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-23BD5-1_S12_L001_R1_001819,018123,015,593100.0%150.2 bases151 bases99.4%
errorsqtrim-23BD5-1_S12_L001_R2_001818,951122,966,104100.0%150.2 bases151 bases98.3%
total1,637,969245,981,697100.0%150.2 bases151 bases98.8%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,65245.01.498.4%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≤ 100000380
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 ≤ 500010
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_0009130.84703

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 input07:59:16 02 Jan 201707:59:46 02 Jan 201730 seconds
Read alignment to reference genome07:59:47 02 Jan 201708:04:38 02 Jan 20174 minutes 51 seconds
Preprocessing alignments for candidate junction identification08:04:38 02 Jan 201708:05:33 02 Jan 201755 seconds
Preliminary analysis of coverage distribution08:05:33 02 Jan 201708:06:59 02 Jan 20171 minute 26 seconds
Identifying junction candidates08:06:59 02 Jan 201708:06:59 02 Jan 20170 seconds
Re-alignment to junction candidates08:06:59 02 Jan 201708:07:53 02 Jan 201754 seconds
Resolving alignments with junction candidates08:07:53 02 Jan 201708:09:27 02 Jan 20171 minute 34 seconds
Creating BAM files08:09:27 02 Jan 201708:10:37 02 Jan 20171 minute 10 seconds
Tabulating error counts08:10:37 02 Jan 201708:11:52 02 Jan 20171 minute 15 seconds
Re-calibrating base error rates08:11:52 02 Jan 201708:11:53 02 Jan 20171 second
Examining read alignment evidence08:11:53 02 Jan 201708:22:21 02 Jan 201710 minutes 28 seconds
Polymorphism statistics08:22:21 02 Jan 201708:22:21 02 Jan 20170 seconds
Output08:22:21 02 Jan 201708:22:36 02 Jan 201715 seconds
Total 23 minutes 19 seconds