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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsPlate-2-BOP-27-PFKA-ALE-1-flask-11_S65_L001_R1_001.good.fq244,98230,265,696100.0%123.5 bases149 bases94.3%
errorsPlate-2-BOP-27-PFKA-ALE-1-flask-11_S65_L001_R2_001.good.fq244,98229,809,293100.0%121.7 bases149 bases97.6%
errorsPlate-2-BOP-27-PFKA-ALE-1-flask-11_S65_L002_R1_001.good.fq198,46424,437,630100.0%123.1 bases149 bases94.0%
errorsPlate-2-BOP-27-PFKA-ALE-1-flask-11_S65_L002_R2_001.good.fq198,46424,074,069100.0%121.3 bases149 bases97.1%
errorsPlate-2-BOP-27-PFKA-ALE-1-flask-11_S65_L003_R1_001.good.fq225,60227,785,372100.0%123.2 bases149 bases94.2%
errorsPlate-2-BOP-27-PFKA-ALE-1-flask-11_S65_L003_R2_001.good.fq225,60227,360,911100.0%121.3 bases149 bases97.6%
errorsPlate-2-BOP-27-PFKA-ALE-1-flask-11_S65_L004_R1_001.good.fq197,05424,206,598100.0%122.8 bases149 bases94.0%
errorsPlate-2-BOP-27-PFKA-ALE-1-flask-11_S65_L004_R2_001.good.fq197,05423,856,367100.0%121.1 bases149 bases96.9%
total1,732,204211,795,936100.0%122.3 bases149 bases95.7%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,65243.32.9100.0%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≤ 10000026730
Coverage evenness (position-hash) score of junction candidates≥ 2≥ 3
Test this many junction candidates (n). May be smaller if not enough passed the coverage evenness threshold100 ≤ n ≤ 5000284
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.019

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.84611

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
bowtie22.2.6
R3.4.4

Execution Times

stepstartendelapsed
Read and reference sequence file input01:14:24 11 Sep 202001:14:49 11 Sep 202025 seconds
Read alignment to reference genome01:14:50 11 Sep 202001:17:49 11 Sep 20202 minutes 59 seconds
Preprocessing alignments for candidate junction identification01:17:49 11 Sep 202001:18:15 11 Sep 202026 seconds
Preliminary analysis of coverage distribution01:18:15 11 Sep 202001:18:58 11 Sep 202043 seconds
Identifying junction candidates01:18:58 11 Sep 202001:20:05 11 Sep 20201 minute 7 seconds
Re-alignment to junction candidates01:20:05 11 Sep 202001:21:05 11 Sep 20201 minute 0 seconds
Resolving best read alignments01:21:05 11 Sep 202001:21:43 11 Sep 202038 seconds
Creating BAM files01:21:43 11 Sep 202001:22:23 11 Sep 202040 seconds
Tabulating error counts01:22:23 11 Sep 202001:22:38 11 Sep 202015 seconds
Re-calibrating base error rates01:22:38 11 Sep 202001:22:41 11 Sep 20203 seconds
Examining read alignment evidence01:22:41 11 Sep 202001:25:55 11 Sep 20203 minutes 14 seconds
Polymorphism statistics01:25:55 11 Sep 202001:25:55 11 Sep 20200 seconds
Output01:25:55 11 Sep 202001:26:12 11 Sep 202017 seconds
Total 11 minutes 47 seconds