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-OCTA1-3_S1_L001_R2_001980,485147,388,424100.0%150.3 bases151 bases98.6%
errorsqtrim-OCTA1-3_S1_L001_R1_001980,513147,474,453100.0%150.4 bases151 bases99.3%
total1,960,998294,862,877100.0%150.4 bases151 bases99.0%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,65263.01.598.3%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≤ 100000971
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 ≤ 500020
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_0009130.81935

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 input12:53:01 02 Jan 201712:53:52 02 Jan 201751 seconds
Read alignment to reference genome12:53:53 02 Jan 201712:59:23 02 Jan 20175 minutes 30 seconds
Preprocessing alignments for candidate junction identification12:59:23 02 Jan 201713:00:31 02 Jan 20171 minute 8 seconds
Preliminary analysis of coverage distribution13:00:31 02 Jan 201713:02:12 02 Jan 20171 minute 41 seconds
Identifying junction candidates13:02:12 02 Jan 201713:02:13 02 Jan 20171 second
Re-alignment to junction candidates13:02:13 02 Jan 201713:03:15 02 Jan 20171 minute 2 seconds
Resolving alignments with junction candidates13:03:15 02 Jan 201713:05:02 02 Jan 20171 minute 47 seconds
Creating BAM files13:05:02 02 Jan 201713:06:25 02 Jan 20171 minute 23 seconds
Tabulating error counts13:06:25 02 Jan 201713:08:00 02 Jan 20171 minute 35 seconds
Re-calibrating base error rates13:08:00 02 Jan 201713:08:02 02 Jan 20172 seconds
Examining read alignment evidence13:08:02 02 Jan 201713:20:14 02 Jan 201712 minutes 12 seconds
Polymorphism statistics13:20:14 02 Jan 201713:20:14 02 Jan 20170 seconds
Output13:20:14 02 Jan 201713:20:35 02 Jan 201721 seconds
Total 27 minutes 33 seconds