| Variant ID: vg0703430302 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 3430302 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.01, others allele: 0.00, population size: 363. )
GGACTTCCCACTGTACTACTATGAACAAAATAATGAATCCACATCAGCATTTCTAAGGATGGACTTCCCATTGTACTACTATACAAATGTGATTAGGCTA[T/C]
GTGATTCTTAATCCAATCAATTAATCGTGGTATCCATGTACTAGAGGCAATTGAGAAGACAGCAGAAACAGTTCAGGAGTAACTGACCTCAAGACAAGTG
CACTTGTCTTGAGGTCAGTTACTCCTGAACTGTTTCTGCTGTCTTCTCAATTGCCTCTAGTACATGGATACCACGATTAATTGATTGGATTAAGAATCAC[A/G]
TAGCCTAATCACATTTGTATAGTAGTACAATGGGAAGTCCATCCTTAGAAATGCTGATGTGGATTCATTATTTTGTTCATAGTAGTACAGTGGGAAGTCC
| 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 | 97.10% | 2.80% | 0.02% | 0.00% | NA |
| All Indica | 2759 | 95.10% | 4.90% | 0.04% | 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 | 96.10% | 3.90% | 0.00% | 0.00% | NA |
| Indica III | 913 | 88.80% | 11.20% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 98.10% | 1.80% | 0.13% | 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 | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0703430302 | T -> C | LOC_Os07g06960.1 | upstream_gene_variant ; 1835.0bp to feature; MODIFIER | silent_mutation | Average:66.762; most accessible tissue: Callus, score: 90.339 | N | N | N | N |
| vg0703430302 | T -> C | LOC_Os07g06970.1 | intron_variant ; MODIFIER | silent_mutation | Average:66.762; most accessible tissue: Callus, score: 90.339 | N | N | N | N |