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-HEXA4-4_S10_L001_R1_0011,253,042188,541,430100.0%150.5 bases151 bases99.7%
errorsqtrim-HEXA4-4_S10_L001_R2_0011,253,020188,300,736100.0%150.3 bases151 bases98.3%
total2,506,062376,842,166100.0%150.4 bases151 bases99.0%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,65280.83.198.2%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≤ 1000002180
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 ≤ 500025
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_0009130.77734

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 input13:32:40 02 Jan 201713:33:28 02 Jan 201748 seconds
Read alignment to reference genome13:33:29 02 Jan 201713:41:38 02 Jan 20178 minutes 9 seconds
Preprocessing alignments for candidate junction identification13:41:38 02 Jan 201713:43:07 02 Jan 20171 minute 29 seconds
Preliminary analysis of coverage distribution13:43:07 02 Jan 201713:45:52 02 Jan 20172 minutes 45 seconds
Identifying junction candidates13:45:52 02 Jan 201713:45:53 02 Jan 20171 second
Re-alignment to junction candidates13:45:53 02 Jan 201713:47:34 02 Jan 20171 minute 41 seconds
Resolving alignments with junction candidates13:47:34 02 Jan 201713:50:06 02 Jan 20172 minutes 32 seconds
Creating BAM files13:50:06 02 Jan 201713:51:56 02 Jan 20171 minute 50 seconds
Tabulating error counts13:51:56 02 Jan 201713:54:14 02 Jan 20172 minutes 18 seconds
Re-calibrating base error rates13:54:14 02 Jan 201713:54:15 02 Jan 20171 second
Examining read alignment evidence13:54:15 02 Jan 201714:11:53 02 Jan 201717 minutes 38 seconds
Polymorphism statistics14:11:53 02 Jan 201714:11:53 02 Jan 20170 seconds
Output14:11:53 02 Jan 201714:12:14 02 Jan 201721 seconds
Total 39 minutes 33 seconds