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_1_56_1_S2262_L006_R1_001.good.fq236,60630,510,481100.0%129.0 bases129 bases97.7%
errorsSNFM_1_56_1_S2262_L006_R2_001.good.fq236,60630,510,481100.0%129.0 bases129 bases89.5%
total473,21261,020,962100.0%129.0 bases129 bases93.6%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionUSA300TCH1516_ALE2,872,91518.41.594.1%Staphylococcus species strain strain.
coveragedistributionCP00073127,04157.21.92.7%Staphylococcus aureus subsp. aureus USA300_TCH1516 plasmid
coveragedistributionNC_0124173,125609.712.13.2%Staphylococcus aureus subsp. aureus USA300_TCH1516 plasmid

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

Number of alignment pairs examined for constructing junction candidates≤ 1000002549
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 ≤ 500081
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.007

Junction Skew Score Calculation

reference sequencepr(no read start)

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

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

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


Execution Times

Read and reference sequence file input06:47:51 24 May 201906:47:58 24 May 20197 seconds
Read alignment to reference genome06:47:58 24 May 201906:49:14 24 May 20191 minute 16 seconds
Preprocessing alignments for candidate junction identification06:49:14 24 May 201906:49:20 24 May 20196 seconds
Preliminary analysis of coverage distribution06:49:20 24 May 201906:49:36 24 May 201916 seconds
Identifying junction candidates06:49:36 24 May 201906:49:36 24 May 20190 seconds
Re-alignment to junction candidates06:49:36 24 May 201906:49:50 24 May 201914 seconds
Resolving best read alignments06:49:50 24 May 201906:49:59 24 May 20199 seconds
Creating BAM files06:49:59 24 May 201906:50:12 24 May 201913 seconds
Tabulating error counts06:50:12 24 May 201906:50:17 24 May 20195 seconds
Re-calibrating base error rates06:50:17 24 May 201906:50:18 24 May 20191 second
Examining read alignment evidence06:50:18 24 May 201906:51:26 24 May 20191 minute 8 seconds
Polymorphism statistics06:51:26 24 May 201906:51:26 24 May 20190 seconds
Output06:51:26 24 May 201906:51:29 24 May 20193 seconds
Total 3 minutes 38 seconds