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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsERR1811607_R1.good.fq724,598120,497,463100.0%166.3 bases275 bases93.3%
errorsERR1811607_R2.good.fq724,588123,489,930100.0%170.4 bases275 bases77.6%
total1,449,186243,987,393100.0%168.4 bases275 bases85.5%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionCP0092734,631,46935.85.6100.0%Escherichia coli BW25113, complete genome.
total4,631,469100.0%

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≤ 10000059038
Coverage evenness (position-hash) score of junction candidates≥ 2≥ 4
Test this many junction candidates (n). May be smaller if not enough passed the coverage evenness threshold100 ≤ n ≤ 5000391
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.047

Junction Skew Score Calculation

reference sequencepr(no read start)
CP0092730.90356

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 input16:36:57 28 Mar 202116:37:26 28 Mar 202129 seconds
Read alignment to reference genome16:37:26 28 Mar 202116:43:24 28 Mar 20215 minutes 58 seconds
Preprocessing alignments for candidate junction identification16:43:24 28 Mar 202116:43:44 28 Mar 202120 seconds
Preliminary analysis of coverage distribution16:43:44 28 Mar 202116:44:38 28 Mar 202154 seconds
Identifying junction candidates16:44:38 28 Mar 202116:45:32 28 Mar 202154 seconds
Re-alignment to junction candidates16:45:32 28 Mar 202116:46:37 28 Mar 20211 minute 5 seconds
Resolving best read alignments16:46:37 28 Mar 202116:47:04 28 Mar 202127 seconds
Creating BAM files16:47:04 28 Mar 202116:47:51 28 Mar 202147 seconds
Tabulating error counts16:47:51 28 Mar 202116:48:11 28 Mar 202120 seconds
Re-calibrating base error rates16:48:11 28 Mar 202116:48:12 28 Mar 20211 second
Examining read alignment evidence16:48:12 28 Mar 202117:04:05 28 Mar 202115 minutes 53 seconds
Polymorphism statistics17:04:05 28 Mar 202117:04:05 28 Mar 20210 seconds
Output17:04:05 28 Mar 202117:04:49 28 Mar 202144 seconds
Total 27 minutes 52 seconds