High throughput sequencing in mice: a platform comparison identifies a preponderance of cryptic SNPs

BMC Genomics

Table 1 Comparison of Illumina and Applied Biosystems realignment data.

	Illumina		SOLiD
	B6	D2	B6	D2
Total basepairs covered	2898101	3000000	2898101	3000000
Ns in realignment	547	23207	82499	116135
Realignment discrepancies to B6 reference or SNPs detected in D2	128	11221	41	9823
Ambiguous alleles	244	2047	37	635

Results are based upon realignments performed by each vendor for chromosome 1 (171.6–174.6 Mb). N's indicate a 'no call' in the realignment. Realignment discrepancies to B6 reference indicate a mismatch to the reference sequence, and SNP detection in D2 indicates a different allele than the B6 reference sequence. An ambiguous allele indicates that more than one base was called at that base, and since these are inbred animals, those calls are ignored and considered the same as a no call or an 'N'.

ISSN: 1471-2164