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_16_1_S2276_L006_R1_001.good.fq328,92146,028,159100.0%139.9 bases140 bases96.9%
errorsSNFM_1_16_1_S2276_L006_R2_001.good.fq328,92146,028,159100.0%139.9 bases140 bases90.3%
total657,84292,056,318100.0%139.9 bases140 bases93.6%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionUSA300TCH1516_ALE2,872,91528.11.694.4%Staphylococcus species strain strain.
coveragedistributionCP00073127,04181.32.42.5%Staphylococcus aureus subsp. aureus USA300_TCH1516 plasmid
coveragedistributionNC_0124173,125873.311.23.0%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≤ 1000003874
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 ≤ 5000192
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.019

Junction Skew Score Calculation

reference sequencepr(no read start)
USA300TCH1516_ALE0.91785
CP0007310.78977
NC_0124170.22046

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 input02:41:48 23 May 201902:41:58 23 May 201910 seconds
Read alignment to reference genome02:41:58 23 May 201902:43:47 23 May 20191 minute 49 seconds
Preprocessing alignments for candidate junction identification02:43:47 23 May 201902:43:55 23 May 20198 seconds
Preliminary analysis of coverage distribution02:43:55 23 May 201902:44:16 23 May 201921 seconds
Identifying junction candidates02:44:16 23 May 201902:44:18 23 May 20192 seconds
Re-alignment to junction candidates02:44:18 23 May 201902:44:39 23 May 201921 seconds
Resolving best read alignments02:44:39 23 May 201902:44:51 23 May 201912 seconds
Creating BAM files02:44:51 23 May 201902:45:10 23 May 201919 seconds
Tabulating error counts02:45:10 23 May 201902:45:16 23 May 20196 seconds
Re-calibrating base error rates02:45:16 23 May 201902:45:17 23 May 20191 second
Examining read alignment evidence02:45:17 23 May 201902:46:47 23 May 20191 minute 30 seconds
Polymorphism statistics02:46:47 23 May 201902:46:47 23 May 20190 seconds
Output02:46:47 23 May 201902:46:50 23 May 20193 seconds
Total 5 minutes 2 seconds