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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsERR1440902_R1.good.fq1,580,282153,266,726100.0%97.0 bases97 bases99.7%
errorsERR1440902_R2.good.fq1,580,282153,266,726100.0%97.0 bases97 bases98.3%
total3,160,564306,533,452100.0%97.0 bases97 bases99.0%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionBX5718572,799,802111.37.198.8%Staphylococcus aureus strain MSSA476, complete genome.
coveragedistributionBX57185820,652187.115.01.2%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.

New Junction Evidence

Junction Candidates Tested

optionlimitactual
Number of alignment pairs examined for constructing junction candidates≤ 100000325
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 ≤ 50006
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.000

Junction Skew Score Calculation

reference sequencepr(no read start)
BX5718570.62461
BX5718580.47635

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 input16:55:48 07 Apr 202016:56:38 07 Apr 202050 seconds
Read alignment to reference genome16:56:38 07 Apr 202017:02:01 07 Apr 20205 minutes 23 seconds
Preprocessing alignments for candidate junction identification17:02:01 07 Apr 202017:02:48 07 Apr 202047 seconds
Preliminary analysis of coverage distribution17:02:48 07 Apr 202017:04:14 07 Apr 20201 minute 26 seconds
Identifying junction candidates17:04:14 07 Apr 202017:04:14 07 Apr 20200 seconds
Re-alignment to junction candidates17:04:14 07 Apr 202017:05:24 07 Apr 20201 minute 10 seconds
Resolving best read alignments17:05:24 07 Apr 202017:06:33 07 Apr 20201 minute 9 seconds
Creating BAM files17:06:33 07 Apr 202017:07:51 07 Apr 20201 minute 18 seconds
Tabulating error counts17:07:51 07 Apr 202017:08:17 07 Apr 202026 seconds
Re-calibrating base error rates17:08:17 07 Apr 202017:08:19 07 Apr 20202 seconds
Examining read alignment evidence17:08:19 07 Apr 202017:24:47 07 Apr 202016 minutes 28 seconds
Polymorphism statistics17:24:47 07 Apr 202017:24:47 07 Apr 20200 seconds
Output17:24:47 07 Apr 202017:24:55 07 Apr 20208 seconds
Total 29 minutes 7 seconds