| Nucleotide polymorphisms |
SNPs |
A variant at a single position where one base replaces another base. SNPs arise from errors during DNA replication or repair. Also referred to as SNV or single-base substitution. |
| Multinucleotide polymorphisms (MNP) |
Changes at two or more adjacent nucleotides, which are relatively rare. |
| Structural variants |
Indels |
A site where DNA is lost (deletion) or gained (insertion), typically describing relatively small (1–20 bp but up to 1,000 bp) changes. Usually classified as sequence differences smaller than PAVs. |
| Simple sequence repeats (SSR) |
Simple sequence repeats are repeats of two to six nucleotides that vary in the number of repeat motifs present. Also referred to as short tandem repeats or microsatellites. Can be considered a type of CNV. |
| CNVs |
Sequences with variable copy number between individuals. The term CNV generally applies to genic regions and can be due to duplications, deletions, or insertions. Simple sequence repeats can be considered as very small CNVs. Typically, CNVs refer to larger sequence repeats (>1 kb for example) and may encompass one or more genes or parts of genes. |
| PAVs |
Large sequence block (>1 kb) present in one line/individual but completely missing in another line. Like CNVs, a PAV typically refers to a region containing genes and can be thought of as an extreme example of CNV. |
| TEs |
Mobile genetic elements. The number and location of each element frequently differ from the reference genome. |
| Large structural variations (SV) and ploidy (whole and partial genome duplication) |
Includes DNA rearrangements such as chromosomal inversions, translocations, partial genome duplications, duplications, etc. |
