breseq  version 0.33.1  revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsPAL15_S15_L007_R1_001.good.fq7,006,213635,718,696100.0%90.7 bases91 bases98.7%
errorsPAL15_S15_L007_R2_001.good.fq7,006,213635,718,696100.0%90.7 bases91 bases97.7%
total14,012,4261,271,437,392100.0%90.7 bases91 bases98.2%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionUSA300TCH1516_ALE2,872,915406.84.994.3%Staphylococcus species strain strain.
coveragedistributionCP00073127,0411511.813.13.1%Staphylococcus aureus subsp. aureus USA300_TCH1516 plasmid
coveragedistributionNC_0124173,12512237.976.72.6%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≤ 10000069488
Coverage evenness (position-hash) score of junction candidates≥ 2≥ 4
Test this many junction candidates (n). May be smaller if not enough passed the coverage evenness threshold100 ≤ n ≤ 5000916
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.060

Junction Skew Score Calculation

reference sequencepr(no read start)
USA300TCH1516_ALE0.22630
CP0007310.03531
NC_0124170.02810

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 input04:29:04 08 Oct 201904:31:55 08 Oct 20192 minutes 51 seconds
Read alignment to reference genome04:31:55 08 Oct 201904:49:39 08 Oct 201917 minutes 44 seconds
Preprocessing alignments for candidate junction identification04:49:39 08 Oct 201904:52:06 08 Oct 20192 minutes 27 seconds
Preliminary analysis of coverage distribution04:52:06 08 Oct 201904:56:33 08 Oct 20194 minutes 27 seconds
Identifying junction candidates04:56:33 08 Oct 201904:57:35 08 Oct 20191 minute 2 seconds
Re-alignment to junction candidates04:57:35 08 Oct 201905:03:54 08 Oct 20196 minutes 19 seconds
Resolving best read alignments05:03:54 08 Oct 201905:08:13 08 Oct 20194 minutes 19 seconds
Creating BAM files05:08:13 08 Oct 201905:12:07 08 Oct 20193 minutes 54 seconds
Tabulating error counts05:12:07 08 Oct 201905:14:06 08 Oct 20191 minute 59 seconds
Re-calibrating base error rates05:14:06 08 Oct 201905:14:08 08 Oct 20192 seconds
Examining read alignment evidence05:14:08 08 Oct 201906:59:20 08 Oct 20191 hour 45 minutes 12 seconds
Polymorphism statistics06:59:20 08 Oct 201906:59:22 08 Oct 20192 seconds
Output06:59:22 08 Oct 201907:00:22 08 Oct 20191 minute 0 seconds
Total 2 hours 31 minutes 18 seconds