Table 2 Location, annotation, and nucleotide types of selected SNPs/InDels in different samples
Variant type | Position | Reference nucleotides | Alternate nucleotides | Zaosu Red | Zaosu | Kuala Pear | Green pool | Red pool | Effect | Gene ID | Nr annotation |
|---|---|---|---|---|---|---|---|---|---|---|---|
SNPs | 9,115,802 | T | A | 0.5 | N | 7.0 | 11.0 | 7.6 | Upstream | Pdr4g010210 | Adenylate kinase 1, chloroplastic-like |
9,212,167 | C | T | 0.1 | N | 2.0 | 6.0 | 5.4 | Upstream | Pdr4g010260 | Zinc finger CCCH domain-containing protein 11-like | |
9,212,608 | G | T | 0.8 | N | 7.0 | 15.0 | 10.7 | Upstream | Pdr4g010260 | ||
9,214,082 | T | C | 0.3 | N | 8.0 | 9.0 | 12.1 | Upstream | Pdr4g010260 | ||
9,214,271 | A | G | 0.4 | N | 8.0 | 11.0 | 12.2 | Upstream | Pdr4g010260 | ||
InDels | 8,553,091 | CTT | C | 2.4 | 0.3 | 0.2 | 0.6 | 6.7 | Intergenic | ||
9,121,649 | GT | G | 5.4 | 5.0 | 17.0 | 28.0 | 19.4 | Intergenic | |||
9,122,408 | G | GA | 11.4 | 8.0 | 7.0 | 20.0 | 20.8 | Intergenic | |||
9,178,944 | TAGA | T | 2.5 | 2.0 | 3.0 | 5.0 | 6.1 | Unknown | |||
9,222,351 | T | TA | 11.4 | 8.0 | 11.0 | 27.0 | 14.5 | Downstream | Pdr4g010260 | Zinc finger CCCH domain-containing protein 11-like | |
9,222,379 | G | GT | 12,4 | 11,0 | 12,0 | 28,0 | 17,6 | Downstream | Pdr4g010260 | ||
18,388,296 | AGCAGCTGAAGTTCC | A | 10,5 | 14,0 | 20,0 | 39,0 | 24,9 | Frame shift | Pdr4g016570 | COL domain-class transcription factor | |
16,860,274 | AG | A | 18,9 | 9,0 | 7,0 | 13,0 | 17,7 | Downstream | Pdr4g015130 | COP9 signalosome complex subunit 7-like |
