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-GLUT4-10_S12_L001_R2_001714,827107,403,675100.0%150.3 bases151 bases97.8%
errorsqtrim-GLUT4-10_S12_L001_R1_001715,156107,615,880100.0%150.5 bases151 bases99.8%
total1,429,983215,019,555100.0%150.4 bases151 bases98.8%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,65245.81.298.3%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≤ 100000846
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_0009130.86400

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 input14:10:15 02 Jan 201714:10:47 02 Jan 201732 seconds
Read alignment to reference genome14:10:47 02 Jan 201714:15:27 02 Jan 20174 minutes 40 seconds
Preprocessing alignments for candidate junction identification14:15:27 02 Jan 201714:16:20 02 Jan 201753 seconds
Preliminary analysis of coverage distribution14:16:20 02 Jan 201714:17:44 02 Jan 20171 minute 24 seconds
Identifying junction candidates14:17:44 02 Jan 201714:17:44 02 Jan 20170 seconds
Re-alignment to junction candidates14:17:44 02 Jan 201714:18:42 02 Jan 201758 seconds
Resolving alignments with junction candidates14:18:42 02 Jan 201714:20:09 02 Jan 20171 minute 27 seconds
Creating BAM files14:20:09 02 Jan 201714:21:18 02 Jan 20171 minute 9 seconds
Tabulating error counts14:21:18 02 Jan 201714:22:38 02 Jan 20171 minute 20 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 201714:33:12 02 Jan 201710 minutes 33 seconds
Polymorphism statistics14:33:12 02 Jan 201714:33:12 02 Jan 20170 seconds
Output14:33:12 02 Jan 201714:33:28 02 Jan 201716 seconds
Total 23 minutes 13 seconds