| Variant ID: vg0221477301 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr02 | Position: 21477301 |
| Reference Allele: GA | Alternative Allele: G |
| Primary Allele: G | Secondary Allele: GA |
Inferred Ancestral Allele: Not determined.
ACCTGCAAACCATTTTCGATTAATTCCTCGCGTGCACACCAACAGATTAAATCCCTGAAGAATCAATTCACGAAACGGATCAATCTCTTTCCGAGGAACA[GA/G]
AAATTAACTGAAAAGAAATTAAAATCAACGCACAATTTCCAGATGATCAAGCAATCATCGGAAGCAATGAGGGGATCGTGGATCAAGAAAACAGAGGATG
CATCCTCTGTTTTCTTGATCCACGATCCCCTCATTGCTTCCGATGATTGCTTGATCATCTGGAAATTGTGCGTTGATTTTAATTTCTTTTCAGTTAATTT[TC/C]
TGTTCCTCGGAAAGAGATTGATCCGTTTCGTGAATTGATTCTTCAGGGATTTAATCTGTTGGTGTGCACGCGAGGAATTAATCGAAAATGGTTTGCAGGT
| Populations | Population Size | Frequency of G(primary allele) | Frequency of GA(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 61.10% | 38.80% | 0.08% | 0.00% | NA |
| All Indica | 2759 | 94.90% | 5.00% | 0.07% | 0.00% | NA |
| All Japonica | 1512 | 3.70% | 96.20% | 0.07% | 0.00% | NA |
| Aus | 269 | 63.20% | 36.80% | 0.00% | 0.00% | NA |
| Indica I | 595 | 98.50% | 1.50% | 0.00% | 0.00% | NA |
| Indica II | 465 | 96.80% | 3.20% | 0.00% | 0.00% | NA |
| Indica III | 913 | 91.70% | 8.20% | 0.11% | 0.00% | NA |
| Indica Intermediate | 786 | 94.90% | 5.00% | 0.13% | 0.00% | NA |
| Temperate Japonica | 767 | 1.40% | 98.40% | 0.13% | 0.00% | NA |
| Tropical Japonica | 504 | 6.90% | 93.10% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 4.10% | 95.90% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 9.40% | 90.60% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 38.90% | 60.00% | 1.11% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0221477301 | GA -> G | LOC_Os02g35750.1 | downstream_gene_variant ; 3480.0bp to feature; MODIFIER | silent_mutation | Average:66.288; most accessible tissue: Zhenshan97 flag leaf, score: 74.825 | N | N | N | N |
| vg0221477301 | GA -> G | LOC_Os02g35750.2 | downstream_gene_variant ; 1834.0bp to feature; MODIFIER | silent_mutation | Average:66.288; most accessible tissue: Zhenshan97 flag leaf, score: 74.825 | N | N | N | N |
| vg0221477301 | GA -> G | LOC_Os02g35750.3 | downstream_gene_variant ; 1669.0bp to feature; MODIFIER | silent_mutation | Average:66.288; most accessible tissue: Zhenshan97 flag leaf, score: 74.825 | N | N | N | N |
| vg0221477301 | GA -> G | LOC_Os02g35760.1 | intron_variant ; MODIFIER | silent_mutation | Average:66.288; most accessible tissue: Zhenshan97 flag leaf, score: 74.825 | N | N | N | N |
| vg0221477301 | GA -> G | LOC_Os02g35760.2 | intron_variant ; MODIFIER | silent_mutation | Average:66.288; most accessible tissue: Zhenshan97 flag leaf, score: 74.825 | N | N | N | N |