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_BC06_R1.good.fq8,984,444682,244,890100.0%75.9 bases76 bases93.7%
errorsR3_Lane2_BC06_R2.good.fq8,984,444682,244,890100.0%75.9 bases76 bases91.4%
total17,968,8881,364,489,780100.0%75.9 bases76 bases92.5%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionREL6064,629,812278.28.9100.0%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≤ 10000018976
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 ≤ 5000338
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.012

Junction Skew Score Calculation

reference sequencepr(no read start)
REL6060.26088

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 input20:51:44 01 Feb 201920:54:57 01 Feb 20193 minutes 13 seconds
Read alignment to reference genome20:54:57 01 Feb 201921:23:38 01 Feb 201928 minutes 41 seconds
Preprocessing alignments for candidate junction identification21:23:38 01 Feb 201921:26:58 01 Feb 20193 minutes 20 seconds
Preliminary analysis of coverage distribution21:26:58 01 Feb 201921:33:51 01 Feb 20196 minutes 53 seconds
Identifying junction candidates21:33:51 01 Feb 201921:33:55 01 Feb 20194 seconds
Re-alignment to junction candidates21:33:55 01 Feb 201921:41:14 01 Feb 20197 minutes 19 seconds
Resolving best read alignments21:41:14 01 Feb 201921:46:25 01 Feb 20195 minutes 11 seconds
Creating BAM files21:46:25 01 Feb 201921:52:41 01 Feb 20196 minutes 16 seconds
Tabulating error counts21:52:41 01 Feb 201921:54:40 01 Feb 20191 minute 59 seconds
Re-calibrating base error rates21:54:40 01 Feb 201921:54:41 01 Feb 20191 second
Examining read alignment evidence21:54:41 01 Feb 201922:12:18 01 Feb 201917 minutes 37 seconds
Polymorphism statistics22:12:18 01 Feb 201922:12:20 01 Feb 20192 seconds
Output22:12:20 01 Feb 201922:12:52 01 Feb 201932 seconds
Total 1 hour 21 minutes 8 seconds