| Variant ID: vg1000677225 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 677225 |
| Reference Allele: T | Alternative Allele: G |
| Primary Allele: T | Secondary Allele: G |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, G: 0.01, others allele: 0.00, population size: 322. )
ATACAGTATATGACCCACCCAATTTAAGGCACATACATTCAGTTCTTTTTTTCCAATGGATCACATCTTTGTTGACGATCAGTTCACAAACTAGTCACAA[T/G]
CACATCGTTATTACTTCTGCTTCTTCAAGCATTCATGTAACATCAAAACATAACACACATCGTCTCAATCGCCTTGTGAAAAGTACAAGAAATTTACTAT
ATAGTAAATTTCTTGTACTTTTCACAAGGCGATTGAGACGATGTGTGTTATGTTTTGATGTTACATGAATGCTTGAAGAAGCAGAAGTAATAACGATGTG[A/C]
TTGTGACTAGTTTGTGAACTGATCGTCAACAAAGATGTGATCCATTGGAAAAAAAGAACTGAATGTATGTGCCTTAAATTGGGTGGGTCATATACTGTAT
| Populations | Population Size | Frequency of T(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 97.20% | 2.80% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 99.50% | 0.50% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 57.20% | 42.80% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.20% | 0.80% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.40% | 0.60% | 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 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 97.80% | 2.20% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1000677225 | T -> G | LOC_Os10g02070.1 | 3_prime_UTR_variant ; 124.0bp to feature; MODIFIER | silent_mutation | Average:62.873; most accessible tissue: Zhenshan97 young leaf, score: 78.044 | N | N | N | N |
| vg1000677225 | T -> G | LOC_Os10g02080.1 | downstream_gene_variant ; 2874.0bp to feature; MODIFIER | silent_mutation | Average:62.873; most accessible tissue: Zhenshan97 young leaf, score: 78.044 | N | N | N | N |