| Variant ID: vg0409081514 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 9081514 |
| 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, others allele: 0.00, population size: 309. )
GGTGGCTGCGGCGACGCTCGCGGACGCATTGGGGGTGACAGCAGCACTCGCGGGCACATCCAACAATGGTGACGGATCTGCAACAGCGGCTGCGACAGCA[C/T]
TCACCGACAGATCTGGTGGGCATCATCACAAGGGTCTTATCTTCTTCGAGAGATAGCATGAGAGGGAATTGTGATTATTTTTTTATTTCTTATGGATGGT
ACCATCCATAAGAAATAAAAAAATAATCACAATTCCCTCTCATGCTATCTCTCGAAGAAGATAAGACCCTTGTGATGATGCCCACCAGATCTGTCGGTGA[G/A]
TGCTGTCGCAGCCGCTGTTGCAGATCCGTCACCATTGTTGGATGTGCCCGCGAGTGCTGCTGTCACCCCCAATGCGTCCGCGAGCGTCGCCGCAGCCACC
| 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 | 99.80% | 0.10% | 0.08% | 0.00% | NA |
| All Indica | 2759 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 99.40% | 0.30% | 0.26% | 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 | 98.80% | 0.70% | 0.52% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0409081514 | C -> T | LOC_Os04g16690.1 | missense_variant ; p.Leu62Phe; MODERATE | N | Average:71.005; most accessible tissue: Zhenshan97 young leaf, score: 86.852 | N | N | N | N |
| vg0409081514 | C -> T | LOC_Os04g16680.1 | upstream_gene_variant ; 3626.0bp to feature; MODIFIER | N | Average:71.005; most accessible tissue: Zhenshan97 young leaf, score: 86.852 | N | N | N | N |
| vg0409081514 | C -> T | LOC_Os04g16700.1 | downstream_gene_variant ; 3550.0bp to feature; MODIFIER | N | Average:71.005; most accessible tissue: Zhenshan97 young leaf, score: 86.852 | N | N | N | N |