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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsPAL19_S19_L007_R1_001.good.fq5,831,690529,005,018100.0%90.7 bases91 bases98.2%
errorsPAL19_S19_L007_R2_001.good.fq5,831,690529,005,018100.0%90.7 bases91 bases96.9%
total11,663,3801,058,010,036100.0%90.7 bases91 bases97.5%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionUSA300TCH1516_ALE2,872,915335.33.493.6%Staphylococcus species strain strain.
coveragedistributionCP00073127,0411286.86.33.3%Staphylococcus aureus subsp. aureus USA300_TCH1516 plasmid
coveragedistributionNC_0124173,12510382.355.83.0%Staphylococcus aureus subsp. aureus USA300_TCH1516 plasmid

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

Number of alignment pairs examined for constructing junction candidates≤ 10000076613
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 ≤ 5000951
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.062

Junction Skew Score Calculation

reference sequencepr(no read start)

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

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

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


Execution Times

Read and reference sequence file input23:30:44 23 May 201923:33:02 23 May 20192 minutes 18 seconds
Read alignment to reference genome23:33:02 23 May 201923:48:28 23 May 201915 minutes 26 seconds
Preprocessing alignments for candidate junction identification23:48:28 23 May 201923:50:42 23 May 20192 minutes 14 seconds
Preliminary analysis of coverage distribution23:50:42 23 May 201923:54:36 23 May 20193 minutes 54 seconds
Identifying junction candidates23:54:36 23 May 201923:55:46 23 May 20191 minute 10 seconds
Re-alignment to junction candidates23:55:46 23 May 201900:01:31 24 May 20195 minutes 45 seconds
Resolving best read alignments00:01:31 24 May 201900:05:05 24 May 20193 minutes 34 seconds
Creating BAM files00:05:05 24 May 201900:08:33 24 May 20193 minutes 28 seconds
Tabulating error counts00:08:33 24 May 201900:10:12 24 May 20191 minute 39 seconds
Re-calibrating base error rates00:10:12 24 May 201900:10:14 24 May 20192 seconds
Examining read alignment evidence00:10:14 24 May 201900:25:43 24 May 201915 minutes 29 seconds
Polymorphism statistics00:25:43 24 May 201900:25:44 24 May 20191 second
Output00:25:44 24 May 201900:26:44 24 May 20191 minute 0 seconds
Total 56 minutes 0 seconds