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_3_18_0_S2697_L006_R1_001.good.fq261,63736,874,801100.0%140.9 bases141 bases99.3%
errorsSNFM_3_18_0_S2697_L006_R2_001.good.fq261,63736,874,801100.0%140.9 bases141 bases98.0%
total523,27473,749,602100.0%140.9 bases141 bases98.7%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionUSA300TCH1516_ALE2,872,91523.52.293.4%Staphylococcus species strain strain.
coveragedistributionCP00073127,04174.72.62.9%Staphylococcus aureus subsp. aureus USA300_TCH1516 plasmid
coveragedistributionNC_0124173,125911.86.13.8%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≤ 1000001187
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 ≤ 500014
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.001

Junction Skew Score Calculation

reference sequencepr(no read start)
USA300TCH1516_ALE0.93530
CP0007310.81116
NC_0124170.19088

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 input07:59:11 23 May 201907:59:19 23 May 20198 seconds
Read alignment to reference genome07:59:19 23 May 201908:00:27 23 May 20191 minute 8 seconds
Preprocessing alignments for candidate junction identification08:00:27 23 May 201908:00:33 23 May 20196 seconds
Preliminary analysis of coverage distribution08:00:33 23 May 201908:00:47 23 May 201914 seconds
Identifying junction candidates08:00:47 23 May 201908:00:47 23 May 20190 seconds
Re-alignment to junction candidates08:00:47 23 May 201908:01:03 23 May 201916 seconds
Resolving best read alignments08:01:03 23 May 201908:01:12 23 May 20199 seconds
Creating BAM files08:01:12 23 May 201908:01:24 23 May 201912 seconds
Tabulating error counts08:01:24 23 May 201908:01:29 23 May 20195 seconds
Re-calibrating base error rates08:01:29 23 May 201908:01:31 23 May 20192 seconds
Examining read alignment evidence08:01:31 23 May 201908:03:51 23 May 20192 minutes 20 seconds
Polymorphism statistics08:03:51 23 May 201908:03:51 23 May 20190 seconds
Output08:03:51 23 May 201908:03:53 23 May 20192 seconds
Total 4 minutes 42 seconds