breseq  version 0.35.7  revision b7a44cd89118
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsSRR258452410,950,064555,577,45715.4%50.7 bases51 bases99.9%
total10,950,064555,577,45715.4%50.7 bases51 bases99.9%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionREL6064,629,812123.23.7100.0%Escherichia coli strain REL606.
total4,629,812100.0%

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≤ 10000065238
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 ≤ 5000185
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.004

Junction Skew Score Calculation

reference sequencepr(no read start)
REL6060.35694

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 cutoffOFF
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
bowtie22.3.4.1
R4.0.0

Execution Times

stepstartendelapsed
Read and reference sequence file input22:20:49 19 Jul 202122:26:41 19 Jul 20215 minutes 52 seconds
Read alignment to reference genome22:26:41 19 Jul 202122:30:35 19 Jul 20213 minutes 54 seconds
Preprocessing alignments for candidate junction identification22:30:35 19 Jul 202122:33:26 19 Jul 20212 minutes 51 seconds
Preliminary analysis of coverage distribution22:33:26 19 Jul 202122:35:45 19 Jul 20212 minutes 19 seconds
Identifying junction candidates22:35:45 19 Jul 202122:35:48 19 Jul 20213 seconds
Re-alignment to junction candidates22:35:48 19 Jul 202122:36:16 19 Jul 202128 seconds
Resolving best read alignments22:36:16 19 Jul 202122:40:03 19 Jul 20213 minutes 47 seconds
Creating BAM files22:40:03 19 Jul 202122:42:06 19 Jul 20212 minutes 3 seconds
Tabulating error counts22:42:06 19 Jul 202122:42:47 19 Jul 202141 seconds
Re-calibrating base error rates22:42:47 19 Jul 202122:42:48 19 Jul 20211 second
Examining read alignment evidence22:42:48 19 Jul 202122:47:40 19 Jul 20214 minutes 52 seconds
Polymorphism statistics22:47:40 19 Jul 202122:47:41 19 Jul 20211 second
Output22:47:41 19 Jul 202122:47:56 19 Jul 202115 seconds
Output :: Mutation Prediction22:47:41 19 Jul 202122:47:42 19 Jul 20211 second
Output :: Mutation Annotation22:47:42 19 Jul 202122:47:42 19 Jul 20210 seconds
Total 27 minutes 8 seconds