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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsBOP1000_aceEF_S2213_L006_R1_001.good.fq1,363,462201,848,116100.0%148.0 bases150 bases94.0%
errorsBOP1000_aceEF_S2213_L006_R2_001.good.fq1,363,462201,848,116100.0%148.0 bases150 bases92.8%
errorsBOP1000_aceEF_S2213_L008_R1_001.good.fq592,22687,562,349100.0%147.9 bases150 bases93.9%
errorsBOP1000_aceEF_S2213_L008_R2_001.good.fq592,22687,562,349100.0%147.9 bases150 bases91.2%
total3,911,376578,820,930100.0%148.0 bases150 bases93.2%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652115.92.4100.0%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≤ 100000100000
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 ≤ 500068
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.004

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.71551

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 input10:17:00 11 Sep 202010:17:59 11 Sep 202059 seconds
Read alignment to reference genome10:18:00 11 Sep 202010:26:11 11 Sep 20208 minutes 11 seconds
Preprocessing alignments for candidate junction identification10:26:11 11 Sep 202010:27:13 11 Sep 20201 minute 2 seconds
Preliminary analysis of coverage distribution10:27:13 11 Sep 202010:29:11 11 Sep 20201 minute 58 seconds
Identifying junction candidates10:29:11 11 Sep 202010:29:36 11 Sep 202025 seconds
Re-alignment to junction candidates10:29:36 11 Sep 202010:31:50 11 Sep 20202 minutes 14 seconds
Resolving best read alignments10:31:50 11 Sep 202010:33:24 11 Sep 20201 minute 34 seconds
Creating BAM files10:33:24 11 Sep 202010:35:11 11 Sep 20201 minute 47 seconds
Tabulating error counts10:35:11 11 Sep 202010:35:53 11 Sep 202042 seconds
Re-calibrating base error rates10:35:53 11 Sep 202010:35:55 11 Sep 20202 seconds
Examining read alignment evidence10:35:55 11 Sep 202010:44:29 11 Sep 20208 minutes 34 seconds
Polymorphism statistics10:44:29 11 Sep 202010:44:29 11 Sep 20200 seconds
Output10:44:29 11 Sep 202010:44:47 11 Sep 202018 seconds
Total 27 minutes 46 seconds