| Variant ID: vg0334132441 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 34132441 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 336. )
TTTTGTATGAATAAAGATATCTTATAATTATTGTATGACTGTCATTATTGTAAGAATAATTATTTGTGTACGGTTTTTTTGACTCATGTAGATGGATCGG[C/T]
AATGGATGTACGCTGACCGGCGGTCCAAAGAGTTTATTGACGGCGTGCACTATTTTTTAAGAGTGGCCGAAGCTAACAGGCAAAGGGGTTTTATTTGTTG
CAACAAATAAAACCCCTTTGCCTGTTAGCTTCGGCCACTCTTAAAAAATAGTGCACGCCGTCAATAAACTCTTTGGACCGCCGGTCAGCGTACATCCATT[G/A]
CCGATCCATCTACATGAGTCAAAAAAACCGTACACAAATAATTATTCTTACAATAATGACAGTCATACAATAATTATAAGATATCTTTATTCATACAAAA
| 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 | 47.30% | 0.10% | 4.89% | 47.69% | NA |
| All Indica | 2759 | 19.40% | 0.20% | 8.01% | 72.38% | NA |
| All Japonica | 1512 | 98.10% | 0.00% | 0.07% | 1.79% | NA |
| Aus | 269 | 27.10% | 0.00% | 1.49% | 71.38% | NA |
| Indica I | 595 | 15.80% | 0.00% | 3.03% | 81.18% | NA |
| Indica II | 465 | 8.00% | 0.00% | 6.88% | 85.16% | NA |
| Indica III | 913 | 28.90% | 0.50% | 10.08% | 60.46% | NA |
| Indica Intermediate | 786 | 17.80% | 0.10% | 10.05% | 72.01% | NA |
| Temperate Japonica | 767 | 99.90% | 0.00% | 0.00% | 0.13% | NA |
| Tropical Japonica | 504 | 95.00% | 0.00% | 0.00% | 4.96% | NA |
| Japonica Intermediate | 241 | 99.20% | 0.00% | 0.41% | 0.41% | NA |
| VI/Aromatic | 96 | 95.80% | 0.00% | 3.12% | 1.04% | NA |
| Intermediate | 90 | 56.70% | 0.00% | 2.22% | 41.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0334132441 | C -> T | LOC_Os03g60010.1 | stop_gained ; p.Gln4*; HIGH | stop_gained | Average:12.835; most accessible tissue: Zhenshan97 root, score: 20.427 | N | N | N | N |
| vg0334132441 | C -> DEL | LOC_Os03g60010.1 | N | frameshift_variant | Average:12.835; most accessible tissue: Zhenshan97 root, score: 20.427 | N | N | N | N |