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_106_1_S2335_L001_R1_001.good.fq681,86092,020,187100.0%135.0 bases135 bases98.5%
errorsSNFR_19_106_1_S2335_L001_R2_001.good.fq681,86092,020,187100.0%135.0 bases135 bases93.2%
total1,363,720184,040,374100.0%135.0 bases135 bases95.8%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionUSA300TCH1516_ALE2,872,91557.43.494.5%Staphylococcus species strain strain.
coveragedistributionCP00073127,041239.57.23.7%Staphylococcus aureus subsp. aureus USA300_TCH1516 plasmid
coveragedistributionNC_0124173,1251044.314.71.8%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≤ 1000006555
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 ≤ 5000320
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.031

Junction Skew Score Calculation

reference sequencepr(no read start)
USA300TCH1516_ALE0.85430
CP0007310.55832
NC_0124170.18166

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 input10:23:34 25 May 201910:23:53 25 May 201919 seconds
Read alignment to reference genome10:23:53 25 May 201910:27:17 25 May 20193 minutes 24 seconds
Preprocessing alignments for candidate junction identification10:27:17 25 May 201910:27:33 25 May 201916 seconds
Preliminary analysis of coverage distribution10:27:33 25 May 201910:28:18 25 May 201945 seconds
Identifying junction candidates10:28:18 25 May 201910:28:25 25 May 20197 seconds
Re-alignment to junction candidates10:28:25 25 May 201910:29:16 25 May 201951 seconds
Resolving best read alignments10:29:16 25 May 201910:29:44 25 May 201928 seconds
Creating BAM files10:29:44 25 May 201910:30:25 25 May 201941 seconds
Tabulating error counts10:30:25 25 May 201910:30:38 25 May 201913 seconds
Re-calibrating base error rates10:30:38 25 May 201910:30:39 25 May 20191 second
Examining read alignment evidence10:30:39 25 May 201910:33:31 25 May 20192 minutes 52 seconds
Polymorphism statistics10:33:31 25 May 201910:33:32 25 May 20191 second
Output10:33:32 25 May 201910:33:38 25 May 20196 seconds
Total 10 minutes 4 seconds