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-BUT3-3_S5_L001_R1_001985,345148,298,327100.0%150.5 bases151 bases99.4%
errorsqtrim-BUT3-3_S5_L001_R2_001985,228148,199,673100.0%150.4 bases151 bases98.3%
total1,970,573296,498,000100.0%150.5 bases151 bases98.9%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,65263.11.298.3%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≤ 1000001105
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 ≤ 500022
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.001

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.81802

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 input15:38:24 02 Jan 201715:39:07 02 Jan 201743 seconds
Read alignment to reference genome15:39:08 02 Jan 201715:45:01 02 Jan 20175 minutes 53 seconds
Preprocessing alignments for candidate junction identification15:45:01 02 Jan 201715:46:03 02 Jan 20171 minute 2 seconds
Preliminary analysis of coverage distribution15:46:03 02 Jan 201715:47:44 02 Jan 20171 minute 41 seconds
Identifying junction candidates15:47:44 02 Jan 201715:47:44 02 Jan 20170 seconds
Re-alignment to junction candidates15:47:44 02 Jan 201715:48:49 02 Jan 20171 minute 5 seconds
Resolving alignments with junction candidates15:48:49 02 Jan 201715:50:38 02 Jan 20171 minute 49 seconds
Creating BAM files15:50:38 02 Jan 201715:51:54 02 Jan 20171 minute 16 seconds
Tabulating error counts15:51:54 02 Jan 201715:53:25 02 Jan 20171 minute 31 seconds
Re-calibrating base error rates15:53:25 02 Jan 201715:53:26 02 Jan 20171 second
Examining read alignment evidence15:53:26 02 Jan 201716:05:56 02 Jan 201712 minutes 30 seconds
Polymorphism statistics16:05:56 02 Jan 201716:05:57 02 Jan 20171 second
Output16:05:57 02 Jan 201716:06:16 02 Jan 201719 seconds
Total 27 minutes 51 seconds