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-OCTA5-9_S12_L001_R2_001967,421145,392,817100.0%150.3 bases151 bases97.8%
errorsqtrim-OCTA5-9_S12_L001_R1_001967,435145,463,590100.0%150.4 bases151 bases98.8%
total1,934,856290,856,407100.0%150.3 bases151 bases98.3%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,65261.51.498.3%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≤ 1000001109
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 ≤ 500019
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_0009130.82234

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 input13:49:47 02 Jan 201713:50:24 02 Jan 201737 seconds
Read alignment to reference genome13:50:25 02 Jan 201713:56:25 02 Jan 20176 minutes 0 seconds
Preprocessing alignments for candidate junction identification13:56:25 02 Jan 201713:57:28 02 Jan 20171 minute 3 seconds
Preliminary analysis of coverage distribution13:57:28 02 Jan 201713:59:18 02 Jan 20171 minute 50 seconds
Identifying junction candidates13:59:18 02 Jan 201713:59:19 02 Jan 20171 second
Re-alignment to junction candidates13:59:19 02 Jan 201714:00:37 02 Jan 20171 minute 18 seconds
Resolving alignments with junction candidates14:00:37 02 Jan 201714:02:31 02 Jan 20171 minute 54 seconds
Creating BAM files14:02:31 02 Jan 201714:03:57 02 Jan 20171 minute 26 seconds
Tabulating error counts14:03:57 02 Jan 201714:05:47 02 Jan 20171 minute 50 seconds
Re-calibrating base error rates14:05:47 02 Jan 201714:05:48 02 Jan 20171 second
Examining read alignment evidence14:05:48 02 Jan 201714:19:46 02 Jan 201713 minutes 58 seconds
Polymorphism statistics14:19:46 02 Jan 201714:19:46 02 Jan 20170 seconds
Output14:19:46 02 Jan 201714:20:05 02 Jan 201719 seconds
Total 30 minutes 17 seconds