4. GS Amplicon Variant Analyzer – Special Topics
:
4.2 Intelligent Variant Naming
: 4.2.2 Tier 2 Naming
4.2.2
Tier 2 Naming
If the attempt to explicitly specify out all the base changes in a Tier 1 name results in an identifier that is longer than 25 characters, Tier 2 naming takes over. Tier 2 names also come in two forms. The first form has the prototype “Position:Modifier[(count/value)]” and the second has the prototype “PositionA-PositionB:Modifier(count/value)”. The modifiers are REF (must match the Reference Sequence), DEL (Deletion), INS (Insertion), and SUB (Substitution). For the first prototype, the “count/value” is optional for single base matches (REF) or single base deletions (DEL). This naming scheme is often more compact than Tier 1 names, especially when stretches of bases can be collapsed into a base count (second prototype), and it maintains the sorting advantage of starting names with the base position on the Reference Sequence. However, exact base changes are not always stated explicitly.
Table 4‑2
shows examples that demonstrate the basics of Tier 2 naming.
Tier 2 Variant Name
Interpretation of the Variant Name
10:REF
base at position 10 must match the reference sequence
10-49:REF(40)
the 40 bases from 10-49 must match the reference sequence
10:DEL
base at position 10 is deleted
10-49:DEL(40)
the 40 bases from 10-49 are deleted
10.5:INS(ACG)
the bases ACG are inserted between positions 10 and 11
10:SUB(G)
base at position 10 has been changed to a G
10:SUB(C),45:SUB(G)
haplotype change at positions 10 (changed to a C) and 45 (changed to a G)
Table 4‑2: Examples of Tier 2 “intelligent” Variant names. Note that some of these (like “10:REF”) would not be used because their Tier 1 equivalent would be preferred. These are shown for illustrative purposes.
