breseq  version 0.27.1  revision 87c22d663cc3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errors9_S9_L001_R2_001472,65070,702,927100.0%149.6 bases151 bases98.2%
errors9_S9_L001_R1_001472,66170,704,935100.0%149.6 bases151 bases99.6%
total945,311141,407,862100.0%149.6 bases151 bases98.9%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,65227.73.0100.0%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≤ 1000005681
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 ≤ 5000216
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.014

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.92647

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 input02:11:27 21 Feb 201602:11:42 21 Feb 201615 seconds
Read alignment to reference genome02:11:42 21 Feb 201602:12:16 21 Feb 201634 seconds
Preprocessing alignments for candidate junction identification02:12:16 21 Feb 201602:12:36 21 Feb 201620 seconds
Preliminary analysis of coverage distribution02:12:36 21 Feb 201602:13:25 21 Feb 201649 seconds
Identifying junction candidates02:13:25 21 Feb 201602:13:26 21 Feb 20161 second
Re-alignment to junction candidates02:13:26 21 Feb 201602:13:34 21 Feb 20168 seconds
Resolving alignments with junction candidates02:13:34 21 Feb 201602:14:15 21 Feb 201641 seconds
Creating BAM files02:14:15 21 Feb 201602:14:45 21 Feb 201630 seconds
Tabulating error counts02:14:45 21 Feb 201602:15:31 21 Feb 201646 seconds
Re-calibrating base error rates02:15:31 21 Feb 201602:15:32 21 Feb 20161 second
Examining read alignment evidence02:15:32 21 Feb 201602:21:38 21 Feb 20166 minutes 6 seconds
Polymorphism statistics02:21:38 21 Feb 201602:21:38 21 Feb 20160 seconds
Output02:21:38 21 Feb 201602:22:12 21 Feb 201634 seconds
Total 10 minutes 45 seconds