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_19_42_1_S2706_L006_R1_001.good.fq305,33743,040,250100.0%141.0 bases141 bases99.3%
errorsSNFM_19_42_1_S2706_L006_R2_001.good.fq305,33743,040,250100.0%141.0 bases141 bases97.7%
total610,67486,080,500100.0%141.0 bases141 bases98.5%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionUSA300TCH1516_ALE2,872,91527.62.194.3%Staphylococcus species strain strain.
coveragedistributionCP00073127,04185.93.22.7%Staphylococcus aureus subsp. aureus USA300_TCH1516 plasmid
coveragedistributionNC_0124173,125842.211.83.0%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≤ 1000002015
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 ≤ 500065
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.007

Junction Skew Score Calculation

reference sequencepr(no read start)
USA300TCH1516_ALE0.92805
CP0007310.80344
NC_0124170.22593

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 input01:29:43 08 Oct 201901:29:53 08 Oct 201910 seconds
Read alignment to reference genome01:29:53 08 Oct 201901:31:14 08 Oct 20191 minute 21 seconds
Preprocessing alignments for candidate junction identification01:31:14 08 Oct 201901:31:21 08 Oct 20197 seconds
Preliminary analysis of coverage distribution01:31:21 08 Oct 201901:31:37 08 Oct 201916 seconds
Identifying junction candidates01:31:37 08 Oct 201901:31:37 08 Oct 20190 seconds
Re-alignment to junction candidates01:31:37 08 Oct 201901:31:55 08 Oct 201918 seconds
Resolving best read alignments01:31:55 08 Oct 201901:32:07 08 Oct 201912 seconds
Creating BAM files01:32:07 08 Oct 201901:32:20 08 Oct 201913 seconds
Tabulating error counts01:32:20 08 Oct 201901:32:26 08 Oct 20196 seconds
Re-calibrating base error rates01:32:26 08 Oct 201901:32:27 08 Oct 20191 second
Examining read alignment evidence01:32:27 08 Oct 201901:33:50 08 Oct 20191 minute 23 seconds
Polymorphism statistics01:33:50 08 Oct 201901:33:50 08 Oct 20190 seconds
Output01:33:50 08 Oct 201901:33:53 08 Oct 20193 seconds
Total 4 minutes 10 seconds