Table 2. Summary, characteristics and distribution of sequence variations between ‘Hainan Tall’ and ‘Catigan Green Dwarf’ (CATD) genomes. Location of variants is based on ‘CATD’ sequence assembly as the reference in this genome mapping analysis.
| Genome Region | |||
|---|---|---|---|
| Variants | Non-repeat region | Genic region | Exonic region |
| (intergenic, gene) | (Intron + Exon) | ||
| Number of SNPs | 57,872 | 21,066 | 5,552 |
| Number of Transversions | 40,233 | 7,192 | 1,664 |
| Number of Transitions | 17,639 | 13,875 | 3,888 |
| Ts/Tv ratio | 2.2809 | 1.93 | 2.34 |
| Number of InDels (1-6 bp) | 631 | 143 | 48 |
| Single-base InDels | 392 | 70 | 17 |
| di-nucleotide InDels | 128 | 32 | 12 |
| >3-bp InDels | 111 | 41 | 19 |
| Total Number of Variants | 58,503 | 21,209 | 5,600 |