84 lines
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2.8 KiB
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84 lines
No EOL
2.8 KiB
HTML
<!DOCTYPE HTML>
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<title>Assembly</title>
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<h3>Assembly</h3><pre>Defined in file <a href="docsum.asn.html">docsum.asn</a>
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C++ class: <a href="../doxyhtml/classCAssembly.html">CAssembly</a>
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Assembly ::= SEQUENCE {
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attlist SET {
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--dbSNP build number defining the rsid set aligned to this
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-- assembly
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dbSnpBuild INTEGER,
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--assembly build number with possible 'subbuild' version
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-- numbers to reflect updates in gene annotation (human e.g. 34_3, 35_1,
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-- 36_1)
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genomeBuild VisibleString,
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--High-level classification of the assembly to distinguish
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-- reference projects from alternate solutions. GroupLabel field from
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-- organism/build-specific ContigInfo tables. "reference" is occasionally used
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-- as the preferred assembly; standards will converge as additional organism
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-- genome projects are finished. Note that some organism assembly names include
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-- extended characters like '~' and '/' that may be incompatible with OS
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-- filename conventions.
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groupLabel VisibleString OPTIONAL,
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--Name of the group(s) or organization(s) that generated the
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-- assembly
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assemblySource VisibleString OPTIONAL,
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current BOOLEAN OPTIONAL, --Marks the current genomic assembly
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reference BOOLEAN OPTIONAL
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},
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component SEQUENCE OF <a href="Component.html">Component</a> OPTIONAL,
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snpStat SEQUENCE {
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attlist SET {
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--summary measure of placement precision in the
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-- assembly
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mapWeight ENUMERATED {
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unmapped (1),
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unique-in-contig (2),
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two-hits-in-contig (3),
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less-10-hits (4),
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multiple-hits (5)
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},
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--number of distinct chromosomes in the
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-- mapset
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chromCount INTEGER OPTIONAL,
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--number of distinct contigs [ gi |
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-- accession[.version] ] in the mapset
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placedContigCount INTEGER OPTIONAL,
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--number of sequence postions to a contig with
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-- unknown chromosomal assignment
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unplacedContigCount INTEGER OPTIONAL,
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--total number of sequence positions in the
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-- mapset
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seqlocCount INTEGER OPTIONAL,
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--Number of hits to alternative genomic haplotypes
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-- (e.g. HLA DR region, KIR, or pseudo-autosomal regions like PAR)
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-- within the assembly mapset. Note that positions on haplotypes
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-- defined in other assemblies (a different assembly_group_label
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-- value) will not be counted in this value.
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hapCount INTEGER OPTIONAL
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},
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snpStat NULL
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}
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}</pre>
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</body>
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