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-COUM8-6_S20_L001_R2_001397,34459,614,297100.0%150.0 bases151 bases95.7%
errorsqtrim-COUM8-6_S20_L001_R1_001397,49159,795,741100.0%150.4 bases151 bases99.5%
total794,835119,410,038100.0%150.2 bases151 bases97.6%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,65225.21.298.3%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≤ 100000162
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 ≤ 500013
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_0009130.92250

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 input10:06:40 03 Jan 201710:06:53 03 Jan 201713 seconds
Read alignment to reference genome10:06:54 03 Jan 201710:08:30 03 Jan 20171 minute 36 seconds
Preprocessing alignments for candidate junction identification10:08:30 03 Jan 201710:08:49 03 Jan 201719 seconds
Preliminary analysis of coverage distribution10:08:49 03 Jan 201710:09:29 03 Jan 201740 seconds
Identifying junction candidates10:09:29 03 Jan 201710:09:29 03 Jan 20170 seconds
Re-alignment to junction candidates10:09:29 03 Jan 201710:09:49 03 Jan 201720 seconds
Resolving alignments with junction candidates10:09:49 03 Jan 201710:10:23 03 Jan 201734 seconds
Creating BAM files10:10:23 03 Jan 201710:10:48 03 Jan 201725 seconds
Tabulating error counts10:10:48 03 Jan 201710:11:20 03 Jan 201732 seconds
Re-calibrating base error rates10:11:20 03 Jan 201710:11:20 03 Jan 20170 seconds
Examining read alignment evidence10:11:20 03 Jan 201710:16:19 03 Jan 20174 minutes 59 seconds
Polymorphism statistics10:16:19 03 Jan 201710:16:19 03 Jan 20170 seconds
Output10:16:19 03 Jan 201710:16:32 03 Jan 201713 seconds
Total 9 minutes 51 seconds