![]() A region found on the X and Y chromosomes of mammals that allow recombination between the sex chromosomes. Any locus may be represented 0, 1 or >1 time, but entire chromosomes are only represented 0 or 1 times. The collection of Chromosome assemblies, unlocalized and unlocalized sequences and alternate loci that represent an organism's genome. NOVEL sequences are sequences that were not in the last full assembly release and will be retained with the next full assembly release. ![]() FIX patches are released to correct an error in the assembly and will be removed when the new full assembly is released. There are two types of patches, FIX and NOVEL. These sequences are meant to add information to the assembly without disrupting the stable coordinate system. Therefore it is not anticipated that alternate loci will be defined for this assembly, although it is possible that unlocalized or unplaced sequences could be part of the assembly.Ī contig sequence that is released outside of the full assembly release cycle. It is anticipated that a diploid genome assembly is representing the genome of an individual. Understanding completeness is important for determining whether we submit chromosome level ASN for that chromosome.Ī genome assembly for which a Chromosome Assembly is available for both sets of an individual's chromosomes, as defined by the NCBI Assembly model. Relatively complete implies that some gaps may still be present in the assembly, but independent measures suggest that most of the sequence is represented by sequenced bases. In many cases, the assembly-units are what many people previously considered ‘assemblies'.Ī relatively complete pseudo-molecule assembled from smaller sequences ( components) that represent a biological chromosome. 129/Sv in mouse) would be considered a separate assembly-unit. Alternate-loci grouped together by a common name (e.g. For example, the Primary assembly is considered one sequence unit. As sequencing technology evolves, it is anticipated that diploid sequences representing an individual's genome will become available.Ĭollections of sequences used to define discrete parts of an assembly. Except in the case of organisms which have been bred to homozygosity, the haploid assembly does not typically represent a single haplotype, but rather a mixture of haplotypes. chimp or mouse) or multiple individuals (e.g. This representation may be obtained from a single individual (e.g. Most current assemblies are a haploid representation of an organism's genome, although some loci may be represented more than once (see Alternate locus, above). Note: an alternate locus group was previously considered an alternate partial assembly.Ī set of chromosomes, unlocalized and unplaced (random) sequences and alternate loci used to represent an organism's genome. Multiple scaffolds from different loci that are considered to be part of the same haplotype should be grouped into alternate locus groups (e.g. Diploid assemblies (which by definition are from a single individual) should not have alternate loci representations. ![]() However, these terms are confusing because they contain terms that have biological implications. Previously these sequences have been referred to as "partial chromosomes", "alternate alleles", and "alternate haplotypes". These sequences don't represent a complete chromosome sequence although there is no hard limit on the size of the alternate locus currently these are less than 1 Mb. Describing AssembliesĪ sequence that provides an alternate representation of a locus found in a largely haploid assembly. Below is a list of commonly used terms and definitions in the field of genomics and used by the NCBI Assembly Model.
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