78 lines
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3.8 KiB
HTML
78 lines
No EOL
3.8 KiB
HTML
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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>
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C++ class: <a href="../doxyhtml/classCVariation__inst.html">CVariation_inst</a>
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Variation-inst ::= SEQUENCE {
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type INTEGER {
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unknown (0), -- delta=[]
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identity (1), -- delta=[]
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inv (2), -- delta=[del, ins.seq=
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-- RevComp(variation-location)]
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snv (3), -- delta=[morph of length 1]
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-- NOTE: this is snV not snP; the latter
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-- requires frequency-based validation to be
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-- established in <a href="VariantProperties.html">VariantProperties</a>
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-- the strict definition of SNP is an SNV with
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-- an established population frequency of at
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-- least 1% in at least 1 popuplation
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mnp (4), -- delta=[morph of length >1]
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delins (5), -- delta=[del, ins]
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del (6), -- delta=[del]
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ins (7), -- delta=[ins]
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microsatellite (8), -- delta=[del, ins.seq= repeat-unit with fuzzy
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-- multiplier]
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-- variation-location is the microsat expansion
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-- on the sequence
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transposon (9), -- delta=[del, ins.seq= known donor or 'this']
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-- variation-location is equiv of transposon
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-- locs.
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cnv (10), -- delta=[del, ins= 'this' with fuzzy
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-- multiplier]
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direct-copy (11), -- delta=[ins.seq= upstream location on the
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-- same strand]
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rev-direct-copy (12), -- delta=[ins.seq= downstream location on the
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-- same strand]
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inverted-copy (13), -- delta=[ins.seq= upstream location on the
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-- opposite strand]
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everted-copy (14), -- delta=[ins.seq= downstream location on the
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-- opposite strand]
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translocation (15), -- delta=like delins
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prot-missense (16), -- delta=[morph of length 1]
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prot-nonsense (17), -- delta=[del]; variation-location is the tail
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-- of the protein being truncated
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prot-neutral (18), -- delta=[morph of length 1]
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prot-silent (19), -- delta=[morph of length 1, same AA as at
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-- variation-location]
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prot-other (20), -- delta=any
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other (255) -- delta=any
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},
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-- Sequence that replaces the location, in biological order.
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delta SEQUENCE OF <a href="Delta-item.html">Delta-item</a>,
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-- 'observation' is used to label items in a <a href="Variation-ref.html">Variation-ref</a> package
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-- This field is explicitly a bit-field, so the bitwise OR (= sum) of any
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-- of the values may be observed.
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observation INTEGER {
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asserted (1), -- inst represents the asserted base at a
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-- position
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reference (2), -- inst represents the reference base at the
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-- position
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variant (4) -- inst represent the observed variant at a
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-- given position
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} OPTIONAL
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}</pre>
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