breseq  version 0.32.1  revision 5f2cb669173e
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsSNFR_15_18_0_S2377_L001_R1_001.good.fq320,73844,872,033100.0%139.9 bases140 bases95.7%
errorsSNFR_15_18_0_S2377_L001_R2_001.good.fq320,73844,872,033100.0%139.9 bases140 bases91.3%
total641,47689,744,066100.0%139.9 bases140 bases93.5%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionCP0007302,872,91528.12.1100.0%Staphylococcus aureus subsp. aureus USA300_TCH1516, complete
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≤ 1000001230
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 ≤ 500011
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.001

Junction Skew Score Calculation

reference sequencepr(no read start)
CP0007300.91613

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≤ 0
Number of bases that at least one read must overlap each uniquely aligned side of a predicted junction≥ 6

Read Alignment Evidence

optionvalue
ModeFull Polymorphism
Ploidy1 (haploid)
Consensus mutation E-value cutoff10
Consensus frequency cutoffOFF
Consensus minimum variant coverage each strandOFF
Consensus minimum total coverage each strandOFF
Consensus minimum variant coverageOFF
Consensus minimum total coverageOFF
Polymorphism E-value cutoff2
Polymorphism frequency cutoff0.025
Polymorphism minimum variant coverage each strand2
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 of ≥3 bases
Skip base substitutions when they create a homopolymer flanked on each side by ≥5 bases

Software Versions

programversion
bowtie22.3.4.1
R3.5.0

Execution Times

stepstartendelapsed
Read and reference sequence file input10:57:22 22 Jun 201810:57:48 22 Jun 201826 seconds
Read alignment to reference genome10:57:48 22 Jun 201810:59:14 22 Jun 20181 minute 26 seconds
Preprocessing alignments for candidate junction identification10:59:14 22 Jun 201810:59:31 22 Jun 201817 seconds
Preliminary analysis of coverage distribution10:59:31 22 Jun 201810:59:58 22 Jun 201827 seconds
Identifying junction candidates10:59:58 22 Jun 201810:59:58 22 Jun 20180 seconds
Re-alignment to junction candidates10:59:58 22 Jun 201811:00:20 22 Jun 201822 seconds
Resolving best read alignments11:00:20 22 Jun 201811:00:49 22 Jun 201829 seconds
Creating BAM files11:00:49 22 Jun 201811:01:11 22 Jun 201822 seconds
Tabulating error counts11:01:11 22 Jun 201811:01:20 22 Jun 20189 seconds
Re-calibrating base error rates11:01:20 22 Jun 201811:01:23 22 Jun 20183 seconds
Examining read alignment evidence11:01:23 22 Jun 201811:06:59 22 Jun 20185 minutes 36 seconds
Polymorphism statistics11:06:59 22 Jun 201811:07:00 22 Jun 20181 second
Output11:07:00 22 Jun 201811:07:07 22 Jun 20187 seconds
Total 9 minutes 45 seconds