Quality Control Statement for Sequence-Based SNP Discovery
1. Sample handling is performed from start to finish in microtiter plates
using robotic pipetting devices; each sample is sequenced in an individual
2. All generated sequences are checked for internal consistency in terms
of their location and orientation (forward or reverse reads) with the
3.Sequence quality, which provides an estimate of the error probabilites
for each base-call, is used to guide SNP analysis to ensure that only
the most accurate regions of the sequence (sequence quality > 30, or <
1 error per 1,000) are used for polymorphism detection.
4. Approximately 30 to 40% of SNPs are confirmed on another strand, due
to redundancy from overlapping sequences produced from the forward and
reverse strands and overlap between adjacent PCR products.
5. All singletons (single heterozygotes among homozygotes) are re-amplified
and re-sequenced for confirmation.
6. Approximately 10% of the samples are resequenced from each gene to
check the accuracy of genotypes and SNPs.