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_5_43_1_S2285_L006_R1_001.good.fq215,58130,382,229100.0%140.9 bases141 bases97.7%
errorsSNFM_5_43_1_S2285_L006_R2_001.good.fq215,58130,382,229100.0%140.9 bases141 bases91.4%
total431,16260,764,458100.0%140.9 bases141 bases94.5%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionUSA300TCH1516_ALE2,872,91518.91.497.1%Staphylococcus species strain strain.
coveragedistributionCP00073127,041NANA0.0%Staphylococcus aureus subsp. aureus USA300_TCH1516 plasmid
coveragedistributionNC_0124173,125571.19.02.9%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.

Insufficient coverage Reference sequence counted as entirely deleted due to low coverage. Try either the -t,--targeted-sequencing or the -c,--contig-reference option if you want mutations called for these reference sequences.

New Junction Evidence

Junction Candidates Tested

optionlimitactual
Number of alignment pairs examined for constructing junction candidates≤ 1000001951
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 ≤ 5000116
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.012

Junction Skew Score Calculation

reference sequencepr(no read start)
USA300TCH1516_ALE0.94254
CP000731NA
NC_0124170.32038

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 input16:51:12 23 May 201916:51:19 23 May 20197 seconds
Read alignment to reference genome16:51:19 23 May 201916:52:30 23 May 20191 minute 11 seconds
Preprocessing alignments for candidate junction identification16:52:30 23 May 201916:52:35 23 May 20195 seconds
Preliminary analysis of coverage distribution16:52:35 23 May 201916:52:49 23 May 201914 seconds
Identifying junction candidates16:52:49 23 May 201916:52:50 23 May 20191 second
Re-alignment to junction candidates16:52:50 23 May 201916:53:04 23 May 201914 seconds
Resolving best read alignments16:53:04 23 May 201916:53:13 23 May 20199 seconds
Creating BAM files16:53:13 23 May 201916:53:25 23 May 201912 seconds
Tabulating error counts16:53:25 23 May 201916:53:29 23 May 20194 seconds
Re-calibrating base error rates16:53:29 23 May 201916:53:30 23 May 20191 second
Examining read alignment evidence16:53:30 23 May 201916:54:36 23 May 20191 minute 6 seconds
Polymorphism statistics16:54:36 23 May 201916:54:37 23 May 20191 second
Output16:54:37 23 May 201916:54:39 23 May 20192 seconds
Total 3 minutes 27 seconds