| Variant ID: vg1020652229 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 20652229 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 313. )
TATTCAATATTCAATTGTCTACTGTGTTTTGCTATGTTCTTTTGTGTTGTTTATTCATTTTTCTCAAGTGTTTTGCTATGGCTCTTGCATTTGCATCTAT[G/A]
ACCCGTACATTCTGCACATGGATAAGCCTAAAACAACGTCCCCTATTACAGTGACAAATCTGAACAAAATGATAATGACACGTGACAAAGGGACTGTGAA
TTCACAGTCCCTTTGTCACGTGTCATTATCATTTTGTTCAGATTTGTCACTGTAATAGGGGACGTTGTTTTAGGCTTATCCATGTGCAGAATGTACGGGT[C/T]
ATAGATGCAAATGCAAGAGCCATAGCAAAACACTTGAGAAAAATGAATAAACAACACAAAAGAACATAGCAAAACACAGTAGACAATTGAATATTGAATA
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 99.90% | 0.10% | 0.02% | 0.00% | NA |
| All Indica | 2759 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 93.80% | 5.20% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1020652229 | G -> A | LOC_Os10g38800.1 | 3_prime_UTR_variant ; 238.0bp to feature; MODIFIER | silent_mutation | Average:60.481; most accessible tissue: Callus, score: 90.967 | N | N | N | N |
| vg1020652229 | G -> A | LOC_Os10g38790.1 | downstream_gene_variant ; 4227.0bp to feature; MODIFIER | silent_mutation | Average:60.481; most accessible tissue: Callus, score: 90.967 | N | N | N | N |