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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsSNFR_19_14_0_S2393_L001_R1_001.good.fq777,486109,600,042100.0%141.0 bases141 bases98.8%
errorsSNFR_19_14_0_S2393_L001_R2_001.good.fq777,486109,600,042100.0%141.0 bases141 bases94.0%
total1,554,972219,200,084100.0%141.0 bases141 bases96.4%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionUSA300TCH1516_ALE2,872,91569.82.295.8%Staphylococcus species strain strain.
coveragedistributionCP00073127,041228.54.22.9%Staphylococcus aureus subsp. aureus USA300_TCH1516 plasmid
coveragedistributionNC_0124173,125930.48.11.3%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≤ 1000002580
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 ≤ 500045
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_ALE0.82078
CP0007310.55827
NC_0124170.19084

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 input11:34:57 25 May 201911:35:21 25 May 201924 seconds
Read alignment to reference genome11:35:21 25 May 201911:39:14 25 May 20193 minutes 53 seconds
Preprocessing alignments for candidate junction identification11:39:14 25 May 201911:39:35 25 May 201921 seconds
Preliminary analysis of coverage distribution11:39:35 25 May 201911:40:25 25 May 201950 seconds
Identifying junction candidates11:40:25 25 May 201911:40:25 25 May 20190 seconds
Re-alignment to junction candidates11:40:25 25 May 201911:41:15 25 May 201950 seconds
Resolving best read alignments11:41:15 25 May 201911:41:48 25 May 201933 seconds
Creating BAM files11:41:48 25 May 201911:42:34 25 May 201946 seconds
Tabulating error counts11:42:34 25 May 201911:42:50 25 May 201916 seconds
Re-calibrating base error rates11:42:50 25 May 201911:42:51 25 May 20191 second
Examining read alignment evidence11:42:51 25 May 201912:01:21 25 May 201918 minutes 30 seconds
Polymorphism statistics12:01:21 25 May 201912:01:21 25 May 20190 seconds
Output12:01:21 25 May 201912:01:28 25 May 20197 seconds
Total 26 minutes 31 seconds