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-OCTA4-9_S7_L001_R2_001884,211132,573,765100.0%149.9 bases151 bases97.4%
errorsqtrim-OCTA4-9_S7_L001_R1_001884,329132,667,127100.0%150.0 bases151 bases98.1%
total1,768,540265,240,892100.0%150.0 bases151 bases97.7%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,65255.41.898.3%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≤ 1000001161
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 ≤ 500044
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.003

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.83770

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 input07:20:30 02 Jan 201707:20:57 02 Jan 201727 seconds
Read alignment to reference genome07:20:58 02 Jan 201707:25:03 02 Jan 20174 minutes 5 seconds
Preprocessing alignments for candidate junction identification07:25:03 02 Jan 201707:25:50 02 Jan 201747 seconds
Preliminary analysis of coverage distribution07:25:50 02 Jan 201707:27:16 02 Jan 20171 minute 26 seconds
Identifying junction candidates07:27:16 02 Jan 201707:27:16 02 Jan 20170 seconds
Re-alignment to junction candidates07:27:16 02 Jan 201707:28:11 02 Jan 201755 seconds
Resolving alignments with junction candidates07:28:11 02 Jan 201707:29:33 02 Jan 20171 minute 22 seconds
Creating BAM files07:29:33 02 Jan 201707:30:40 02 Jan 20171 minute 7 seconds
Tabulating error counts07:30:40 02 Jan 201707:31:53 02 Jan 20171 minute 13 seconds
Re-calibrating base error rates07:31:53 02 Jan 201707:31:54 02 Jan 20171 second
Examining read alignment evidence07:31:54 02 Jan 201707:41:27 02 Jan 20179 minutes 33 seconds
Polymorphism statistics07:41:27 02 Jan 201707:41:27 02 Jan 20170 seconds
Output07:41:27 02 Jan 201707:41:41 02 Jan 201714 seconds
Total 21 minutes 10 seconds