breseq  version 0.33.1  revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsSNFR_21_117_1_S160_S2000_L006_R1_001.good.fq1,030,518140,546,017100.0%136.4 bases141 bases92.0%
errorsSNFR_21_117_1_S160_S2000_L006_R2_001.good.fq1,030,518140,546,017100.0%136.4 bases141 bases91.2%
total2,061,036281,092,034100.0%136.4 bases141 bases91.6%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionCP0007302,872,91589.22.7100.0%Staphylococcus aureus subsp. aureus USA300_TCH1516, complete genome.
total2,872,915100.0%

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≤ 10000090728
Coverage evenness (position-hash) score of junction candidates≥ 2≥ 3
Test this many junction candidates (n). May be smaller if not enough passed the coverage evenness threshold100 ≤ n ≤ 5000344
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.035

Junction Skew Score Calculation

reference sequencepr(no read start)
CP0007300.75083

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 cutoff0.8
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
bowtie22.3.4.3
R3.5.1

Execution Times

stepstartendelapsed
Read and reference sequence file input19:04:00 29 Oct 201819:04:38 29 Oct 201838 seconds
Read alignment to reference genome19:04:38 29 Oct 201819:09:03 29 Oct 20184 minutes 25 seconds
Preprocessing alignments for candidate junction identification19:09:03 29 Oct 201819:09:36 29 Oct 201833 seconds
Preliminary analysis of coverage distribution19:09:36 29 Oct 201819:10:26 29 Oct 201850 seconds
Identifying junction candidates19:10:26 29 Oct 201819:11:10 29 Oct 201844 seconds
Re-alignment to junction candidates19:11:10 29 Oct 201819:12:24 29 Oct 20181 minute 14 seconds
Resolving best read alignments19:12:24 29 Oct 201819:13:21 29 Oct 201857 seconds
Creating BAM files19:13:21 29 Oct 201819:14:05 29 Oct 201844 seconds
Tabulating error counts19:14:05 29 Oct 201819:14:23 29 Oct 201818 seconds
Re-calibrating base error rates19:14:23 29 Oct 201819:14:24 29 Oct 20181 second
Examining read alignment evidence19:14:24 29 Oct 201819:16:53 29 Oct 20182 minutes 29 seconds
Polymorphism statistics19:16:53 29 Oct 201819:16:53 29 Oct 20180 seconds
Output19:16:53 29 Oct 201819:17:01 29 Oct 20188 seconds
Total 13 minutes 1 second