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-OCTA8-7_S20_L001_R1_0011,421,882213,868,727100.0%150.4 bases151 bases99.2%
errorsqtrim-OCTA8-7_S20_L001_R2_0011,421,856213,792,072100.0%150.4 bases151 bases98.7%
total2,843,738427,660,799100.0%150.4 bases151 bases99.0%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,65291.51.598.3%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≤ 1000001398
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 ≤ 500017
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_0009130.75196

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 input07:41:41 02 Jan 201707:42:25 02 Jan 201744 seconds
Read alignment to reference genome07:42:26 02 Jan 201707:50:21 02 Jan 20177 minutes 55 seconds
Preprocessing alignments for candidate junction identification07:50:21 02 Jan 201707:51:49 02 Jan 20171 minute 28 seconds
Preliminary analysis of coverage distribution07:51:49 02 Jan 201707:54:32 02 Jan 20172 minutes 43 seconds
Identifying junction candidates07:54:32 02 Jan 201707:54:32 02 Jan 20170 seconds
Re-alignment to junction candidates07:54:32 02 Jan 201707:56:07 02 Jan 20171 minute 35 seconds
Resolving alignments with junction candidates07:56:07 02 Jan 201707:58:37 02 Jan 20172 minutes 30 seconds
Creating BAM files07:58:37 02 Jan 201708:00:28 02 Jan 20171 minute 51 seconds
Tabulating error counts08:00:28 02 Jan 201708:02:36 02 Jan 20172 minutes 8 seconds
Re-calibrating base error rates08:02:36 02 Jan 201708:02:37 02 Jan 20171 second
Examining read alignment evidence08:02:37 02 Jan 201708:20:16 02 Jan 201717 minutes 39 seconds
Polymorphism statistics08:20:16 02 Jan 201708:20:18 02 Jan 20172 seconds
Output08:20:18 02 Jan 201708:20:36 02 Jan 201718 seconds
Total 38 minutes 54 seconds