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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsEEP_appC-cydB-ndh_A9F30I0R1_S57_L003_R1_001.good.fq10,298,8701,539,060,941100.0%149.4 bases150 bases99.3%
errorsEEP_appC-cydB-ndh_A9F30I0R1_S57_L003_R2_001.good.fq10,298,8701,539,060,941100.0%149.4 bases150 bases98.7%
total20,597,7403,078,121,882100.0%149.4 bases150 bases99.0%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652651.417.3100.0%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≤ 10000071630
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 ≤ 5000145
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.010

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.31103

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≤ 0
Number of bases that at least one read must overlap each uniquely aligned side of a predicted junction≥ 6

Read Alignment Evidence

optionvalue
ModeFull Polymorphism
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 cutoff2
Polymorphism frequency cutoff0.05
Polymorphism minimum variant coverage each strand2
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 of ≥3 bases
Skip base substitutions when they create a homopolymer flanked on each side by ≥5 bases

Software Versions

programversion
bowtie22.2.6
R3.4.4

Execution Times

stepstartendelapsed
Read and reference sequence file input20:54:43 15 Apr 202121:00:45 15 Apr 20216 minutes 2 seconds
Read alignment to reference genome21:00:45 15 Apr 202121:47:55 15 Apr 202147 minutes 10 seconds
Preprocessing alignments for candidate junction identification21:47:55 15 Apr 202121:53:24 15 Apr 20215 minutes 29 seconds
Preliminary analysis of coverage distribution21:53:24 15 Apr 202122:04:16 15 Apr 202110 minutes 52 seconds
Identifying junction candidates22:04:16 15 Apr 202122:04:53 15 Apr 202137 seconds
Re-alignment to junction candidates22:04:53 15 Apr 202122:17:06 15 Apr 202112 minutes 13 seconds
Resolving best read alignments22:17:06 15 Apr 202122:24:14 15 Apr 20217 minutes 8 seconds
Creating BAM files22:24:14 15 Apr 202122:33:51 15 Apr 20219 minutes 37 seconds
Tabulating error counts22:33:51 15 Apr 202122:38:21 15 Apr 20214 minutes 30 seconds
Re-calibrating base error rates22:38:21 15 Apr 202122:38:22 15 Apr 20211 second
Examining read alignment evidence22:38:22 15 Apr 202105:12:20 16 Apr 20216 hours 33 minutes 58 seconds
Polymorphism statistics05:12:20 16 Apr 202105:12:29 16 Apr 20219 seconds
Output05:12:29 16 Apr 202105:13:34 16 Apr 20211 minute 5 seconds
Total 8 hours 18 minutes 51 seconds