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-GLUT1-3_S1_L001_R1_001628,20494,531,781100.0%150.5 bases151 bases99.8%
errorsqtrim-GLUT1-3_S1_L001_R2_001628,00094,357,131100.0%150.3 bases151 bases97.5%
total1,256,204188,888,912100.0%150.4 bases151 bases98.6%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,65240.21.298.3%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≤ 100000549
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 ≤ 500021
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_0009130.88015

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 input23:27:29 02 Jan 201723:27:49 02 Jan 201720 seconds
Read alignment to reference genome23:27:49 02 Jan 201723:30:14 02 Jan 20172 minutes 25 seconds
Preprocessing alignments for candidate junction identification23:30:14 02 Jan 201723:30:45 02 Jan 201731 seconds
Preliminary analysis of coverage distribution23:30:45 02 Jan 201723:31:44 02 Jan 201759 seconds
Identifying junction candidates23:31:44 02 Jan 201723:31:44 02 Jan 20170 seconds
Re-alignment to junction candidates23:31:44 02 Jan 201723:32:17 02 Jan 201733 seconds
Resolving alignments with junction candidates23:32:17 02 Jan 201723:33:11 02 Jan 201754 seconds
Creating BAM files23:33:11 02 Jan 201723:33:51 02 Jan 201740 seconds
Tabulating error counts23:33:51 02 Jan 201723:34:41 02 Jan 201750 seconds
Re-calibrating base error rates23:34:41 02 Jan 201723:34:42 02 Jan 20171 second
Examining read alignment evidence23:34:42 02 Jan 201723:41:44 02 Jan 20177 minutes 2 seconds
Polymorphism statistics23:41:44 02 Jan 201723:41:44 02 Jan 20170 seconds
Output23:41:44 02 Jan 201723:41:56 02 Jan 201712 seconds
Total 14 minutes 27 seconds