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_19_14_1_S2349_L001_R1_001.good.fq1,415,303209,418,266100.0%148.0 bases148 bases93.4%
errorsSNFR_19_14_1_S2349_L001_R2_001.good.fq1,415,303209,418,266100.0%148.0 bases148 bases90.6%
total2,830,606418,836,532100.0%148.0 bases148 bases92.0%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionCP0007302,872,915132.77.1100.0%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≤ 10000013129
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 ≤ 5000675
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.072

Junction Skew Score Calculation

reference sequencepr(no read start)
CP0007300.74883

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 input16:16:10 29 Oct 201816:17:04 29 Oct 201854 seconds
Read alignment to reference genome16:17:04 29 Oct 201816:23:10 29 Oct 20186 minutes 6 seconds
Preprocessing alignments for candidate junction identification16:23:10 29 Oct 201816:23:57 29 Oct 201847 seconds
Preliminary analysis of coverage distribution16:23:57 29 Oct 201816:25:46 29 Oct 20181 minute 49 seconds
Identifying junction candidates16:25:46 29 Oct 201816:26:19 29 Oct 201833 seconds
Re-alignment to junction candidates16:26:19 29 Oct 201816:28:15 29 Oct 20181 minute 56 seconds
Resolving best read alignments16:28:15 29 Oct 201816:29:37 29 Oct 20181 minute 22 seconds
Creating BAM files16:29:37 29 Oct 201816:31:18 29 Oct 20181 minute 41 seconds
Tabulating error counts16:31:18 29 Oct 201816:31:46 29 Oct 201828 seconds
Re-calibrating base error rates16:31:46 29 Oct 201816:31:47 29 Oct 20181 second
Examining read alignment evidence16:31:47 29 Oct 201816:35:35 29 Oct 20183 minutes 48 seconds
Polymorphism statistics16:35:35 29 Oct 201816:35:36 29 Oct 20181 second
Output16:35:36 29 Oct 201816:35:46 29 Oct 201810 seconds
Total 19 minutes 36 seconds