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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsERR1579168_R1.good.fq3,362,224329,447,043100.0%98.0 bases98 bases99.7%
errorsERR1579168_R2.good.fq3,362,224329,447,043100.0%98.0 bases98 bases97.6%
total6,724,448658,894,086100.0%98.0 bases98 bases98.7%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionBX5718572,799,802242.630.799.2%Staphylococcus aureus strain MSSA476, complete genome.
coveragedistributionBX57185820,652235.220.10.8%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≤ 100000908
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 ≤ 50007
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.001

Junction Skew Score Calculation

reference sequencepr(no read start)
BX5718570.40818
BX5718580.38885

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 input23:50:25 07 Apr 202023:52:05 07 Apr 20201 minute 40 seconds
Read alignment to reference genome23:52:06 07 Apr 202000:03:02 08 Apr 202010 minutes 56 seconds
Preprocessing alignments for candidate junction identification00:03:02 08 Apr 202000:04:40 08 Apr 20201 minute 38 seconds
Preliminary analysis of coverage distribution00:04:40 08 Apr 202000:07:36 08 Apr 20202 minutes 56 seconds
Identifying junction candidates00:07:36 08 Apr 202000:07:36 08 Apr 20200 seconds
Re-alignment to junction candidates00:07:36 08 Apr 202000:10:07 08 Apr 20202 minutes 31 seconds
Resolving best read alignments00:10:07 08 Apr 202000:12:36 08 Apr 20202 minutes 29 seconds
Creating BAM files00:12:36 08 Apr 202000:15:12 08 Apr 20202 minutes 36 seconds
Tabulating error counts00:15:12 08 Apr 202000:16:13 08 Apr 20201 minute 1 second
Re-calibrating base error rates00:16:13 08 Apr 202000:16:15 08 Apr 20202 seconds
Examining read alignment evidence00:16:15 08 Apr 202001:06:27 08 Apr 202050 minutes 12 seconds
Polymorphism statistics01:06:27 08 Apr 202001:06:27 08 Apr 20200 seconds
Output01:06:27 08 Apr 202001:06:41 08 Apr 202014 seconds
Total 1 hour 16 minutes 15 seconds