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-OCTA2-14_S5_L001_R2_001718,731107,832,086100.0%150.0 bases151 bases93.4%
errorsqtrim-OCTA2-14_S5_L001_R1_001718,818108,003,078100.0%150.3 bases151 bases94.7%
total1,437,549215,835,164100.0%150.1 bases151 bases94.1%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,65243.81.598.3%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≤ 100000791
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_0009130.86978

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 input10:55:50 02 Jan 201710:56:17 02 Jan 201727 seconds
Read alignment to reference genome10:56:17 02 Jan 201711:00:40 02 Jan 20174 minutes 23 seconds
Preprocessing alignments for candidate junction identification11:00:40 02 Jan 201711:01:22 02 Jan 201742 seconds
Preliminary analysis of coverage distribution11:01:22 02 Jan 201711:02:36 02 Jan 20171 minute 14 seconds
Identifying junction candidates11:02:36 02 Jan 201711:02:36 02 Jan 20170 seconds
Re-alignment to junction candidates11:02:36 02 Jan 201711:03:26 02 Jan 201750 seconds
Resolving alignments with junction candidates11:03:26 02 Jan 201711:04:39 02 Jan 20171 minute 13 seconds
Creating BAM files11:04:39 02 Jan 201711:05:36 02 Jan 201757 seconds
Tabulating error counts11:05:36 02 Jan 201711:06:43 02 Jan 20171 minute 7 seconds
Re-calibrating base error rates11:06:43 02 Jan 201711:06:44 02 Jan 20171 second
Examining read alignment evidence11:06:44 02 Jan 201711:15:53 02 Jan 20179 minutes 9 seconds
Polymorphism statistics11:15:53 02 Jan 201711:15:54 02 Jan 20171 second
Output11:15:54 02 Jan 201711:16:11 02 Jan 201717 seconds
Total 20 minutes 21 seconds