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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsDRR075743_R1.good.fq1,914,602522,396,065100.0%272.8 bases289 bases99.5%
errorsDRR075743_R2.good.fq1,914,602522,683,133100.0%273.0 bases289 bases93.7%
total3,829,2041,045,079,198100.0%272.9 bases289 bases96.6%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionCP0425833,977,116262.85.7100.0%Escherichia coli str. K-12 substr. MDS42 strain SynAC chromosome,
total3,977,116100.0%

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≤ 10000010173
Coverage evenness (position-hash) score of junction candidates≥ 2≥ 3
Test this many junction candidates (n). May be smaller if not enough passed the coverage evenness threshold100 ≤ n ≤ 500052
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.008

Junction Skew Score Calculation

reference sequencepr(no read start)
CP0425830.76609

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 cutoff0.75
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
bowtie22.2.6
R3.4.4

Execution Times

stepstartendelapsed
Read and reference sequence file input09:13:48 07 Mar 202009:14:59 07 Mar 20201 minute 11 seconds
Read alignment to reference genome09:14:59 07 Mar 202009:32:24 07 Mar 202017 minutes 25 seconds
Preprocessing alignments for candidate junction identification09:32:24 07 Mar 202009:33:39 07 Mar 20201 minute 15 seconds
Preliminary analysis of coverage distribution09:33:39 07 Mar 202009:36:31 07 Mar 20202 minutes 52 seconds
Identifying junction candidates09:36:31 07 Mar 202009:36:57 07 Mar 202026 seconds
Re-alignment to junction candidates09:36:57 07 Mar 202009:39:54 07 Mar 20202 minutes 57 seconds
Resolving best read alignments09:39:54 07 Mar 202009:42:01 07 Mar 20202 minutes 7 seconds
Creating BAM files09:42:01 07 Mar 202009:44:28 07 Mar 20202 minutes 27 seconds
Tabulating error counts09:44:28 07 Mar 202009:46:09 07 Mar 20201 minute 41 seconds
Re-calibrating base error rates09:46:09 07 Mar 202009:46:10 07 Mar 20201 second
Examining read alignment evidence09:46:10 07 Mar 202010:04:42 07 Mar 202018 minutes 32 seconds
Polymorphism statistics10:04:42 07 Mar 202010:04:51 07 Mar 20209 seconds
Output10:04:51 07 Mar 202010:18:15 07 Mar 202013 minutes 24 seconds
Total 1 hour 4 minutes 27 seconds