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_11_18_1_S2699_L006_R1_001.good.fq86,86512,245,517100.0%141.0 bases141 bases93.5%
errorsSNFM_11_18_1_S2699_L006_R2_001.good.fq86,86512,245,517100.0%141.0 bases141 bases92.7%
total173,73024,491,034100.0%141.0 bases141 bases93.1%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionCP0007302,872,9157.91.3100.0%Staphylococcus aureus subsp. aureus USA300_TCH1516, complete genome.
total2,872,915100.0%

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≤ 100000552
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 ≤ 500026
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.003

Junction Skew Score Calculation

reference sequencepr(no read start)
CP0007300.97431

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 cutoff0.8
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
bowtie22.3.4.3
R3.5.1

Execution Times

stepstartendelapsed
Read and reference sequence file input09:36:17 26 Oct 201809:36:21 26 Oct 20184 seconds
Read alignment to reference genome09:36:21 26 Oct 201809:36:46 26 Oct 201825 seconds
Preprocessing alignments for candidate junction identification09:36:46 26 Oct 201809:36:49 26 Oct 20183 seconds
Preliminary analysis of coverage distribution09:36:49 26 Oct 201809:36:55 26 Oct 20186 seconds
Identifying junction candidates09:36:55 26 Oct 201809:36:55 26 Oct 20180 seconds
Re-alignment to junction candidates09:36:55 26 Oct 201809:37:02 26 Oct 20187 seconds
Resolving best read alignments09:37:02 26 Oct 201809:37:07 26 Oct 20185 seconds
Creating BAM files09:37:07 26 Oct 201809:37:12 26 Oct 20185 seconds
Tabulating error counts09:37:12 26 Oct 201809:37:14 26 Oct 20182 seconds
Re-calibrating base error rates09:37:14 26 Oct 201809:37:15 26 Oct 20181 second
Examining read alignment evidence09:37:15 26 Oct 201809:37:54 26 Oct 201839 seconds
Polymorphism statistics09:37:54 26 Oct 201809:37:56 26 Oct 20182 seconds
Output09:37:56 26 Oct 201809:38:50 26 Oct 201854 seconds
Total 2 minutes 33 seconds