breseq  version 0.29.0  revision 8f9c342918e4
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsqtrim-COUM3-9_S6_L001_R1_001957,634144,048,878100.0%150.4 bases151 bases99.8%
errorsqtrim-COUM3-9_S6_L001_R2_001957,326143,765,479100.0%150.2 bases151 bases97.8%
total1,914,960287,814,357100.0%150.3 bases151 bases98.8%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,65261.31.398.3%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≤ 1000001314
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 ≤ 500024
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.002

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.82375

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 cutoff0.8
Consensus minimum coverage each strandOFF
Polymorphism E-value cutoff10
Polymorphism frequency cutoff0.2
Polymorphism minimum coverage each strandOFF
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

Execution Times

stepstartendelapsed
Read and reference sequence file input09:17:42 03 Jan 201709:18:10 03 Jan 201728 seconds
Read alignment to reference genome09:18:11 03 Jan 201709:21:55 03 Jan 20173 minutes 44 seconds
Preprocessing alignments for candidate junction identification09:21:55 03 Jan 201709:22:45 03 Jan 201750 seconds
Preliminary analysis of coverage distribution09:22:45 03 Jan 201709:24:14 03 Jan 20171 minute 29 seconds
Identifying junction candidates09:24:14 03 Jan 201709:24:14 03 Jan 20170 seconds
Re-alignment to junction candidates09:24:14 03 Jan 201709:25:06 03 Jan 201752 seconds
Resolving alignments with junction candidates09:25:06 03 Jan 201709:26:29 03 Jan 20171 minute 23 seconds
Creating BAM files09:26:29 03 Jan 201709:27:40 03 Jan 20171 minute 11 seconds
Tabulating error counts09:27:40 03 Jan 201709:28:56 03 Jan 20171 minute 16 seconds
Re-calibrating base error rates09:28:56 03 Jan 201709:28:57 03 Jan 20171 second
Examining read alignment evidence09:28:57 03 Jan 201709:38:53 03 Jan 20179 minutes 56 seconds
Polymorphism statistics09:38:53 03 Jan 201709:38:54 03 Jan 20171 second
Output09:38:54 03 Jan 201709:39:10 03 Jan 201716 seconds
Total 21 minutes 27 seconds