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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsJ3-E2_S99_R1_001.good.fq5,189,613322,804,646100.0%62.2 bases71 bases98.4%
total5,189,613322,804,646100.0%62.2 bases71 bases98.4%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionAP0090484,646,33268.85.5100.0%Escherichia coli str. K-12 substr. W3110 DNA, complete genome.
total4,646,332100.0%

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≤ 10000053776
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 ≤ 50001239
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.039

Junction Skew Score Calculation

reference sequencepr(no read start)
AP0090480.63729

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≤ 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
bowtie22.3.4.1
R3.4.4

Execution Times

stepstartendelapsed
Read and reference sequence file input13:31:08 01 Jul 201913:32:00 01 Jul 201952 seconds
Read alignment to reference genome13:32:00 01 Jul 201913:38:11 01 Jul 20196 minutes 11 seconds
Preprocessing alignments for candidate junction identification13:38:11 01 Jul 201913:39:12 01 Jul 20191 minute 1 second
Preliminary analysis of coverage distribution13:39:12 01 Jul 201913:40:54 01 Jul 20191 minute 42 seconds
Identifying junction candidates13:40:54 01 Jul 201913:41:12 01 Jul 201918 seconds
Re-alignment to junction candidates13:41:12 01 Jul 201913:43:13 01 Jul 20192 minutes 1 second
Resolving best read alignments13:43:13 01 Jul 201913:44:42 01 Jul 20191 minute 29 seconds
Creating BAM files13:44:42 01 Jul 201913:46:15 01 Jul 20191 minute 33 seconds
Tabulating error counts13:46:15 01 Jul 201913:46:44 01 Jul 201929 seconds
Re-calibrating base error rates13:46:44 01 Jul 201913:46:45 01 Jul 20191 second
Examining read alignment evidence13:46:45 01 Jul 201913:54:57 01 Jul 20198 minutes 12 seconds
Polymorphism statistics13:54:57 01 Jul 201913:54:57 01 Jul 20190 seconds
Output13:54:57 01 Jul 201913:55:36 01 Jul 201939 seconds
Total 24 minutes 28 seconds