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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsSRR3190692_S1_L001_R1_001.good.fq8,348,2912,481,670,054100.0%297.3 bases298 bases99.2%
errorsSRR3190692_S1_L001_R2_001.good.fq8,348,2912,482,342,552100.0%297.3 bases298 bases97.0%
total16,696,5824,964,012,606100.0%297.3 bases298 bases98.1%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0104684,746,2181096.5279.9100.0%Escherichia coli ATCC 8739, complete genome.
total4,746,218100.0%

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≤ 1000006198
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 ≤ 5000276
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.036

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0104680.30335

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
bowtie22.3.4.1
R3.4.4

Execution Times

stepstartendelapsed
Read and reference sequence file input17:49:45 25 Feb 202017:54:27 25 Feb 20204 minutes 42 seconds
Read alignment to reference genome17:54:28 25 Feb 202019:14:06 25 Feb 20201 hour 19 minutes 38 seconds
Preprocessing alignments for candidate junction identification19:14:06 25 Feb 202019:19:34 25 Feb 20205 minutes 28 seconds
Preliminary analysis of coverage distribution19:19:34 25 Feb 202019:32:58 25 Feb 202013 minutes 24 seconds
Identifying junction candidates19:32:58 25 Feb 202019:33:14 25 Feb 202016 seconds
Re-alignment to junction candidates19:33:14 25 Feb 202019:59:09 25 Feb 202025 minutes 55 seconds
Resolving best read alignments19:59:09 25 Feb 202020:07:48 25 Feb 20208 minutes 39 seconds
Creating BAM files20:07:48 25 Feb 202020:19:00 25 Feb 202011 minutes 12 seconds
Tabulating error counts20:19:00 25 Feb 202020:28:24 25 Feb 20209 minutes 24 seconds
Re-calibrating base error rates20:28:24 25 Feb 202020:28:25 25 Feb 20201 second
Examining read alignment evidence20:28:25 25 Feb 202021:48:54 25 Feb 20201 hour 20 minutes 29 seconds
Polymorphism statistics21:48:54 25 Feb 202021:48:55 25 Feb 20201 second
Output21:48:55 25 Feb 202021:50:24 25 Feb 20201 minute 29 seconds
Total 4 hours 38 seconds