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-12PD1-2_S1_L001_R1_0011,473,866221,640,369100.0%150.4 bases151 bases98.4%
errorsqtrim-12PD1-2_S1_L001_R2_0011,473,756221,511,353100.0%150.3 bases151 bases97.8%
total2,947,622443,151,722100.0%150.3 bases151 bases98.1%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,65293.71.598.3%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≤ 100000765
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 ≤ 500012
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_0009130.74665

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 input08:30:05 02 Jan 201708:30:58 02 Jan 201753 seconds
Read alignment to reference genome08:30:59 02 Jan 201708:39:21 02 Jan 20178 minutes 22 seconds
Preprocessing alignments for candidate junction identification08:39:21 02 Jan 201708:40:55 02 Jan 20171 minute 34 seconds
Preliminary analysis of coverage distribution08:40:55 02 Jan 201708:43:44 02 Jan 20172 minutes 49 seconds
Identifying junction candidates08:43:44 02 Jan 201708:43:45 02 Jan 20171 second
Re-alignment to junction candidates08:43:45 02 Jan 201708:45:27 02 Jan 20171 minute 42 seconds
Resolving alignments with junction candidates08:45:27 02 Jan 201708:48:10 02 Jan 20172 minutes 43 seconds
Creating BAM files08:48:10 02 Jan 201708:50:06 02 Jan 20171 minute 56 seconds
Tabulating error counts08:50:06 02 Jan 201708:52:29 02 Jan 20172 minutes 23 seconds
Re-calibrating base error rates08:52:29 02 Jan 201708:52:30 02 Jan 20171 second
Examining read alignment evidence08:52:30 02 Jan 201709:10:38 02 Jan 201718 minutes 8 seconds
Polymorphism statistics09:10:38 02 Jan 201709:10:40 02 Jan 20172 seconds
Output09:10:40 02 Jan 201709:11:42 02 Jan 20171 minute 2 seconds
Total 41 minutes 36 seconds