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<title>Variation-inst</title>
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<h3>Variation-inst</h3><pre>Defined in file <a href="seqfeat.asn.html">seqfeat.asn</a>
C++ class: <a href="../doxyhtml/classCVariation__inst.html">CVariation_inst</a>
Variation-inst ::= SEQUENCE {
type INTEGER {
unknown (0), -- delta=[]
identity (1), -- delta=[]
inv (2), -- delta=[del, ins.seq=
-- RevComp(variation-location)]
snv (3), -- delta=[morph of length 1]
-- NOTE: this is snV not snP; the latter
-- requires frequency-based validation to be
-- established in <a href="VariantProperties.html">VariantProperties</a>
-- the strict definition of SNP is an SNV with
-- an established population frequency of at
-- least 1% in at least 1 popuplation
mnp (4), -- delta=[morph of length >1]
delins (5), -- delta=[del, ins]
del (6), -- delta=[del]
ins (7), -- delta=[ins]
microsatellite (8), -- delta=[del, ins.seq= repeat-unit with fuzzy
-- multiplier]
-- variation-location is the microsat expansion
-- on the sequence
transposon (9), -- delta=[del, ins.seq= known donor or 'this']
-- variation-location is equiv of transposon
-- locs.
cnv (10), -- delta=[del, ins= 'this' with fuzzy
-- multiplier]
direct-copy (11), -- delta=[ins.seq= upstream location on the
-- same strand]
rev-direct-copy (12), -- delta=[ins.seq= downstream location on the
-- same strand]
inverted-copy (13), -- delta=[ins.seq= upstream location on the
-- opposite strand]
everted-copy (14), -- delta=[ins.seq= downstream location on the
-- opposite strand]
translocation (15), -- delta=like delins
prot-missense (16), -- delta=[morph of length 1]
prot-nonsense (17), -- delta=[del]; variation-location is the tail
-- of the protein being truncated
prot-neutral (18), -- delta=[morph of length 1]
prot-silent (19), -- delta=[morph of length 1, same AA as at
-- variation-location]
prot-other (20), -- delta=any
other (255) -- delta=any
},
-- Sequence that replaces the location, in biological order.
delta SEQUENCE OF <a href="Delta-item.html">Delta-item</a>,
-- 'observation' is used to label items in a <a href="Variation-ref.html">Variation-ref</a> package
-- This field is explicitly a bit-field, so the bitwise OR (= sum) of any
-- of the values may be observed.
observation INTEGER {
asserted (1), -- inst represents the asserted base at a
-- position
reference (2), -- inst represents the reference base at the
-- position
variant (4) -- inst represent the observed variant at a
-- given position
} OPTIONAL
}</pre>
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