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-COUM2-7_S4_L001_R1_001861,314129,502,194100.0%150.4 bases151 bases99.8%
errorsqtrim-COUM2-7_S4_L001_R2_001861,047129,222,697100.0%150.1 bases151 bases97.5%
total1,722,361258,724,891100.0%150.2 bases151 bases98.6%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,65255.01.398.3%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≤ 1000001152
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_0009130.83967

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 input17:36:36 03 Jan 201717:37:14 03 Jan 201738 seconds
Read alignment to reference genome17:37:15 03 Jan 201717:43:00 03 Jan 20175 minutes 45 seconds
Preprocessing alignments for candidate junction identification17:43:00 03 Jan 201717:44:00 03 Jan 20171 minute 0 seconds
Preliminary analysis of coverage distribution17:44:00 03 Jan 201717:45:37 03 Jan 20171 minute 37 seconds
Identifying junction candidates17:45:37 03 Jan 201717:45:38 03 Jan 20171 second
Re-alignment to junction candidates17:45:38 03 Jan 201717:46:52 03 Jan 20171 minute 14 seconds
Resolving alignments with junction candidates17:46:52 03 Jan 201717:48:35 03 Jan 20171 minute 43 seconds
Creating BAM files17:48:35 03 Jan 201717:50:00 03 Jan 20171 minute 25 seconds
Tabulating error counts17:50:00 03 Jan 201717:51:32 03 Jan 20171 minute 32 seconds
Re-calibrating base error rates17:51:32 03 Jan 201717:51:33 03 Jan 20171 second
Examining read alignment evidence17:51:33 03 Jan 201707:55:31 04 Jan 201714 hours 3 minutes 58 seconds
Polymorphism statistics07:55:31 04 Jan 201707:55:31 04 Jan 20170 seconds
Output07:55:31 04 Jan 201707:55:46 04 Jan 201715 seconds
Total 14 hours 19 minutes 9 seconds