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-COUM5-3_S11_L001_R1_0011,447,141217,632,752100.0%150.4 bases151 bases99.2%
errorsqtrim-COUM5-3_S11_L001_R2_0011,446,711217,115,891100.0%150.1 bases151 bases96.4%
total2,893,852434,748,643100.0%150.2 bases151 bases97.8%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,65291.51.498.3%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≤ 1000003960
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 ≤ 500039
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_0009130.75151

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 input11:12:48 03 Jan 201711:13:31 03 Jan 201743 seconds
Read alignment to reference genome11:13:31 03 Jan 201711:19:30 03 Jan 20175 minutes 59 seconds
Preprocessing alignments for candidate junction identification11:19:30 03 Jan 201711:20:47 03 Jan 20171 minute 17 seconds
Preliminary analysis of coverage distribution11:20:47 03 Jan 201711:23:32 03 Jan 20172 minutes 45 seconds
Identifying junction candidates11:23:32 03 Jan 201711:23:33 03 Jan 20171 second
Re-alignment to junction candidates11:23:33 03 Jan 201711:25:17 03 Jan 20171 minute 44 seconds
Resolving alignments with junction candidates11:25:17 03 Jan 201711:27:50 03 Jan 20172 minutes 33 seconds
Creating BAM files11:27:50 03 Jan 201711:30:17 03 Jan 20172 minutes 27 seconds
Tabulating error counts11:30:17 03 Jan 201711:32:32 03 Jan 20172 minutes 15 seconds
Re-calibrating base error rates11:32:32 03 Jan 201711:32:33 03 Jan 20171 second
Examining read alignment evidence11:32:33 03 Jan 201711:52:43 03 Jan 201720 minutes 10 seconds
Polymorphism statistics11:52:43 03 Jan 201711:52:45 03 Jan 20172 seconds
Output11:52:45 03 Jan 201711:53:17 03 Jan 201732 seconds
Total 40 minutes 29 seconds