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_178_1_S2367_L001_R1_001.good.fq1,007,653141,018,680100.0%139.9 bases140 bases98.6%
errorsSNFR_5_178_1_S2367_L001_R2_001.good.fq1,007,653141,018,680100.0%139.9 bases140 bases92.9%
total2,015,306282,037,360100.0%139.9 bases140 bases95.8%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionUSA300TCH1516_ALE2,872,91589.42.595.8%Staphylococcus species strain strain.
coveragedistributionCP00073127,0410.51.00.0%Staphylococcus aureus subsp. aureus USA300_TCH1516 plasmid
coveragedistributionNC_0124173,1253785.650.84.2%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≤ 1000009851
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 ≤ 5000587
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.059

Junction Skew Score Calculation

reference sequencepr(no read start)
USA300TCH1516_ALE0.79698
CP0007310.99992
NC_0124170.05910

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≤ 3
Number of bases that at least one read must overlap each uniquely aligned side of a predicted junction≥ 1

Read Alignment Evidence

optionvalue
ModeConsensus/Mixed Base
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 cutoff10
Polymorphism frequency cutoff0.2
Polymorphism minimum variant coverage each strandOFF
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 ofOFF
Skip base substitutions when they create a homopolymer flanked on each side byOFF

Software Versions

programversion
bowtie22.3.4.1
R3.4.4

Execution Times

stepstartendelapsed
Read and reference sequence file input00:11:54 26 May 201900:12:23 26 May 201929 seconds
Read alignment to reference genome00:12:23 26 May 201900:17:38 26 May 20195 minutes 15 seconds
Preprocessing alignments for candidate junction identification00:17:38 26 May 201900:18:08 26 May 201930 seconds
Preliminary analysis of coverage distribution00:18:08 26 May 201900:19:16 26 May 20191 minute 8 seconds
Identifying junction candidates00:19:16 26 May 201900:19:30 26 May 201914 seconds
Re-alignment to junction candidates00:19:30 26 May 201900:21:02 26 May 20191 minute 32 seconds
Resolving best read alignments00:21:02 26 May 201900:21:47 26 May 201945 seconds
Creating BAM files00:21:47 26 May 201900:22:46 26 May 201959 seconds
Tabulating error counts00:22:46 26 May 201900:23:07 26 May 201921 seconds
Re-calibrating base error rates00:23:07 26 May 201900:23:08 26 May 20191 second
Examining read alignment evidence00:23:08 26 May 201900:27:32 26 May 20194 minutes 24 seconds
Polymorphism statistics00:27:32 26 May 201900:27:33 26 May 20191 second
Output00:27:33 26 May 201900:27:44 26 May 201911 seconds
Total 15 minutes 50 seconds