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-12PD3-7_S5_L001_R2_0011,740,934261,509,011100.0%150.2 bases151 bases97.3%
errorsqtrim-12PD3-7_S5_L001_R1_0011,741,104261,863,072100.0%150.4 bases151 bases98.7%
errorsqtrim-12PD3-7_S6_L001_R1_001597,67389,216,135100.0%149.3 bases151 bases81.2%
errorsqtrim-12PD3-7_S6_L001_R2_001597,65189,072,430100.0%149.0 bases151 bases80.6%
total4,677,362701,660,648100.0%150.0 bases151 bases93.6%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652141.81.798.3%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≤ 1000001218
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 ≤ 500018
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_0009130.65020

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 input07:14:32 02 Jan 201707:15:42 02 Jan 20171 minute 10 seconds
Read alignment to reference genome07:15:43 02 Jan 201707:25:54 02 Jan 201710 minutes 11 seconds
Preprocessing alignments for candidate junction identification07:25:54 02 Jan 201707:27:53 02 Jan 20171 minute 59 seconds
Preliminary analysis of coverage distribution07:27:53 02 Jan 201707:31:52 02 Jan 20173 minutes 59 seconds
Identifying junction candidates07:31:52 02 Jan 201707:31:52 02 Jan 20170 seconds
Re-alignment to junction candidates07:31:52 02 Jan 201707:34:17 02 Jan 20172 minutes 25 seconds
Resolving alignments with junction candidates07:34:17 02 Jan 201707:37:52 02 Jan 20173 minutes 35 seconds
Creating BAM files07:37:52 02 Jan 201707:40:40 02 Jan 20172 minutes 48 seconds
Tabulating error counts07:40:40 02 Jan 201707:43:55 02 Jan 20173 minutes 15 seconds
Re-calibrating base error rates07:43:55 02 Jan 201707:43:56 02 Jan 20171 second
Examining read alignment evidence07:43:56 02 Jan 201708:10:11 02 Jan 201726 minutes 15 seconds
Polymorphism statistics08:10:11 02 Jan 201708:10:13 02 Jan 20172 seconds
Output08:10:13 02 Jan 201708:11:08 02 Jan 201755 seconds
Total 56 minutes 35 seconds