breseq  version 0.33.1  revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsC13-Redo-1-58_S1_L001_R1_001.good.fq1,656,751428,164,755100.0%258.4 bases281 bases98.6%
errorsC13-Redo-1-58_S1_L001_R2_001.good.fq1,656,751429,880,030100.0%259.5 bases281 bases90.3%
total3,313,502858,044,785100.0%259.0 bases281 bases94.5%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652174.15.2100.0%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≤ 1000004571
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 ≤ 5000654
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.080

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.81090

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 cutoff0.75
Consensus minimum variant coverage each strandOFF
Consensus minimum total coverage each strandOFF
Consensus minimum variant coverageOFF
Consensus minimum total coverageOFF
Polymorphism E-value cutoff10
Polymorphism frequency cutoff0.2
Polymorphism minimum variant coverage each strandOFF
Polymorphism minimum total coverage each strandOFF
Polymorphism minimum variant coverageOFF
Polymorphism minimum total coverageOFF
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

Software Versions

programversion
bowtie22.3.4.1
R3.4.4

Execution Times

stepstartendelapsed
Read and reference sequence file input03:20:48 16 May 201903:21:41 16 May 201953 seconds
Read alignment to reference genome03:21:41 16 May 201903:40:27 16 May 201918 minutes 46 seconds
Preprocessing alignments for candidate junction identification03:40:27 16 May 201903:41:21 16 May 201954 seconds
Preliminary analysis of coverage distribution03:41:21 16 May 201903:44:38 16 May 20193 minutes 17 seconds
Identifying junction candidates03:44:38 16 May 201903:44:44 16 May 20196 seconds
Re-alignment to junction candidates03:44:44 16 May 201903:49:38 16 May 20194 minutes 54 seconds
Resolving best read alignments03:49:38 16 May 201903:51:16 16 May 20191 minute 38 seconds
Creating BAM files03:51:16 16 May 201903:54:06 16 May 20192 minutes 50 seconds
Tabulating error counts03:54:06 16 May 201903:55:22 16 May 20191 minute 16 seconds
Re-calibrating base error rates03:55:22 16 May 201903:55:23 16 May 20191 second
Examining read alignment evidence03:55:23 16 May 201904:08:51 16 May 201913 minutes 28 seconds
Polymorphism statistics04:08:51 16 May 201904:08:52 16 May 20191 second
Output04:08:52 16 May 201904:09:11 16 May 201919 seconds
Total 48 minutes 23 seconds