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_19_18_1_S2709_L006_R1_001.good.fq568,57680,150,859100.0%141.0 bases141 bases98.6%
errorsSNFM_19_18_1_S2709_L006_R2_001.good.fq568,57680,150,859100.0%141.0 bases141 bases97.0%
total1,137,152160,301,718100.0%141.0 bases141 bases97.8%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionUSA300TCH1516_ALE2,872,91550.92.894.4%Staphylococcus species strain strain.
coveragedistributionCP00073127,041157.14.62.7%Staphylococcus aureus subsp. aureus USA300_TCH1516 plasmid
coveragedistributionNC_0124173,1251513.718.22.9%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≤ 1000003448
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 ≤ 5000111
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.011

Junction Skew Score Calculation

reference sequencepr(no read start)
USA300TCH1516_ALE0.88787
CP0007310.71229
NC_0124170.13854

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 input23:27:57 07 Oct 201923:28:17 07 Oct 201920 seconds
Read alignment to reference genome23:28:17 07 Oct 201923:30:47 07 Oct 20192 minutes 30 seconds
Preprocessing alignments for candidate junction identification23:30:47 07 Oct 201923:31:00 07 Oct 201913 seconds
Preliminary analysis of coverage distribution23:31:00 07 Oct 201923:31:30 07 Oct 201930 seconds
Identifying junction candidates23:31:30 07 Oct 201923:31:31 07 Oct 20191 second
Re-alignment to junction candidates23:31:31 07 Oct 201923:32:08 07 Oct 201937 seconds
Resolving best read alignments23:32:08 07 Oct 201923:32:29 07 Oct 201921 seconds
Creating BAM files23:32:29 07 Oct 201923:32:56 07 Oct 201927 seconds
Tabulating error counts23:32:56 07 Oct 201923:33:07 07 Oct 201911 seconds
Re-calibrating base error rates23:33:07 07 Oct 201923:33:08 07 Oct 20191 second
Examining read alignment evidence23:33:08 07 Oct 201923:35:29 07 Oct 20192 minutes 21 seconds
Polymorphism statistics23:35:29 07 Oct 201923:35:29 07 Oct 20190 seconds
Output23:35:29 07 Oct 201923:35:34 07 Oct 20195 seconds
Total 7 minutes 37 seconds