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_3_44_0_S2694_L006_R1_001.good.fq460,63364,930,541100.0%141.0 bases141 bases95.0%
errorsSNFM_3_44_0_S2694_L006_R2_001.good.fq460,63364,930,541100.0%141.0 bases141 bases94.3%
total921,266129,861,082100.0%141.0 bases141 bases94.6%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionCP0007302,872,91542.13.1100.0%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≤ 1000001243
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 ≤ 500013
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.001

Junction Skew Score Calculation

reference sequencepr(no read start)
CP0007300.90750

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 cutoff0.05
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
bowtie22.3.4.3
R3.5.1

Execution Times

stepstartendelapsed
Read and reference sequence file input06:45:49 28 Oct 201808:32:48 28 Oct 20181 hour 46 minutes 59 seconds
Read alignment to reference genome08:32:48 28 Oct 201808:45:45 28 Oct 201812 minutes 57 seconds
Preprocessing alignments for candidate junction identification08:45:45 28 Oct 201808:46:00 28 Oct 201815 seconds
Preliminary analysis of coverage distribution08:46:00 28 Oct 201808:59:08 28 Oct 201813 minutes 8 seconds
Identifying junction candidates08:59:08 28 Oct 201808:59:08 28 Oct 20180 seconds
Re-alignment to junction candidates08:59:08 28 Oct 201808:59:48 28 Oct 201840 seconds
Resolving best read alignments08:59:48 28 Oct 201811:00:10 28 Oct 20182 hours 22 seconds
Creating BAM files11:00:10 28 Oct 201811:00:33 28 Oct 201823 seconds
Tabulating error counts11:00:33 28 Oct 201811:00:42 28 Oct 20189 seconds
Re-calibrating base error rates11:00:42 28 Oct 201811:00:42 28 Oct 20180 seconds
Examining read alignment evidence11:00:42 28 Oct 201816:50:08 28 Oct 20185 hours 49 minutes 26 seconds
Polymorphism statistics16:50:08 28 Oct 201816:50:09 28 Oct 20181 second
Output16:50:09 28 Oct 201818:50:17 28 Oct 20182 hours 8 seconds
Total 12 hours 4 minutes 28 seconds