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-OCTA2-10_S4_L001_R2_0011,255,153188,601,373100.0%150.3 bases151 bases97.4%
errorsqtrim-OCTA2-10_S4_L001_R1_0011,255,279188,705,818100.0%150.3 bases151 bases98.0%
total2,510,432377,307,191100.0%150.3 bases151 bases97.7%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,65279.41.698.3%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≤ 1000001337
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 ≤ 500022
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_0009130.77967

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 input08:42:55 02 Jan 201708:43:44 02 Jan 201749 seconds
Read alignment to reference genome08:43:45 02 Jan 201708:50:57 02 Jan 20177 minutes 12 seconds
Preprocessing alignments for candidate junction identification08:50:57 02 Jan 201708:52:21 02 Jan 20171 minute 24 seconds
Preliminary analysis of coverage distribution08:52:21 02 Jan 201708:54:41 02 Jan 20172 minutes 20 seconds
Identifying junction candidates08:54:41 02 Jan 201708:54:42 02 Jan 20171 second
Re-alignment to junction candidates08:54:42 02 Jan 201708:56:10 02 Jan 20171 minute 28 seconds
Resolving alignments with junction candidates08:56:10 02 Jan 201708:58:26 02 Jan 20172 minutes 16 seconds
Creating BAM files08:58:26 02 Jan 201709:00:06 02 Jan 20171 minute 40 seconds
Tabulating error counts09:00:06 02 Jan 201709:02:04 02 Jan 20171 minute 58 seconds
Re-calibrating base error rates09:02:04 02 Jan 201709:02:05 02 Jan 20171 second
Examining read alignment evidence09:02:05 02 Jan 201709:18:58 02 Jan 201716 minutes 53 seconds
Polymorphism statistics09:18:58 02 Jan 201709:18:59 02 Jan 20171 second
Output09:18:59 02 Jan 201709:19:23 02 Jan 201724 seconds
Total 36 minutes 27 seconds