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-BUT9-7_S19_L001_R1_0011,001,187150,682,643100.0%150.5 bases151 bases99.7%
errorsqtrim-BUT9-7_S19_L001_R2_0011,001,056150,592,913100.0%150.4 bases151 bases99.1%
total2,002,243301,275,556100.0%150.5 bases151 bases99.4%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,65264.61.298.3%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≤ 100000343
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_0009130.81452

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 input08:09:01 02 Jan 201708:09:37 02 Jan 201736 seconds
Read alignment to reference genome08:09:38 02 Jan 201708:15:06 02 Jan 20175 minutes 28 seconds
Preprocessing alignments for candidate junction identification08:15:06 02 Jan 201708:16:06 02 Jan 20171 minute 0 seconds
Preliminary analysis of coverage distribution08:16:06 02 Jan 201708:17:51 02 Jan 20171 minute 45 seconds
Identifying junction candidates08:17:51 02 Jan 201708:17:51 02 Jan 20170 seconds
Re-alignment to junction candidates08:17:51 02 Jan 201708:19:08 02 Jan 20171 minute 17 seconds
Resolving alignments with junction candidates08:19:08 02 Jan 201708:20:56 02 Jan 20171 minute 48 seconds
Creating BAM files08:20:56 02 Jan 201708:22:16 02 Jan 20171 minute 20 seconds
Tabulating error counts08:22:16 02 Jan 201708:23:50 02 Jan 20171 minute 34 seconds
Re-calibrating base error rates08:23:50 02 Jan 201708:23:51 02 Jan 20171 second
Examining read alignment evidence08:23:51 02 Jan 201708:36:01 02 Jan 201712 minutes 10 seconds
Polymorphism statistics08:36:01 02 Jan 201708:36:01 02 Jan 20170 seconds
Output08:36:01 02 Jan 201708:36:23 02 Jan 201722 seconds
Total 27 minutes 21 seconds