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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorspgi-13-1_S26_L001_R1_001.good.fq1,208,663320,939,305100.0%265.5 bases289 bases99.3%
errorspgi-13-1_S26_L001_R2_001.good.fq1,208,663321,730,326100.0%266.2 bases289 bases91.8%
total2,417,326642,669,631100.0%265.9 bases289 bases95.5%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652132.84.9100.0%Escherichia coli str. K-12 substr. MG1655, complete genome.
total4,641,652100.0%

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≤ 1000007322
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 ≤ 5000625
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.079

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.84113

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 input11:32:55 29 Feb 202011:33:32 29 Feb 202037 seconds
Read alignment to reference genome11:33:33 29 Feb 202011:45:24 29 Feb 202011 minutes 51 seconds
Preprocessing alignments for candidate junction identification11:45:24 29 Feb 202011:46:05 29 Feb 202041 seconds
Preliminary analysis of coverage distribution11:46:05 29 Feb 202011:48:19 29 Feb 20202 minutes 14 seconds
Identifying junction candidates11:48:19 29 Feb 202011:48:33 29 Feb 202014 seconds
Re-alignment to junction candidates11:48:33 29 Feb 202011:52:04 29 Feb 20203 minutes 31 seconds
Resolving best read alignments11:52:04 29 Feb 202011:53:12 29 Feb 20201 minute 8 seconds
Creating BAM files11:53:12 29 Feb 202011:55:08 29 Feb 20201 minute 56 seconds
Tabulating error counts11:55:08 29 Feb 202011:56:12 29 Feb 20201 minute 4 seconds
Re-calibrating base error rates11:56:12 29 Feb 202011:56:13 29 Feb 20201 second
Examining read alignment evidence11:56:13 29 Feb 202013:05:36 29 Feb 20201 hour 9 minutes 23 seconds
Polymorphism statistics13:05:36 29 Feb 202013:05:37 29 Feb 20201 second
Output13:05:37 29 Feb 202013:06:02 29 Feb 202025 seconds
Total 1 hour 33 minutes 6 seconds