| Variant ID: vg0334098334 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 34098334 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 313. )
CTCAGCTGGAGTCGTATGCAACCTACGGGTTGCGAGAGATGTACAACTCCGGTGTTGACGACATCGACGATCGTCCCACTATGGGATCTTTGTGGACACA[C/T]
TGTGAGGTAAATTTTGTTTAATTCGTTTGTGTTCTCATTATGAACAGTTCCGTATTAGTTCAATACTTTCCTGATATAACTAATCATAACTATTATCTTC
GAAGATAATAGTTATGATTAGTTATATCAGGAAAGTATTGAACTAATACGGAACTGTTCATAATGAGAACACAAACGAATTAAACAAAATTTACCTCACA[G/A]
TGTGTCCACAAAGATCCCATAGTGGGACGATCGTCGATGTCGTCAACACCGGAGTTGTACATCTCTCGCAACCCGTAGGTTGCATACGACTCCAGCTGAG
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 99.60% | 0.40% | 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 | 98.50% | 1.50% | 0.00% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.60% | 0.40% | 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 | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0334098334 | C -> T | LOC_Os03g59910.1 | synonymous_variant ; p.His21His; LOW | N | Average:48.119; most accessible tissue: Minghui63 panicle, score: 59.629 | N | N | N | N |
| vg0334098334 | C -> T | LOC_Os03g59894.1 | downstream_gene_variant ; 1667.0bp to feature; MODIFIER | N | Average:48.119; most accessible tissue: Minghui63 panicle, score: 59.629 | N | N | N | N |
| vg0334098334 | C -> T | LOC_Os03g59920.1 | downstream_gene_variant ; 1227.0bp to feature; MODIFIER | N | Average:48.119; most accessible tissue: Minghui63 panicle, score: 59.629 | N | N | N | N |