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-OCTA4-10_S8_L001_R2_0011,023,108153,414,930100.0%149.9 bases151 bases96.4%
errorsqtrim-OCTA4-10_S8_L001_R1_0011,023,173153,530,473100.0%150.1 bases151 bases97.2%
total2,046,281306,945,403100.0%150.0 bases151 bases96.8%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,65263.61.998.3%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≤ 1000001487
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 ≤ 500052
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.003

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.81728

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 input06:56:28 02 Jan 201706:56:59 02 Jan 201731 seconds
Read alignment to reference genome06:56:59 02 Jan 201707:01:37 02 Jan 20174 minutes 38 seconds
Preprocessing alignments for candidate junction identification07:01:37 02 Jan 201707:02:33 02 Jan 201756 seconds
Preliminary analysis of coverage distribution07:02:33 02 Jan 201707:04:09 02 Jan 20171 minute 36 seconds
Identifying junction candidates07:04:09 02 Jan 201707:04:10 02 Jan 20171 second
Re-alignment to junction candidates07:04:10 02 Jan 201707:05:08 02 Jan 201758 seconds
Resolving alignments with junction candidates07:05:08 02 Jan 201707:06:41 02 Jan 20171 minute 33 seconds
Creating BAM files07:06:41 02 Jan 201707:07:56 02 Jan 20171 minute 15 seconds
Tabulating error counts07:07:56 02 Jan 201707:09:19 02 Jan 20171 minute 23 seconds
Re-calibrating base error rates07:09:19 02 Jan 201707:09:20 02 Jan 20171 second
Examining read alignment evidence07:09:20 02 Jan 201707:20:16 02 Jan 201710 minutes 56 seconds
Polymorphism statistics07:20:16 02 Jan 201707:20:17 02 Jan 20171 second
Output07:20:17 02 Jan 201707:20:29 02 Jan 201712 seconds
Total 24 minutes 1 second