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_5_18_0_S2345_L001_R1_001.good.fq766,775108,080,352100.0%141.0 bases141 bases98.8%
errorsSNFR_5_18_0_S2345_L001_R2_001.good.fq766,775108,080,352100.0%141.0 bases141 bases94.4%
total1,533,550216,160,704100.0%141.0 bases141 bases96.6%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionUSA300TCH1516_ALE2,872,91569.12.195.9%Staphylococcus species strain strain.
coveragedistributionCP00073127,041210.34.22.8%Staphylococcus aureus subsp. aureus USA300_TCH1516 plasmid
coveragedistributionNC_0124173,125915.27.11.3%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≤ 1000004058
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 ≤ 500083
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.008

Junction Skew Score Calculation

reference sequencepr(no read start)
USA300TCH1516_ALE0.81309
CP0007310.56084
NC_0124170.18752

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 input18:53:24 25 May 201918:53:46 25 May 201922 seconds
Read alignment to reference genome18:53:46 25 May 201918:57:32 25 May 20193 minutes 46 seconds
Preprocessing alignments for candidate junction identification18:57:32 25 May 201918:57:50 25 May 201918 seconds
Preliminary analysis of coverage distribution18:57:50 25 May 201918:58:39 25 May 201949 seconds
Identifying junction candidates18:58:39 25 May 201918:58:40 25 May 20191 second
Re-alignment to junction candidates18:58:40 25 May 201918:59:29 25 May 201949 seconds
Resolving best read alignments18:59:29 25 May 201919:00:00 25 May 201931 seconds
Creating BAM files19:00:00 25 May 201919:00:44 25 May 201944 seconds
Tabulating error counts19:00:44 25 May 201919:00:59 25 May 201915 seconds
Re-calibrating base error rates19:00:59 25 May 201919:01:01 25 May 20192 seconds
Examining read alignment evidence19:01:01 25 May 201919:18:55 25 May 201917 minutes 54 seconds
Polymorphism statistics19:18:55 25 May 201919:18:55 25 May 20190 seconds
Output19:18:55 25 May 201919:19:01 25 May 20196 seconds
Total 25 minutes 37 seconds