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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsR2_Lane7_BC04_R1.good.fq1,666,429126,606,489100.0%76.0 bases76 bases97.7%
errorsR2_Lane7_BC04_R2.good.fq1,666,429126,606,489100.0%76.0 bases76 bases95.4%
total3,332,858253,212,978100.0%76.0 bases76 bases96.5%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionREL6064,629,81252.22.7100.0%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≤ 1000004163
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 ≤ 500069
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.002

Junction Skew Score Calculation

reference sequencepr(no read start)
REL6060.73016

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 input12:54:03 01 Feb 201912:54:37 01 Feb 201934 seconds
Read alignment to reference genome12:54:38 01 Feb 201912:59:23 01 Feb 20194 minutes 45 seconds
Preprocessing alignments for candidate junction identification12:59:23 01 Feb 201913:00:01 01 Feb 201938 seconds
Preliminary analysis of coverage distribution13:00:01 01 Feb 201913:01:24 01 Feb 20191 minute 23 seconds
Identifying junction candidates13:01:24 01 Feb 201913:01:24 01 Feb 20190 seconds
Re-alignment to junction candidates13:01:24 01 Feb 201913:02:37 01 Feb 20191 minute 13 seconds
Resolving best read alignments13:02:37 01 Feb 201913:03:33 01 Feb 201956 seconds
Creating BAM files13:03:33 01 Feb 201913:04:50 01 Feb 20191 minute 17 seconds
Tabulating error counts13:04:50 01 Feb 201913:05:12 01 Feb 201922 seconds
Re-calibrating base error rates13:05:12 01 Feb 201913:05:13 01 Feb 20191 second
Examining read alignment evidence13:05:13 01 Feb 201913:08:45 01 Feb 20193 minutes 32 seconds
Polymorphism statistics13:08:45 01 Feb 201913:08:45 01 Feb 20190 seconds
Output13:08:45 01 Feb 201913:08:55 01 Feb 201910 seconds
Total 14 minutes 51 seconds