Variation-inst

Defined in file seqfeat.asn
C++ class: CVariation_inst


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 VariantProperties
                                -- 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 Delta-item,

    -- 'observation' is used to label items in a Variation-ref 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
}