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-12PD8-7_S19_L001_R1_0011,066,394160,278,131100.0%150.3 bases151 bases99.1%
errorsqtrim-12PD8-7_S19_L001_R2_0011,066,351160,159,375100.0%150.2 bases151 bases98.3%
total2,132,745320,437,506100.0%150.2 bases151 bases98.7%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,65268.21.598.3%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≤ 100000811
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_0009130.80578

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 input06:28:50 02 Jan 201706:29:24 02 Jan 201734 seconds
Read alignment to reference genome06:29:24 02 Jan 201706:34:25 02 Jan 20175 minutes 1 second
Preprocessing alignments for candidate junction identification06:34:25 02 Jan 201706:35:24 02 Jan 201759 seconds
Preliminary analysis of coverage distribution06:35:24 02 Jan 201706:37:10 02 Jan 20171 minute 46 seconds
Identifying junction candidates06:37:10 02 Jan 201706:37:11 02 Jan 20171 second
Re-alignment to junction candidates06:37:11 02 Jan 201706:38:12 02 Jan 20171 minute 1 second
Resolving alignments with junction candidates06:38:12 02 Jan 201706:39:50 02 Jan 20171 minute 38 seconds
Creating BAM files06:39:50 02 Jan 201706:41:12 02 Jan 20171 minute 22 seconds
Tabulating error counts06:41:12 02 Jan 201706:42:40 02 Jan 20171 minute 28 seconds
Re-calibrating base error rates06:42:40 02 Jan 201706:42:41 02 Jan 20171 second
Examining read alignment evidence06:42:41 02 Jan 201706:54:01 02 Jan 201711 minutes 20 seconds
Polymorphism statistics06:54:01 02 Jan 201706:54:01 02 Jan 20170 seconds
Output06:54:01 02 Jan 201706:54:41 02 Jan 201740 seconds
Total 25 minutes 51 seconds