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_5_71_0_S2299_L006_R1_001.good.fq755,247106,464,170100.0%141.0 bases141 bases98.1%
errorsSNFM_5_71_0_S2299_L006_R2_001.good.fq755,247106,464,170100.0%141.0 bases141 bases92.1%
total1,510,494212,928,340100.0%141.0 bases141 bases95.1%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionUSA300TCH1516_ALE2,872,91565.22.196.0%Staphylococcus species strain strain.
coveragedistributionCP00073127,041175.72.52.4%Staphylococcus aureus subsp. aureus USA300_TCH1516 plasmid
coveragedistributionNC_0124173,1251089.014.31.6%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≤ 1000002766
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 ≤ 500048
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_ALE0.82208
CP0007310.62636
NC_0124170.19606

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≤ 0
Number of bases that at least one read must overlap each uniquely aligned side of a predicted junction≥ 6

Read Alignment Evidence

optionvalue
ModeFull Polymorphism
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 cutoff2
Polymorphism frequency cutoff0.05
Polymorphism minimum variant coverage each strand2
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 of ≥3 bases
Skip base substitutions when they create a homopolymer flanked on each side by ≥5 bases

Software Versions

programversion
bowtie22.3.4.1
R3.4.4

Execution Times

stepstartendelapsed
Read and reference sequence file input10:07:58 24 May 201910:08:21 24 May 201923 seconds
Read alignment to reference genome10:08:21 24 May 201910:12:34 24 May 20194 minutes 13 seconds
Preprocessing alignments for candidate junction identification10:12:34 24 May 201910:12:54 24 May 201920 seconds
Preliminary analysis of coverage distribution10:12:54 24 May 201910:13:44 24 May 201950 seconds
Identifying junction candidates10:13:44 24 May 201910:13:45 24 May 20191 second
Re-alignment to junction candidates10:13:45 24 May 201910:14:33 24 May 201948 seconds
Resolving best read alignments10:14:33 24 May 201910:15:03 24 May 201930 seconds
Creating BAM files10:15:03 24 May 201910:15:47 24 May 201944 seconds
Tabulating error counts10:15:47 24 May 201910:16:03 24 May 201916 seconds
Re-calibrating base error rates10:16:03 24 May 201910:16:04 24 May 20191 second
Examining read alignment evidence10:16:04 24 May 201910:35:59 24 May 201919 minutes 55 seconds
Polymorphism statistics10:35:59 24 May 201910:36:00 24 May 20191 second
Output10:36:00 24 May 201910:36:06 24 May 20196 seconds
Total 28 minutes 8 seconds