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-COUM3-1_S5_L001_R1_001999,741150,386,437100.0%150.4 bases151 bases99.8%
errorsqtrim-COUM3-1_S5_L001_R2_001999,477150,068,467100.0%150.1 bases151 bases97.1%
total1,999,218300,454,904100.0%150.3 bases151 bases98.4%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,65263.91.398.3%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≤ 1000001509
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 ≤ 500028
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.002

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.81778

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 input10:50:14 03 Jan 201710:50:43 03 Jan 201729 seconds
Read alignment to reference genome10:50:44 03 Jan 201710:54:41 03 Jan 20173 minutes 57 seconds
Preprocessing alignments for candidate junction identification10:54:41 03 Jan 201710:55:31 03 Jan 201750 seconds
Preliminary analysis of coverage distribution10:55:31 03 Jan 201710:57:05 03 Jan 20171 minute 34 seconds
Identifying junction candidates10:57:05 03 Jan 201710:57:05 03 Jan 20170 seconds
Re-alignment to junction candidates10:57:05 03 Jan 201710:58:03 03 Jan 201758 seconds
Resolving alignments with junction candidates10:58:03 03 Jan 201710:59:30 03 Jan 20171 minute 27 seconds
Creating BAM files10:59:30 03 Jan 201711:00:43 03 Jan 20171 minute 13 seconds
Tabulating error counts11:00:43 03 Jan 201711:02:02 03 Jan 20171 minute 19 seconds
Re-calibrating base error rates11:02:02 03 Jan 201711:02:03 03 Jan 20171 second
Examining read alignment evidence11:02:03 03 Jan 201711:12:32 03 Jan 201710 minutes 29 seconds
Polymorphism statistics11:12:32 03 Jan 201711:12:32 03 Jan 20170 seconds
Output11:12:32 03 Jan 201711:12:48 03 Jan 201716 seconds
Total 22 minutes 33 seconds