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_BC05_R1.good.fq6,319,878479,924,697100.0%75.9 bases76 bases94.4%
errorsR3_Lane2_BC05_R2.good.fq6,319,878479,924,697100.0%75.9 bases76 bases92.2%
total12,639,756959,849,394100.0%75.9 bases76 bases93.3%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionREL6064,629,812195.15.6100.0%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≤ 10000012132
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 ≤ 500083
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.003

Junction Skew Score Calculation

reference sequencepr(no read start)
REL6060.35471

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 input15:27:27 31 Jan 201915:29:39 31 Jan 20192 minutes 12 seconds
Read alignment to reference genome15:29:39 31 Jan 201915:49:46 31 Jan 201920 minutes 7 seconds
Preprocessing alignments for candidate junction identification15:49:46 31 Jan 201915:52:04 31 Jan 20192 minutes 18 seconds
Preliminary analysis of coverage distribution15:52:04 31 Jan 201915:56:56 31 Jan 20194 minutes 52 seconds
Identifying junction candidates15:56:56 31 Jan 201915:56:58 31 Jan 20192 seconds
Re-alignment to junction candidates15:56:58 31 Jan 201916:01:32 31 Jan 20194 minutes 34 seconds
Resolving best read alignments16:01:32 31 Jan 201916:05:11 31 Jan 20193 minutes 39 seconds
Creating BAM files16:05:11 31 Jan 201916:09:38 31 Jan 20194 minutes 27 seconds
Tabulating error counts16:09:38 31 Jan 201916:11:01 31 Jan 20191 minute 23 seconds
Re-calibrating base error rates16:11:01 31 Jan 201916:11:02 31 Jan 20191 second
Examining read alignment evidence16:11:02 31 Jan 201916:23:20 31 Jan 201912 minutes 18 seconds
Polymorphism statistics16:23:20 31 Jan 201916:23:21 31 Jan 20191 second
Output16:23:21 31 Jan 201916:23:49 31 Jan 201928 seconds
Total 56 minutes 22 seconds