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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsERR1440904_R1.good.fq8,186802,142100.0%98.0 bases98 bases99.6%
errorsERR1440904_R2.good.fq8,186802,142100.0%98.0 bases98 bases94.6%
total16,3721,604,284100.0%98.0 bases98 bases97.1%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionBX5718572,799,802NANA99.1%Staphylococcus aureus strain MSSA476, complete genome.
coveragedistributionBX57185820,652NANA0.9%Staphylococcus aureus plasmid pSAS, complete genome.
total2,820,454100.0%

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.

Insufficient coverage Reference sequence counted as entirely deleted due to low coverage. Try either the -t,--targeted-sequencing or the -c,--contig-reference option if you want mutations called for these reference sequences.

New Junction Evidence

Junction Candidates Tested

optionlimitactual
Number of alignment pairs examined for constructing junction candidates≤ 10000013
Coverage evenness (position-hash) score of junction candidates≥ 2≥ 0
Test this many junction candidates (n). May be smaller if not enough passed the coverage evenness threshold100 ≤ n ≤ 50000
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.000

Junction Skew Score Calculation

reference sequencepr(no read start)
BX5718570.99736
BX5718580.99671

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 cutoff0.75
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
bowtie22.3.4.1
R3.4.4

Execution Times

stepstartendelapsed
Read and reference sequence file input21:39:47 07 Apr 202021:39:48 07 Apr 20201 second
Read alignment to reference genome21:39:48 07 Apr 202021:39:52 07 Apr 20204 seconds
Preprocessing alignments for candidate junction identification21:39:52 07 Apr 202021:39:52 07 Apr 20200 seconds
Preliminary analysis of coverage distribution21:39:52 07 Apr 202021:39:54 07 Apr 20202 seconds
Identifying junction candidates21:39:54 07 Apr 202021:39:54 07 Apr 20200 seconds
Re-alignment to junction candidates21:39:54 07 Apr 202021:39:54 07 Apr 20200 seconds
Resolving best read alignments21:39:54 07 Apr 202021:39:54 07 Apr 20200 seconds
Creating BAM files21:39:54 07 Apr 202021:39:55 07 Apr 20201 second
Tabulating error counts21:39:55 07 Apr 202021:39:55 07 Apr 20200 seconds
Re-calibrating base error rates21:39:55 07 Apr 202021:39:56 07 Apr 20201 second
Examining read alignment evidence21:39:56 07 Apr 202021:39:58 07 Apr 20202 seconds
Polymorphism statistics21:39:58 07 Apr 202021:39:58 07 Apr 20200 seconds
Output21:39:58 07 Apr 202021:39:59 07 Apr 20201 second
Total 12 seconds