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Interpreting results

Results

A resultsStats + extension file

The first line is the fasta description line taken from the input file with GenBank identifier and RefSeq number.

>gi|116048575|ref|NC_008463.1| Pseudomonas aeruginosa UCBPP-PA14, complete genome

Line 2 lists the number of base pairs counted in the genome.

Genome size: 6537637

The third line contains the column headers.

ID Oligo Freq Exp.Freq ChiSq 

Explanation of column headers

ID is an internal number required for sorting some data
Oligo is the oligonucleotide string
Freq is the number of instances counted of this oligo in the genome (observed count)
Exp.Freq is the number of instances expected of this oligo in the genome (expected count) according
to a simple zero order markov model
ChiSq is the chi-squared statistic derived from the observed and expected values.

Sample

gi|121582657|ref|NC_008770.1| Campylobacter jejuni subsp. jejuni 81-176 plasmid pVir, complete sequence
Genome size: 37473
ID Oligo Freq Exp.Freq ChiSq
8 AAAAAAGG 29 4.143 149
7 GAAAAAGA 27 4.143 126


A resultsPositions + extension file

As above except:

No is the instance of the oligo, from first to last
Start is the genomic position where this oligo instance begins.

>gi|121582657|ref|NC_008770.1| Campylobacter jejuni subsp. jejuni 81-176 plasmid pVir, complete sequence
Genome size: 37473
hitID oligo No. start
8 AAAAAAGG 1 1491
8 AAAAAAGG 2 4806
8 AAAAAAGG 3 6442