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-12PD8-6_S18_L001_R1_001767,401115,198,108100.0%150.1 bases151 bases99.1%
errorsqtrim-12PD8-6_S18_L001_R2_001767,354115,080,014100.0%150.0 bases151 bases98.2%
total1,534,755230,278,122100.0%150.0 bases151 bases98.6%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,65255.03.198.1%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≤ 100000912
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 ≤ 500018
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_0009130.85649

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 input06:54:41 02 Jan 201706:55:06 02 Jan 201725 seconds
Read alignment to reference genome06:55:06 02 Jan 201706:58:30 02 Jan 20173 minutes 24 seconds
Preprocessing alignments for candidate junction identification06:58:30 02 Jan 201706:59:13 02 Jan 201743 seconds
Preliminary analysis of coverage distribution06:59:13 02 Jan 201707:00:29 02 Jan 20171 minute 16 seconds
Identifying junction candidates07:00:29 02 Jan 201707:00:30 02 Jan 20171 second
Re-alignment to junction candidates07:00:30 02 Jan 201707:01:17 02 Jan 201747 seconds
Resolving alignments with junction candidates07:01:17 02 Jan 201707:02:32 02 Jan 20171 minute 15 seconds
Creating BAM files07:02:32 02 Jan 201707:03:32 02 Jan 20171 minute 0 seconds
Tabulating error counts07:03:32 02 Jan 201707:04:36 02 Jan 20171 minute 4 seconds
Re-calibrating base error rates07:04:36 02 Jan 201707:04:37 02 Jan 20171 second
Examining read alignment evidence07:04:37 02 Jan 201707:13:19 02 Jan 20178 minutes 42 seconds
Polymorphism statistics07:13:19 02 Jan 201707:13:20 02 Jan 20171 second
Output07:13:20 02 Jan 201707:14:31 02 Jan 20171 minute 11 seconds
Total 19 minutes 50 seconds