| Variant ID: vg0424199800 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 24199800 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 254. )
TTTAAACTAAGCGTTTGAGAGTTATTGATGCTAAAAATTTTAGAAGTTTATGAATTATGGTTAGAGTGTGTATTACTGTTGTGTTGTCTAGTAAGTGAGA[A/G]
CGAAGAACGAAGGCAGTACCGAAATACTAAGTATCTTCAAAAGAGGTGCTGCTTCCAAAAGAAACAGCGTCCAATTGATGCCACAGTTTGGATGAATGCG
CGCATTCATCCAAACTGTGGCATCAATTGGACGCTGTTTCTTTTGGAAGCAGCACCTCTTTTGAAGATACTTAGTATTTCGGTACTGCCTTCGTTCTTCG[T/C]
TCTCACTTACTAGACAACACAACAGTAATACACACTCTAACCATAATTCATAAACTTCTAAAATTTTTAGCATCAATAACTCTCAAACGCTTAGTTTAAA
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 97.50% | 1.10% | 0.08% | 1.38% | NA |
| All Indica | 2759 | 96.70% | 1.80% | 0.11% | 1.45% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 90.70% | 0.00% | 0.37% | 8.92% | NA |
| Indica I | 595 | 94.80% | 4.70% | 0.34% | 0.17% | NA |
| Indica II | 465 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica III | 913 | 95.60% | 1.00% | 0.00% | 3.40% | NA |
| Indica Intermediate | 786 | 97.50% | 1.40% | 0.13% | 1.02% | 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% | 1.10% | 0.00% | 1.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0424199800 | A -> DEL | N | N | silent_mutation | Average:37.226; most accessible tissue: Callus, score: 79.457 | N | N | N | N |
| vg0424199800 | A -> G | LOC_Os04g40770.1 | downstream_gene_variant ; 4450.0bp to feature; MODIFIER | silent_mutation | Average:37.226; most accessible tissue: Callus, score: 79.457 | N | N | N | N |
| vg0424199800 | A -> G | LOC_Os04g40790.1 | downstream_gene_variant ; 2513.0bp to feature; MODIFIER | silent_mutation | Average:37.226; most accessible tissue: Callus, score: 79.457 | N | N | N | N |
| vg0424199800 | A -> G | LOC_Os04g40780.1 | intron_variant ; MODIFIER | silent_mutation | Average:37.226; most accessible tissue: Callus, score: 79.457 | N | N | N | N |