Using structural bioinformatics to investigate the impact of non synonymous SNPs and disease mutations: scope and limitations

Table 1 Summary of structural coverage of SNP data.

Properties	# SNPs	% SNPs
nsSNPs covered by high quality structural data
No additional criteria	9877	7.4
Sequence coverage > 80 or alignment length > 100	8238	6.2
Sequence identity > 80	5416	4.1
Sequence coverage > 80 or alignment length > 100, and sequence identity > 80	5318	4.0
Highly reliable nsSNPs covered by high quality structural data
Doublehit validation status, MAF > 0.01	680	0.51
Doublehit validation status, MAF > 0.01, sequence identity > 80	229	0.17
Doublehit validation status, MAF > 0.01, sequence coverage > 80 or alignment length > 100	446	0.33
Doublehit validation status, MAF > 0.01, sequence coverage > 80 or alignment length > 100, and sequence identity > 80	209	0.16

Several criteria resulting from the above analyses are applied to assess the structural coverage and reliability of that coverage of human SNPs in the Ensembl database, as well as the overlap of the structural coverage with quality parameters for the validation and frequency status of the polymorphism data.

ISSN: 1471-2105