breseq  version 0.39.0  
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsME8562_S14_R1_RMDUP_RM-R2-DUP.cutadapt877,185260,233,870100.0%296.7 bases300 bases92.4%
errorsME8562_S14_R2_RMDUP_RM-R1-DUP.cutadapt877,483258,368,886100.0%294.4 bases300 bases95.6%
total1,754,668518,602,756100.0%295.6 bases300 bases94.0%

Reference Sequence Information

seq idlengthfit meanfit relative_variance% mapped readsdescription
coveragedistributionNC_0009134,641,652103.74.8100.0%Escherichia coli str. K-12 substr. MG1655, complete genome.
total4,641,652100.0%

fit relative_variance 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≤ 1000005060
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 ≤ 5000160
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.021

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.89028

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
Minimum probablilty assigned that no mapped read will start at a given position and strand for junction prediction0.1
Junction allow suboptimal matchesFALSE
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 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
bowtie22.5.1
R4.0.3

Execution Times

stepstartendelapsed
Read and reference sequence file input14:32:56 10 Oct 202514:33:23 10 Oct 202527 seconds
Read alignment to reference genome14:33:23 10 Oct 202514:34:50 10 Oct 20251 minute 27 seconds
Preprocessing alignments for candidate junction identification14:34:50 10 Oct 202514:35:16 10 Oct 202526 seconds
Preliminary analysis of coverage distribution14:35:16 10 Oct 202514:36:25 10 Oct 20251 minute 9 seconds
Identifying junction candidates14:36:25 10 Oct 202514:36:29 10 Oct 20254 seconds
Re-alignment to junction candidates14:36:29 10 Oct 202514:36:44 10 Oct 202515 seconds
Resolving best read alignments14:36:44 10 Oct 202514:37:33 10 Oct 202549 seconds
Creating BAM files14:37:33 10 Oct 202514:38:31 10 Oct 202558 seconds
Tabulating error counts14:38:31 10 Oct 202514:39:16 10 Oct 202545 seconds
Re-calibrating base error rates14:39:16 10 Oct 202514:39:17 10 Oct 20251 second
Examining read alignment evidence14:39:17 10 Oct 202514:45:31 10 Oct 20256 minutes 14 seconds
Polymorphism statistics14:45:31 10 Oct 202514:45:32 10 Oct 20251 second
Output14:45:32 10 Oct 202514:45:39 10 Oct 20257 seconds
Output :: Mutation Prediction14:45:32 10 Oct 202514:45:32 10 Oct 20250 seconds
Output :: Mutation Annotation14:45:32 10 Oct 202514:45:32 10 Oct 20250 seconds
Total 12 minutes 43 seconds