breseq  version 0.35.4  revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsSvNSRound3_24_106_2_S362_L002_R1_001.good.fq575,11582,704,895100.0%143.8 bases149 bases97.9%
errorsSvNSRound3_24_106_2_S362_L002_R2_001.good.fq575,11582,704,895100.0%143.8 bases149 bases89.1%
total1,150,230165,409,790100.0%143.8 bases149 bases93.5%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_000913_3_pae_tpiA4,641,56833.21.6100.0%Escherichia coli str. K-12 substr. MG1655, P. aerophilum tpiA gene, complete genome.
total4,641,568100.0%

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≤ 1000005068
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 ≤ 5000663
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.044

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_000913_3_pae_tpiA0.90210

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 cutoff0.75
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 input18:03:17 19 Dec 202018:04:27 19 Dec 20201 minute 10 seconds
Read alignment to reference genome18:04:27 19 Dec 202018:16:03 19 Dec 202011 minutes 36 seconds
Preprocessing alignments for candidate junction identification18:16:03 19 Dec 202018:16:57 19 Dec 202054 seconds
Preliminary analysis of coverage distribution18:16:57 19 Dec 202018:19:14 19 Dec 20202 minutes 17 seconds
Identifying junction candidates18:19:14 19 Dec 202018:19:21 19 Dec 20207 seconds
Re-alignment to junction candidates18:19:21 19 Dec 202018:22:01 19 Dec 20202 minutes 40 seconds
Resolving best read alignments18:22:01 19 Dec 202018:23:17 19 Dec 20201 minute 16 seconds
Creating BAM files18:23:17 19 Dec 202018:25:20 19 Dec 20202 minutes 3 seconds
Tabulating error counts18:25:20 19 Dec 202018:26:07 19 Dec 202047 seconds
Re-calibrating base error rates18:26:07 19 Dec 202018:26:11 19 Dec 20204 seconds
Examining read alignment evidence18:26:11 19 Dec 202018:37:53 19 Dec 202011 minutes 42 seconds
Polymorphism statistics18:37:53 19 Dec 202018:37:53 19 Dec 20200 seconds
Output18:37:53 19 Dec 202018:38:18 19 Dec 202025 seconds
Total 35 minutes 1 second