Reporting Differences To The Revised Cambridge Reference Sequence

For reporting purposes, sequences are listed in a minimum data format as differences relative to the rCRS. When differences are observed, the nucleotide position is cited followed by the base present at that site. For example in Figure 10.8a, differences are observed at positions 16093 and 16129 and are noted in Figure 10.8b in their minimum data format at 16093C and 16129A. In this format, all other nucleotides are assumed to be identical to the revised Cambridge Reference Sequence. Bases that cannot unambiguously be determined are usually coded N. At confirmed positions of ambiguity (e.g., sequence heteroplasmy), the International Union of Pure and Applied Chemistry (IUPAC) codes should be used, such as A/G = R and C/T = Y (SWGDAM 2003).

Insertions in a DNA sequence relative to the rCRS are described by noting the site immediately 5' to the insertion as compared to the rCRS followed by a point and a '1' (for the first insertion), a '2' (if there is a second insertion), and so on, and then by the nucleotide that is inserted (Isenberg 2004). For example, 315.1C is a common observation where six Cs are observed following the T at position 310 in the rCRS. The rCRS contains only five Cs in positions 311-315 (Andrews et al. 1999). Therefore, the notation 315.1C describes the presence of five cytosines at positions 311-315 and an extra C as an insertion ('.1C') prior to position 316.

Deletions are noted by a dash ('-') or a 'D', 'd' or 'del' following the nucleotide position where the deletion was observed relative to the rCRS (e.g., 309D, 309-, or 309del). Some insertion and deletion combinations can lead to multiple possibilities for reporting a result in terms of differences from the reference sequence. Therefore, recommendations have been made for consistent treatment of length variants as will be described in the next section.

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