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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsR3_Lane2_BC02_R1.good.fq9,025,674685,154,461100.0%75.9 bases76 bases94.2%
errorsR3_Lane2_BC02_R2.good.fq9,025,674685,154,461100.0%75.9 bases76 bases91.7%
total18,051,3481,370,308,922100.0%75.9 bases76 bases92.9%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionREL6064,629,812277.38.4100.0%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≤ 10000025724
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 ≤ 5000447
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.015

Junction Skew Score Calculation

reference sequencepr(no read start)
REL6060.26351

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
bowtie22.3.4.1
R3.4.4

Execution Times

stepstartendelapsed
Read and reference sequence file input21:30:44 31 Jan 201921:33:57 31 Jan 20193 minutes 13 seconds
Read alignment to reference genome21:33:57 31 Jan 201922:02:36 31 Jan 201928 minutes 39 seconds
Preprocessing alignments for candidate junction identification22:02:36 31 Jan 201922:05:53 31 Jan 20193 minutes 17 seconds
Preliminary analysis of coverage distribution22:05:53 31 Jan 201922:12:47 31 Jan 20196 minutes 54 seconds
Identifying junction candidates22:12:47 31 Jan 201922:12:51 31 Jan 20194 seconds
Re-alignment to junction candidates22:12:51 31 Jan 201922:20:13 31 Jan 20197 minutes 22 seconds
Resolving best read alignments22:20:13 31 Jan 201922:25:30 31 Jan 20195 minutes 17 seconds
Creating BAM files22:25:30 31 Jan 201922:31:45 31 Jan 20196 minutes 15 seconds
Tabulating error counts22:31:45 31 Jan 201922:33:47 31 Jan 20192 minutes 2 seconds
Re-calibrating base error rates22:33:47 31 Jan 201922:33:48 31 Jan 20191 second
Examining read alignment evidence22:33:48 31 Jan 201922:51:27 31 Jan 201917 minutes 39 seconds
Polymorphism statistics22:51:27 31 Jan 201922:51:28 31 Jan 20191 second
Output22:51:28 31 Jan 201922:52:04 31 Jan 201936 seconds
Total 1 hour 21 minutes 20 seconds