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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsSSW-KHP-SSW-4-165-2-1_S19_L001_R2_001298,38489,599,43599.9%300.3 bases301 bases79.3%
errorsSSW-KHP-SSW-4-165-2-1_S19_L001_R1_001298,76489,799,358100.0%300.6 bases301 bases82.0%
total597,148179,398,79399.9%300.4 bases301 bases80.7%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,65231.01.8100.0%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≤ 1000002812
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 ≤ 5000256
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.033

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.95869

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 input17:58:41 05 Mar 201617:59:01 05 Mar 201620 seconds
Read alignment to reference genome17:59:01 05 Mar 201618:00:39 05 Mar 20161 minute 38 seconds
Preprocessing alignments for candidate junction identification18:00:39 05 Mar 201618:00:57 05 Mar 201618 seconds
Preliminary analysis of coverage distribution18:00:57 05 Mar 201618:01:41 05 Mar 201644 seconds
Identifying junction candidates18:01:41 05 Mar 201618:01:41 05 Mar 20160 seconds
Re-alignment to junction candidates18:01:41 05 Mar 201618:01:52 05 Mar 201611 seconds
Resolving alignments with junction candidates18:01:52 05 Mar 201618:02:30 05 Mar 201638 seconds
Creating BAM files18:02:30 05 Mar 201618:02:54 05 Mar 201624 seconds
Tabulating error counts18:02:54 05 Mar 201618:03:42 05 Mar 201648 seconds
Re-calibrating base error rates18:03:42 05 Mar 201618:03:43 05 Mar 20161 second
Examining read alignment evidence18:03:43 05 Mar 201618:10:31 05 Mar 20166 minutes 48 seconds
Polymorphism statistics18:10:31 05 Mar 201618:10:31 05 Mar 20160 seconds
Output18:10:31 05 Mar 201618:10:52 05 Mar 201621 seconds
Total 12 minutes 11 seconds