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-OCTA7-2_S16_L001_R1_0011,047,917157,579,714100.0%150.4 bases151 bases98.3%
errorsqtrim-OCTA7-2_S16_L001_R2_0011,047,868157,473,067100.0%150.3 bases151 bases97.4%
total2,095,785315,052,781100.0%150.3 bases151 bases97.9%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,65266.61.398.3%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≤ 100000342
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 ≤ 500011
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_0009130.81005

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 input11:16:11 02 Jan 201711:16:53 02 Jan 201742 seconds
Read alignment to reference genome11:16:53 02 Jan 201711:22:57 02 Jan 20176 minutes 4 seconds
Preprocessing alignments for candidate junction identification11:22:57 02 Jan 201711:24:04 02 Jan 20171 minute 7 seconds
Preliminary analysis of coverage distribution11:24:04 02 Jan 201711:25:56 02 Jan 20171 minute 52 seconds
Identifying junction candidates11:25:56 02 Jan 201711:25:56 02 Jan 20170 seconds
Re-alignment to junction candidates11:25:56 02 Jan 201711:27:09 02 Jan 20171 minute 13 seconds
Resolving alignments with junction candidates11:27:09 02 Jan 201711:28:59 02 Jan 20171 minute 50 seconds
Creating BAM files11:28:59 02 Jan 201711:30:22 02 Jan 20171 minute 23 seconds
Tabulating error counts11:30:22 02 Jan 201711:32:00 02 Jan 20171 minute 38 seconds
Re-calibrating base error rates11:32:00 02 Jan 201711:32:01 02 Jan 20171 second
Examining read alignment evidence11:32:01 02 Jan 201711:45:03 02 Jan 201713 minutes 2 seconds
Polymorphism statistics11:45:03 02 Jan 201711:45:04 02 Jan 20171 second
Output11:45:04 02 Jan 201711:45:21 02 Jan 201717 seconds
Total 29 minutes 10 seconds