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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsIH84_rmdup_R1714,197214,259,100100.0%300.0 bases300 bases97.7%
errorsIH84_rmdup_R2698,053209,415,900100.0%300.0 bases300 bases97.0%
total1,412,250423,675,000100.0%300.0 bases300 bases97.4%

Reference Sequence Information

seq idlengthfit meanfit relative_variance% mapped readsdescription
coveragedistributionNC_0009134,641,65287.44.1100.0%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≤ 10000010639
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 ≤ 500090
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.012

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.90145

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 input00:06:52 04 Jun 202500:07:15 04 Jun 202523 seconds
Read alignment to reference genome00:07:15 04 Jun 202500:08:29 04 Jun 20251 minute 14 seconds
Preprocessing alignments for candidate junction identification00:08:29 04 Jun 202500:08:51 04 Jun 202522 seconds
Preliminary analysis of coverage distribution00:08:51 04 Jun 202500:09:48 04 Jun 202557 seconds
Identifying junction candidates00:09:48 04 Jun 202500:09:51 04 Jun 20253 seconds
Re-alignment to junction candidates00:09:51 04 Jun 202500:10:02 04 Jun 202511 seconds
Resolving best read alignments00:10:02 04 Jun 202500:10:43 04 Jun 202541 seconds
Creating BAM files00:10:43 04 Jun 202500:11:31 04 Jun 202548 seconds
Tabulating error counts00:11:31 04 Jun 202500:12:08 04 Jun 202537 seconds
Re-calibrating base error rates00:12:08 04 Jun 202500:12:09 04 Jun 20251 second
Examining read alignment evidence00:12:09 04 Jun 202500:17:25 04 Jun 20255 minutes 16 seconds
Polymorphism statistics00:17:25 04 Jun 202500:17:26 04 Jun 20251 second
Output00:17:26 04 Jun 202500:17:32 04 Jun 20256 seconds
Output :: Mutation Prediction00:17:26 04 Jun 202500:17:26 04 Jun 20250 seconds
Output :: Mutation Annotation00:17:26 04 Jun 202500:17:26 04 Jun 20250 seconds
Total 10 minutes 40 seconds