192 minutes 12 seconds
Creating BAM files04:53:45 25 May 201904:55:45 25 May 20192 minutes 0 seconds
Tabulating error counts04:55:45 25 May 201904:56:38 25 May 201953 seconds
Re-calibrating base error rates04:56:38 25 May 201904:56:40 25 May 20192 seconds
Examining read alignment evidence04:56:40 25 May 201905:05:48 25 May 20199 minutes 8 seconds
Polymorphism statistics05:05:48 25 May 201905:05:49 25 May 20191 second
Output05:05:49 25 May 201905:06:46 25 May 201957 seconds
Total 37 minutes 26 seconds