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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsSNFM_21_42_1_S2710_L006_R1_001.good.fq435,72861,420,024100.0%141.0 bases141 bases99.0%
errorsSNFM_21_42_1_S2710_L006_R2_001.good.fq435,72861,420,024100.0%141.0 bases141 bases97.3%
total871,456122,840,048100.0%141.0 bases141 bases98.2%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionUSA300TCH1516_ALE2,872,91539.52.494.7%Staphylococcus species strain strain.
coveragedistributionCP00073127,041118.72.72.7%Staphylococcus aureus subsp. aureus USA300_TCH1516 plasmid
coveragedistributionNC_0124173,1251036.817.02.6%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≤ 1000002214
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 ≤ 500047
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.005

Junction Skew Score Calculation

reference sequencepr(no read start)
USA300TCH1516_ALE0.90377
CP0007310.74938
NC_0124170.19481

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 input15:27:55 23 May 201915:28:08 23 May 201913 seconds
Read alignment to reference genome15:28:08 23 May 201915:30:07 23 May 20191 minute 59 seconds
Preprocessing alignments for candidate junction identification15:30:07 23 May 201915:30:18 23 May 201911 seconds
Preliminary analysis of coverage distribution15:30:18 23 May 201915:30:41 23 May 201923 seconds
Identifying junction candidates15:30:41 23 May 201915:30:41 23 May 20190 seconds
Re-alignment to junction candidates15:30:41 23 May 201915:31:09 23 May 201928 seconds
Resolving best read alignments15:31:09 23 May 201915:31:28 23 May 201919 seconds
Creating BAM files15:31:28 23 May 201915:31:47 23 May 201919 seconds
Tabulating error counts15:31:47 23 May 201915:31:55 23 May 20198 seconds
Re-calibrating base error rates15:31:55 23 May 201915:31:57 23 May 20192 seconds
Examining read alignment evidence15:31:57 23 May 201915:33:51 23 May 20191 minute 54 seconds
Polymorphism statistics15:33:51 23 May 201915:33:51 23 May 20190 seconds
Output15:33:51 23 May 201915:33:55 23 May 20194 seconds
Total 6 minutes 0 seconds