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_13_68_0_S1828_L005_R1_001.good.fq608,61981,523,714100.0%133.9 bases134 bases95.5%
errorsSNFM_13_68_0_S1828_L005_R2_001.good.fq608,61981,523,714100.0%133.9 bases134 bases91.1%
total1,217,238163,047,428100.0%133.9 bases134 bases93.3%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionUSA300TCH1516_ALE2,872,91550.42.195.7%Staphylococcus species strain strain.
coveragedistributionCP00073127,041135.82.52.5%Staphylococcus aureus subsp. aureus USA300_TCH1516 plasmid
coveragedistributionNC_0124173,125934.15.31.9%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≤ 1000002725
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 ≤ 500054
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_ALE0.86136
CP0007310.68490
NC_0124170.18366

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 input18:06:26 23 May 201918:06:43 23 May 201917 seconds
Read alignment to reference genome18:06:43 23 May 201918:09:59 23 May 20193 minutes 16 seconds
Preprocessing alignments for candidate junction identification18:09:59 23 May 201918:10:14 23 May 201915 seconds
Preliminary analysis of coverage distribution18:10:14 23 May 201918:10:52 23 May 201938 seconds
Identifying junction candidates18:10:52 23 May 201918:10:52 23 May 20190 seconds
Re-alignment to junction candidates18:10:52 23 May 201918:11:28 23 May 201936 seconds
Resolving best read alignments18:11:28 23 May 201918:11:54 23 May 201926 seconds
Creating BAM files18:11:54 23 May 201918:12:28 23 May 201934 seconds
Tabulating error counts18:12:28 23 May 201918:12:39 23 May 201911 seconds
Re-calibrating base error rates18:12:39 23 May 201918:12:41 23 May 20192 seconds
Examining read alignment evidence18:12:41 23 May 201918:27:36 23 May 201914 minutes 55 seconds
Polymorphism statistics18:27:36 23 May 201918:27:36 23 May 20190 seconds
Output18:27:36 23 May 201918:27:41 23 May 20195 seconds
Total 21 minutes 15 seconds