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_1_15_0_S2329_L001_R1_001.good.fq667,94193,487,458100.0%140.0 bases140 bases95.5%
errorsSNFR_1_15_0_S2329_L001_R2_001.good.fq667,94193,487,458100.0%140.0 bases140 bases91.6%
total1,335,882186,974,916100.0%140.0 bases140 bases93.5%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionCP0007302,872,91560.32.2100.0%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≤ 1000002509
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 ≤ 500083
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.008

Junction Skew Score Calculation

reference sequencepr(no read start)
CP0007300.83894

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 input17:56:05 29 Oct 201817:56:30 29 Oct 201825 seconds
Read alignment to reference genome17:56:30 29 Oct 201817:59:45 29 Oct 20183 minutes 15 seconds
Preprocessing alignments for candidate junction identification17:59:45 29 Oct 201818:00:06 29 Oct 201821 seconds
Preliminary analysis of coverage distribution18:00:06 29 Oct 201818:00:57 29 Oct 201851 seconds
Identifying junction candidates18:00:57 29 Oct 201818:00:57 29 Oct 20180 seconds
Re-alignment to junction candidates18:00:57 29 Oct 201818:01:39 29 Oct 201842 seconds
Resolving best read alignments18:01:39 29 Oct 201818:02:16 29 Oct 201837 seconds
Creating BAM files18:02:16 29 Oct 201818:03:02 29 Oct 201846 seconds
Tabulating error counts18:03:02 29 Oct 201818:03:15 29 Oct 201813 seconds
Re-calibrating base error rates18:03:15 29 Oct 201818:03:16 29 Oct 20181 second
Examining read alignment evidence18:03:16 29 Oct 201818:12:44 29 Oct 20189 minutes 28 seconds
Polymorphism statistics18:12:44 29 Oct 201818:12:44 29 Oct 20180 seconds
Output18:12:44 29 Oct 201818:12:50 29 Oct 20186 seconds
Total 16 minutes 45 seconds