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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorspgi-KO_S9_L001_R2_001948,660201,880,906100.0%212.8 bases218 bases98.5%
errorspgi-KO_S9_L001_R1_001948,702272,834,228100.0%287.6 bases301 bases99.0%
total1,897,362474,715,134100.0%250.2 bases301 bases98.8%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652108.73.1100.0%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≤ 1000001833
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 ≤ 500091
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.012

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.87316

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 input23:30:10 17 Jun 201623:30:50 17 Jun 201640 seconds
Read alignment to reference genome23:30:50 17 Jun 201623:33:34 17 Jun 20162 minutes 44 seconds
Preprocessing alignments for candidate junction identification23:33:34 17 Jun 201623:34:25 17 Jun 201651 seconds
Preliminary analysis of coverage distribution23:34:25 17 Jun 201623:37:06 17 Jun 20162 minutes 41 seconds
Identifying junction candidates23:37:06 17 Jun 201623:37:06 17 Jun 20160 seconds
Re-alignment to junction candidates23:37:06 17 Jun 201623:37:30 17 Jun 201624 seconds
Resolving alignments with junction candidates23:37:30 17 Jun 201623:39:33 17 Jun 20162 minutes 3 seconds
Creating BAM files23:39:33 17 Jun 201623:41:10 17 Jun 20161 minute 37 seconds
Tabulating error counts23:41:10 17 Jun 201623:43:45 17 Jun 20162 minutes 35 seconds
Re-calibrating base error rates23:43:45 17 Jun 201623:43:46 17 Jun 20161 second
Examining read alignment evidence23:43:46 17 Jun 201600:02:28 18 Jun 201618 minutes 42 seconds
Polymorphism statistics00:02:28 18 Jun 201600:02:28 18 Jun 20160 seconds
Output00:02:28 18 Jun 201600:03:20 18 Jun 201652 seconds
Total 33 minutes 10 seconds