In the field of genetic variation, the term variant is used to refer to a specific region of the genome which differs between two genomes.
通常我們所說的變異其實是相對於參考基因組來說的。如果沒有這個參考基因組，何談變異。按照這個定義，變異其實說的是兩個基因組不同的區域。那麽，單核苷酸變異說的不同人之間單個base的變異。可以叫做snv （single-nucleotide variant)），但是還不能被叫snp (single-nucleotide polymorphism) 。
snv和snp之間區別請移步公眾號搜索“理清SNP、SNV、CNV等壹些概念”。
snp和snv很多時候被混著叫。snp的概念重心在於多態性，描述的是壹個群體性的概念。這個單位點的變異存在於壹個群體之中，當然這個頻率是多少不壹定。
snv描述的是少數個體之間，相對於參考基因組，某個位點的變異。
那麽知道snp後，後面壹個概念是allele，翻譯過來是等位基因。
關於等位基因概念allele請移步公眾號搜索“壹葉知因丨基因科普微視頻之Allele”。
說簡單點，就是同源染色體上，同壹個基因座上的壹對基因。壹個來自父親，壹個來自母親。當然，等位基因可能完全壹樣，也可能部分序列不壹樣。
這個和我們遺傳學上課本學的等位基因的概念還有些不同。
進行群體的重測序後，我們要call snp。
按照以下EBI的描述，說的是同壹個snp位置，參考基因組那個堿基就是 reference allele ；妳的重測序個體那個snp就是 alternative allele 。
那麽，接下來就引出另壹個概念，snp二態性（snp biallelic）。
雖然base有acgt四種，但是對於基因組某個位置確定的堿基只有壹個，也就是說具體到某個snp其實就是兩種形態，比如C/T。他們非此即彼。
有了snp allele的概念，就很容易理解haplotype了。翻譯為單倍型。簡單理解就是壹條染色體上，連續的壹段snp。下圖清晰地展示了haplotype。AGT/GTA/AGA是三種不同類型的單倍型。
那麽問題來了，為了什麽要區分不同的單倍型？
Different versions of the same variant are called alleles . For example, a SNP may have two alternative bases, or alleles, C and T 4 .
When working with genome scale data the term reference allele refers to the base that is found in the reference genome. Since the reference is just somebody’s genome, it is not always the major allele. In contrast, the alternative allele refers to any base, other than the reference, that is found at that locus. The alternative allele is not necessarily the minor allele and it may, or may not, be linked to a phenotype. There can be more than one alternative allele per variant.
In the genome, alleles at variants close together on the same chromosome tend to occur together more often than is expected by chance. These blocks of alleles are called haplotypes. Linkage disequilibrium (LD) is a measure of how often two alleles or specific sequences are inherited together, with alleles that are always co-inherited said to be in linkage disequilibrium.
不知道理解到位不？後續再理解，加點圖
未完，待續