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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsERR1440905_R1.good.fq3,646,974357,355,779100.0%98.0 bases98 bases99.8%
errorsERR1440905_R2.good.fq3,646,974357,355,779100.0%98.0 bases98 bases98.1%
total7,293,948714,711,558100.0%98.0 bases98 bases98.9%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionBX5718572,799,802262.615.599.2%Staphylococcus aureus strain MSSA476, complete genome.
coveragedistributionBX57185820,652303.133.50.8%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≤ 100000800
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 ≤ 500010
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.001

Junction Skew Score Calculation

reference sequencepr(no read start)
BX5718570.37094
BX5718580.34026

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 input18:52:27 07 Apr 202018:54:18 07 Apr 20201 minute 51 seconds
Read alignment to reference genome18:54:18 07 Apr 202019:06:35 07 Apr 202012 minutes 17 seconds
Preprocessing alignments for candidate junction identification19:06:35 07 Apr 202019:08:18 07 Apr 20201 minute 43 seconds
Preliminary analysis of coverage distribution19:08:18 07 Apr 202019:11:26 07 Apr 20203 minutes 8 seconds
Identifying junction candidates19:11:26 07 Apr 202019:11:26 07 Apr 20200 seconds
Re-alignment to junction candidates19:11:26 07 Apr 202019:14:04 07 Apr 20202 minutes 38 seconds
Resolving best read alignments19:14:04 07 Apr 202019:16:45 07 Apr 20202 minutes 41 seconds
Creating BAM files19:16:45 07 Apr 202019:19:32 07 Apr 20202 minutes 47 seconds
Tabulating error counts19:19:32 07 Apr 202019:20:31 07 Apr 202059 seconds
Re-calibrating base error rates19:20:31 07 Apr 202019:20:33 07 Apr 20202 seconds
Examining read alignment evidence19:20:33 07 Apr 202020:15:21 07 Apr 202054 minutes 48 seconds
Polymorphism statistics20:15:21 07 Apr 202020:15:22 07 Apr 20201 second
Output20:15:22 07 Apr 202020:15:37 07 Apr 202015 seconds
Total 1 hour 23 minutes 10 seconds