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_17_172_1_S191_S1999_L006_R1_001.good.fq872,157121,401,233100.0%139.2 bases141 bases96.6%
errorsSNFR_17_172_1_S191_S1999_L006_R2_001.good.fq872,157121,401,233100.0%139.2 bases141 bases95.2%
errorsSNFR_17_172_1_S191_S1999_L008_R1_001.good.fq372,95751,842,638100.0%139.0 bases141 bases96.6%
errorsSNFR_17_172_1_S191_S1999_L008_R2_001.good.fq372,95751,842,638100.0%139.0 bases141 bases93.5%
total2,490,228346,487,742100.0%139.1 bases141 bases95.6%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionUSA300TCH1516_ALE2,872,915114.81.699.9%Staphylococcus species strain strain.
coveragedistributionCP00073127,0413.51.00.0%Staphylococcus aureus subsp. aureus USA300_TCH1516 plasmid
coveragedistributionNC_0124173,12582.41.10.1%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≤ 10000052087
Coverage evenness (position-hash) score of junction candidates≥ 2≥ 3
Test this many junction candidates (n). May be smaller if not enough passed the coverage evenness threshold100 ≤ n ≤ 5000352
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.035

Junction Skew Score Calculation

reference sequencepr(no read start)
USA300TCH1516_ALE0.70031
CP0007310.98768
NC_0124170.78133

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 input21:34:16 25 May 201921:34:51 25 May 201935 seconds
Read alignment to reference genome21:34:51 25 May 201921:40:30 25 May 20195 minutes 39 seconds
Preprocessing alignments for candidate junction identification21:40:30 25 May 201921:41:04 25 May 201934 seconds
Preliminary analysis of coverage distribution21:41:04 25 May 201921:42:16 25 May 20191 minute 12 seconds
Identifying junction candidates21:42:16 25 May 201921:42:45 25 May 201929 seconds
Re-alignment to junction candidates21:42:45 25 May 201921:44:15 25 May 20191 minute 30 seconds
Resolving best read alignments21:44:15 25 May 201921:45:12 25 May 201957 seconds
Creating BAM files21:45:12 25 May 201921:46:15 25 May 20191 minute 3 seconds
Tabulating error counts21:46:15 25 May 201921:46:41 25 May 201926 seconds
Re-calibrating base error rates21:46:41 25 May 201921:46:43 25 May 20192 seconds
Examining read alignment evidence21:46:43 25 May 201921:51:47 25 May 20195 minutes 4 seconds
Polymorphism statistics21:51:47 25 May 201921:51:47 25 May 20190 seconds
Output21:51:47 25 May 201921:52:02 25 May 201915 seconds
Total 17 minutes 46 seconds