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-12PD6-9_S15_L001_R2_0014,108,121601,204,806100.0%146.3 bases151 bases13.7%
errorsqtrim-12PD6-9_S15_L001_R1_0014,108,310604,295,791100.0%147.1 bases151 bases12.9%
total8,216,4311,205,500,597100.0%146.7 bases151 bases13.3%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,65237.11.898.2%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≤ 100000631
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 ≤ 500051
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_0009130.89531

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 input13:46:50 02 Jan 201713:49:53 02 Jan 20173 minutes 3 seconds
Read alignment to reference genome13:49:54 02 Jan 201714:10:42 02 Jan 201720 minutes 48 seconds
Preprocessing alignments for candidate junction identification14:10:42 02 Jan 201714:11:35 02 Jan 201753 seconds
Preliminary analysis of coverage distribution14:11:35 02 Jan 201714:12:43 02 Jan 20171 minute 8 seconds
Identifying junction candidates14:12:43 02 Jan 201714:12:44 02 Jan 20171 second
Re-alignment to junction candidates14:12:44 02 Jan 201714:18:06 02 Jan 20175 minutes 22 seconds
Resolving alignments with junction candidates14:18:06 02 Jan 201714:20:54 02 Jan 20172 minutes 48 seconds
Creating BAM files14:20:54 02 Jan 201714:21:38 02 Jan 201744 seconds
Tabulating error counts14:21:38 02 Jan 201714:22:38 02 Jan 20171 minute 0 seconds
Re-calibrating base error rates14:22:38 02 Jan 201714:22:39 02 Jan 20171 second
Examining read alignment evidence14:22:39 02 Jan 201714:31:39 02 Jan 20179 minutes 0 seconds
Polymorphism statistics14:31:39 02 Jan 201714:31:40 02 Jan 20171 second
Output14:31:40 02 Jan 201714:32:04 02 Jan 201724 seconds
Total 45 minutes 13 seconds