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-GLUT1-10_S3_L001_R1_001714,655107,540,823100.0%150.5 bases151 bases99.6%
errorsqtrim-GLUT1-10_S3_L001_R2_001714,442107,407,696100.0%150.3 bases151 bases98.5%
total1,429,097214,948,519100.0%150.4 bases151 bases99.0%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,65245.91.298.3%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≤ 1000001027
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 ≤ 500027
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.002

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.86378

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 input15:04:44 02 Jan 201715:05:10 02 Jan 201726 seconds
Read alignment to reference genome15:05:11 02 Jan 201715:09:23 02 Jan 20174 minutes 12 seconds
Preprocessing alignments for candidate junction identification15:09:23 02 Jan 201715:10:09 02 Jan 201746 seconds
Preliminary analysis of coverage distribution15:10:09 02 Jan 201715:11:27 02 Jan 20171 minute 18 seconds
Identifying junction candidates15:11:27 02 Jan 201715:11:28 02 Jan 20171 second
Re-alignment to junction candidates15:11:28 02 Jan 201715:12:20 02 Jan 201752 seconds
Resolving alignments with junction candidates15:12:20 02 Jan 201715:13:34 02 Jan 20171 minute 14 seconds
Creating BAM files15:13:34 02 Jan 201715:14:34 02 Jan 20171 minute 0 seconds
Tabulating error counts15:14:34 02 Jan 201715:15:42 02 Jan 20171 minute 8 seconds
Re-calibrating base error rates15:15:42 02 Jan 201715:15:43 02 Jan 20171 second
Examining read alignment evidence15:15:43 02 Jan 201715:25:22 02 Jan 20179 minutes 39 seconds
Polymorphism statistics15:25:22 02 Jan 201715:25:23 02 Jan 20171 second
Output15:25:23 02 Jan 201715:25:41 02 Jan 201718 seconds
Total 20 minutes 56 seconds