| Variant ID: vg0302880739 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 2880739 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, C: 0.01, others allele: 0.00, population size: 254. )
AAGCTCGATGATATTTTCTCTTTTCATTTTCCCTTTTTTTTTTGTCATTCTTGTTAAGAATTCGTTGCCAACTCAATCTGGCTGGCAAATAAAAGTGTAT[T/C]
AAATTTCCCCTTTTTATATAGAGAGACAGGTACACAATTGTAATTGTTTTTTTAGATCAACCAATGCATGTGAAACGATATACGTGCTACTACCATGTAA
TTACATGGTAGTAGCACGTATATCGTTTCACATGCATTGGTTGATCTAAAAAAACAATTACAATTGTGTACCTGTCTCTCTATATAAAAAGGGGAAATTT[A/G]
ATACACTTTTATTTGCCAGCCAGATTGAGTTGGCAACGAATTCTTAACAAGAATGACAAAAAAAAAAGGGAAAATGAAAAGAGAAAATATCATCGAGCTT
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 96.50% | 3.50% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 98.90% | 1.10% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 54.60% | 45.40% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.20% | 0.80% | 0.00% | 0.00% | NA |
| Indica II | 465 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 97.60% | 2.40% | 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 | 89.60% | 10.40% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 96.70% | 3.30% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0302880739 | T -> C | LOC_Os03g05770.1 | 3_prime_UTR_variant ; 323.0bp to feature; MODIFIER | silent_mutation | Average:47.022; most accessible tissue: Callus, score: 89.101 | N | N | N | N |
| vg0302880739 | T -> C | LOC_Os03g05780.1 | downstream_gene_variant ; 2266.0bp to feature; MODIFIER | silent_mutation | Average:47.022; most accessible tissue: Callus, score: 89.101 | N | N | N | N |