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-OCTA1-5_S2_L001_R2_001801,529120,334,209100.0%150.1 bases151 bases96.0%
errorsqtrim-OCTA1-5_S2_L001_R1_001801,465120,478,752100.0%150.3 bases151 bases97.1%
total1,602,994240,812,961100.0%150.2 bases151 bases96.6%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,65250.11.598.2%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≤ 100000864
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 ≤ 500013
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_0009130.85259

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 input08:20:37 02 Jan 201708:21:06 02 Jan 201729 seconds
Read alignment to reference genome08:21:07 02 Jan 201708:25:36 02 Jan 20174 minutes 29 seconds
Preprocessing alignments for candidate junction identification08:25:36 02 Jan 201708:26:22 02 Jan 201746 seconds
Preliminary analysis of coverage distribution08:26:22 02 Jan 201708:27:47 02 Jan 20171 minute 25 seconds
Identifying junction candidates08:27:47 02 Jan 201708:27:48 02 Jan 20171 second
Re-alignment to junction candidates08:27:48 02 Jan 201708:28:45 02 Jan 201757 seconds
Resolving alignments with junction candidates08:28:45 02 Jan 201708:30:05 02 Jan 20171 minute 20 seconds
Creating BAM files08:30:05 02 Jan 201708:31:11 02 Jan 20171 minute 6 seconds
Tabulating error counts08:31:11 02 Jan 201708:32:23 02 Jan 20171 minute 12 seconds
Re-calibrating base error rates08:32:23 02 Jan 201708:32:24 02 Jan 20171 second
Examining read alignment evidence08:32:24 02 Jan 201708:42:38 02 Jan 201710 minutes 14 seconds
Polymorphism statistics08:42:38 02 Jan 201708:42:38 02 Jan 20170 seconds
Output08:42:38 02 Jan 201708:42:55 02 Jan 201717 seconds
Total 22 minutes 17 seconds