4. GS Amplicon Variant Analyzer – Special Topics
:
4.2 Intelligent Variant Naming
: 4.2.1 Tier 1 Naming
4.2.1
Tier 1 Naming
Tier 1 names are the preferred, and come in two forms. The first form has the prototype “Position:From-Sequence/To-Sequence” and the second has the prototype “PositionA-PositionB:From-Sequence/To-Sequence”. Complicated Variants may be described using multiple names of either form, separated by commas. This is the most precise naming scheme as it explicitly specifies each base requirement that defines the Variant. Also, starting the name with the base position (relative to the Reference Sequence), is convenient for sorting a Table of Variants.
Table 4‑1
, below, shows some example Tier 1 names and what they mean.
Tier 1 Variant Name
Interpretation of the Variant Name
10:A/C
position 10 has a change from an A to a C
10-12:ACT/ATG
position 10 must match the Reference Sequence (and remain an A), while positions 11 and 12 change from a CT to a TG
10-12:ACT/ANG
position 10 must remain an A, position 11 can be any base, and position 12 has a change from a T to a G
10-12:ACT/---
the bases ACT at positions 10-12 are deleted
10.5:-/A
an A is inserted between positions 10 and 11
10-11:A-T/ACT
a C is inserted between A and T, which must be maintained, at positions 10 and 11
10:A/C,45:T/G
haplotype change including an A changed to a C at position 10 and a T changed to a G at position 45
Table 4‑1: Examples of Tier 1 “intelligent” Variant names
