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_70_1_S2255_L006_R1_001.good.fq322,76845,490,366100.0%140.9 bases141 bases97.8%
errorsSNFM_1_70_1_S2255_L006_R2_001.good.fq322,76845,490,366100.0%140.9 bases141 bases90.9%
total645,53690,980,732100.0%140.9 bases141 bases94.4%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionUSA300TCH1516_ALE2,872,91527.51.894.1%Staphylococcus species strain strain.
coveragedistributionCP00073127,04187.72.32.8%Staphylococcus aureus subsp. aureus USA300_TCH1516 plasmid
coveragedistributionNC_0124173,125893.714.33.1%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≤ 1000003468
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 ≤ 5000152
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.015

Junction Skew Score Calculation

reference sequencepr(no read start)
USA300TCH1516_ALE0.91925
CP0007310.77961
NC_0124170.23274

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 input09:13:21 23 May 201909:13:30 23 May 20199 seconds
Read alignment to reference genome09:13:30 23 May 201909:15:12 23 May 20191 minute 42 seconds
Preprocessing alignments for candidate junction identification09:15:12 23 May 201909:15:19 23 May 20197 seconds
Preliminary analysis of coverage distribution09:15:19 23 May 201909:15:39 23 May 201920 seconds
Identifying junction candidates09:15:39 23 May 201909:15:41 23 May 20192 seconds
Re-alignment to junction candidates09:15:41 23 May 201909:16:01 23 May 201920 seconds
Resolving best read alignments09:16:01 23 May 201909:16:14 23 May 201913 seconds
Creating BAM files09:16:14 23 May 201909:16:31 23 May 201917 seconds
Tabulating error counts09:16:31 23 May 201909:16:37 23 May 20196 seconds
Re-calibrating base error rates09:16:37 23 May 201909:16:39 23 May 20192 seconds
Examining read alignment evidence09:16:39 23 May 201909:18:08 23 May 20191 minute 29 seconds
Polymorphism statistics09:18:08 23 May 201909:18:08 23 May 20190 seconds
Output09:18:08 23 May 201909:18:12 23 May 20194 seconds
Total 4 minutes 51 seconds